---------------------------------------------------------------------------
        UniProt - Swiss-Prot Protein Knowledgebase
        SIB Swiss Institute of Bioinformatics; Geneva, Switzerland
        European Bioinformatics Institute (EBI); Hinxton, United Kingdom
        Protein Information Resource (PIR); Washington DC, USA
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Description: Controlled vocabulary of subcellular locations and membrane
             topologies and orientations
Name:        subcell.txt
Release:     2022_03 of 03-Aug-2022

---------------------------------------------------------------------------

 This document lists the UniProtKB controlled vocabulary used for the
 subcellular locations (including the membrane topologies and orientations
 terms) in the SUBCELLULAR LOCATION lines.

 It provides definitions of the terms as well as other relevant information
 in the following format:

  ---------  -------------------------------   ----------------------------
  Line code  Content                           Occurrence in an entry
  ---------  -------------------------------   ----------------------------
  ID         Identifier (location)             Once; starts an entry
  IT         Identifier (topology)             Once; starts a 'topology' entry
  IO         Identifier (orientation)          Once; starts an 'orientation' entry
  AC         Accession (SL-xxxx)               Once
  DE         Definition                        Once or more
  SY         Synonyms                          Optional; Once or more
  SL         Content of subc. loc. lines       Once
  HI         Hierarchy ('is-a')                Optional; Once or more
  HP         Hierarchy ('part-of')             Optional; Once or more
  KW         Associated keyword (accession)    Optional; Once
  GO         Gene ontology (GO) mapping        Optional; Once or more
  AN         Annotation note                   Optional; Once or more
  RX         Interesting references            Optional; Once or more
  WW         Interesting links                 Optional; Once or more
  //         Terminator                        Once; ends an entry


AN   Next free AC: SL-0551
___________________________________________________________________________
ID   A band.
AC   SL-0476
DE   The appearance of the striated muscle is created by a pattern of
DE   alternating dark A bands and light I bands. A bands comprise thick
DE   filaments of myosin and proteins that bind myosin. They are bisected
DE   by the H zone, a paler region where the thick and the thin filaments
DE   do not overlap. The exact center of the A band is termed the M line.
SY   A-band; A line.
SL   Cytoplasm, myofibril, sarcomere, A band.
HP   Sarcomere.
GO   GO:0031672; A band
//
ID   Acidocalcisome.
AC   SL-0002
DE   The acidocalcisome is an electron-dense acidic organelle which
DE   contains a matrix of pyrophosphate and polyphosphates with bound
DE   calcium and other cations. Its limiting membrane possesses a number of
DE   pumps and exchangers for the uptake and release of these elements. The
DE   acidocalcisome does not belong to the endocytic pathway and may
DE   represent a branch of the secretory pathway in trypanosomatids and
DE   apicomplexan parasites. The acidocalcisome is possibly involved in
DE   polyphosphate and cation storage and in adaptation of these
DE   microoganisms to environmental stress.
SL   Acidocalcisome.
GO   GO:0020022; acidocalcisome
RX   PubMed=15738951; DOI=10.1038/nrmicro1097;
//
ID   Acidocalcisome lumen.
AC   SL-0316
DE   The acidocalcisome compartment bounded by the acidocalcisomal
DE   membrane.
SY   Acidocalcisomal lumen.
SL   Acidocalcisome lumen.
HP   Acidocalcisome.
GO   GO:0033985; acidocalcisome lumen
//
ID   Acidocalcisome membrane.
AC   SL-0003
DE   The membrane of an acidocalcisome.
SY   Acidocalcisomal membrane.
SL   Acidocalcisome membrane.
HI   Membrane.
HP   Acidocalcisome.
HP   Endomembrane system.
GO   GO:0033102; acidocalcisome membrane
//
ID   Acrosome.
AC   SL-0007
DE   The acrosome is a large lysosome-like vesicle overlying the sperm
DE   nucleus. This spermatid specific organelle, derived from the Golgi
DE   during spermatogenesis, contains both unique acrosomal enzymes and
DE   common enzymes associated with lysosomes in somatic cells. Only sperm
DE   that have undergone the acrosome reaction can fuse with egg plasma
DE   membrane. The acrosome reaction is characterized by multiple fusions
DE   of the outer acrosomal membrane with the sperm cell membrane.
SY   Acrosomal vesicle.
SL   Cytoplasmic vesicle, secretory vesicle, acrosome.
HI   Secretory vesicle.
GO   GO:0001669; acrosomal vesicle
//
ID   Acrosome inner membrane.
AC   SL-0004
DE   The portion of the acrosomal membrane closely associated with the
DE   anterior region of the nuclear envelope.
SY   Acrosomal inner membrane; IAM; Inner acrosomal membrane.
SL   Cytoplasmic vesicle, secretory vesicle, acrosome inner membrane.
HP   Acrosome membrane.
GO   GO:0002079; inner acrosomal membrane
//
ID   Acrosome lumen.
AC   SL-0005
DE   The lumen of the acrosome.
SY   Acrosomal lumen.
SL   Cytoplasmic vesicle, secretory vesicle, acrosome lumen.
HI   Secretory vesicle lumen.
HP   Acrosome.
GO   GO:0043160; acrosomal lumen
//
ID   Acrosome membrane.
AC   SL-0006
DE   The membrane of the acrosome.
SY   Acrosomal membrane.
SL   Cytoplasmic vesicle, secretory vesicle, acrosome membrane.
HI   Secretory vesicle membrane.
HP   Acrosome.
HP   Endomembrane system.
GO   GO:0002080; acrosomal membrane
//
ID   Acrosome outer membrane.
AC   SL-0447
DE   The portion of the acrosomal membrane just beneath the sperm cell
DE   membrane.
SY   Acrosomal outer membrane; Outer acrosomal membrane.
SL   Cytoplasmic vesicle, secretory vesicle, acrosome outer membrane.
HP   Acrosome membrane.
GO   GO:0002081; outer acrosomal membrane
//
ID   Actin patch.
AC   SL-0008
DE   The actin patch is a highly dynamic actin structure in fungi required
DE   primarily for endocytosis but possibly also coupled to exocytosis.
DE   Actin patches are highly motile, they first assemble at sites of
DE   polarized cell growth and then move slowly and nondirectionally along
DE   the cell cortex.
SY   Actin cortical patch.
SL   Cytoplasm, cytoskeleton, actin patch.
HP   Cytoskeleton.
GO   GO:0030479; actin cortical patch
AN   The actin patch is a specialised structure which is specific to fungi
AN   so this term should be used only for fungal species.
//
ID   Adherens junction.
AC   SL-0009
DE   The adherens junction is an adhesion complex that localizes close to
DE   the apical membrane in epithelial cells. These junctions join the
DE   actin cytoskeleton to the plasma membrane to form adhesive contacts
DE   between cells or between cells and extracellular matrix. AJs mediate
DE   both cell adhesion and signaling.
SY   AJ; ZA; Zonula adherens.
SL   Cell junction, adherens junction.
HI   Cell junction.
GO   GO:0005912; adherens junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
//
ID   Aleurone grain.
AC   SL-0010
DE   The aleurone grain (protein body), is a specialized dry vacuole where
DE   storage proteins accumulate in a stable form in seeds, usually in the
DE   endosperm. Cells containing aleurones form the aleurone layer. These
DE   act as a source of amino acids for various synthetic activities during
DE   germination, but also represent immensely important nutritional
DE   sources for humans and ruminants. In most seeds, the aleuron grains
DE   contain three morphologically distinct regions: the matrix,
DE   crystalloid, and globoid.
SY   Protein body.
SL   Vacuole, aleurone grain.
HI   Vacuole.
GO   GO:0033095; aleurone grain
//
ID   Aleurone grain lumen.
AC   SL-0317
DE   The aleurone grain compartment bounded by the aleurone grain membrane.
SY   Protein body lumen.
SL   Vacuole, aleurone grain lumen.
HI   Vacuole lumen.
HP   Aleurone grain.
GO   GO:0034422; aleurone grain lumen
//
ID   Aleurone grain membrane.
AC   SL-0011
DE   The membrane of an aleurone grain.
SY   Protein body membrane.
SL   Vacuole, aleurone grain membrane.
HI   Vacuole membrane.
HP   Aleurone grain.
GO   GO:0032578; aleurone grain membrane
//
ID   Amyloplast.
AC   SL-0012
DE   The amyloplast is a colorless plant plastid that forms and stores
DE   starch. Amyloplasts are found in many tissues, particularly in storage
DE   tissues. They are found in both photosynthetic and parasitic plants,
DE   i.e. even in plants that are not capable of photosynthesis. Many
DE   amyloplast proteins are also expressed in photosynthetic tissue.
SL   Plastid, amyloplast.
HI   Plastid.
KW   KW-0035
GO   GO:0009501; amyloplast
//
ID   Amyloplast inner membrane.
AC   SL-0013
DE   The inner membrane of an amyloplast.
SY   Inner amyloplastic membrane.
SL   Plastid, amyloplast inner membrane.
HI   Amyloplast membrane.
HI   Plastid inner membrane.
GO   GO:0033098; amyloplast inner membrane
//
ID   Amyloplast membrane.
AC   SL-0014
DE   The membrane surrounding the amyloplast. Also used when it is not
DE   clear in which amyloplast membrane a protein is found.
SL   Plastid, amyloplast membrane.
HI   Plastid membrane.
HP   Amyloplast.
GO   GO:0033097; amyloplast membrane
//
ID   Anammoxosome.
AC   SL-0491
DE   The anammoxosome is a large intracytoplasmic compartment bounded by a
DE   single bilayer, ladderane-lipid-containing membrane present in
DE   bacteria that perform anaerobic ammonium oxidation (anammox). This
DE   organelle is the site of the anammox process, in which nitrite is used
DE   as the electron acceptor in the conversion of ammonium to dinitrogen
DE   (N2) gas and water. Anammox bacteria belong to the phylum
DE   Planctomycetes and are recognized as major players in the global
DE   nitrogen cycle.
SL   Anammoxosome.
//
ID   Anammoxosome membrane.
AC   SL-0492
DE   The membrane of the anammoxosome, a single bilayer membrane that
DE   contains unusual lipids, i.e. the so-called ladderane lipids, which
DE   appear to be unique for anammox bacteria.
SL   Anammoxosome membrane.
HI   Membrane.
HP   Anammoxosome.
//
ID   Apical cell membrane.
AC   SL-0015
DE   The fraction of the cell membrane at the apical end of the cell, which
DE   faces the outside world or the lumen of the cavity.
SY   Apical plasma membrane.
SL   Apical cell membrane.
HP   Cell membrane.
GO   GO:0016324; apical plasma membrane
//
ID   Apical lamina.
AC   SL-0016
DE   In the sea urchin embryos the apical lamina is a fibrous meshwork that
DE   remains after removal of hyalin from the hyalin layer.
SL   Secreted, extracellular space, extracellular matrix, apical lamina.
HI   Extracellular matrix.
GO   GO:0032579; apical lamina of hyaline layer
//
ID   Apicolateral cell membrane.
AC   SL-0017
DE   The fraction of the cell membrane at the apical end of the lateral
DE   plasma membrane of the cell.
SY   Apicolateral plasma membrane.
SL   Apicolateral cell membrane.
HP   Cell membrane.
GO   GO:0016327; apicolateral plasma membrane
//
ID   Apicoplast.
AC   SL-0018
DE   The apicoplast is a plastid found in some apicocomplexan parasites
DE   which is a non-photosynthetic plastid relict. Apicoplasts do not
DE   contain thylakoids; it is not yet clear if they contain internal
DE   membranes.
SY   Golgi-adjunct organelle; Thick-walled organelle.
SL   Plastid, apicoplast.
HI   Plastid.
KW   KW-0933
GO   GO:0020011; apicoplast
//
ID   Apoplast.
AC   SL-0019
DE   The apoplast is the "non-living" extracellular space that surrounds
DE   the symplast. It consists of cell walls and spaces between cells.
DE   Water and solutes can move freely in this framework, except at the
DE   endodermis in roots and stems where the apoplastic flow of ions is
DE   interrupted by the Casparian strip, forcing water to flow to symplast.
SL   Secreted, extracellular space, apoplast.
HI   Extracellular space.
KW   KW-0052
GO   GO:0048046; apoplast
//
ID   Archaeal flagellum.
AC   SL-0306
DE   The flagellum of Archaea is a long hair-like cell surface appendage
DE   made of polymerized flagellin with an attached hook. This rotating
DE   structure with switches propels the cell through a liquid medium. The
DE   archaeal flagellum is distinct from its bacterial equivalent in terms
DE   of architecture, composition and mechanism of assembly. Thinner (10-15
DE   nm) compared to the bacterial flagellum (18-24 nm), it is usually
DE   composed of several types of flagellins and is glycosylated. The
DE   archeal flagellum is considered as a type IV pilus-like structure.
SY   Archaeal flagella; Archaeal flagellar apparatus.
SL   Archaeal flagellum.
KW   KW-0974
GO   GO:0097589; archaeal-type flagellum
//
ID   Ascus epiplasm.
AC   SL-0538
DE   Ascus cytoplasm that is not packaged into ascospores.
SL   Ascus epiplasm.
//
ID   Attachment organelle.
AC   SL-0020
DE   The attachment organelle is a multifunctional polar structure found in
DE   several Mycoplasma species. This large and complex cell extension,
DE   whose predicted mass is greater than that of a vertebrate nuclear pore
DE   complex, is essential for adherence to host cells, is involved in
DE   gliding motility, and is associated with cell division.
SY   Terminal organelle.
SL   Cell projection, attachment organelle.
HI   Cell projection.
GO   GO:0033099; attachment organelle
//
ID   Attachment organelle membrane.
AC   SL-0021
DE   The membrane surrounding the attachment organelle.
SY   Terminal organelle membrane.
SL   Cell projection, attachment organelle membrane.
HP   Attachment organelle.
HP   Cell membrane.
GO   GO:0033111; attachment organelle membrane
//
ID   Autolysosome.
AC   SL-0535
DE   The autolysosome is a single-membrane organelle resulting from the
DE   fusion of a double-membrane autophagosome with a lysosome during
DE   macroautophagy. The outer membrane of the autophagosome fuses with the
DE   lysosome membrane whereas the inner membrane and the autophagic cargo
DE   are released into the lumen and degraded. Alternatively, the
DE   convergence of macroautophagy and endocytosis produces a single-
DE   membrane amphisome that also results in an autolysosome upon fusion
DE   with a lysosome.
SY   Degrading autophagic vacuole.
SL   Autolysosome.
HI   Autophagosome.
HI   Lysosome.
GO   GO:0044754; autolysosome
//
ID   Autolysosome lumen.
AC   SL-0537
DE   The autolysosome lumen is the area enclosed by the autolysosomal
DE   membrane.
SY   Degrading autophagic vacuole lumen.
SL   Autolysosome lumen.
HP   Autolysosome.
//
ID   Autolysosome membrane.
AC   SL-0536
DE   The membrane surrounding the autolysosome.
SL   Autolysosome membrane.
HI   Membrane.
HP   Autolysosome.
//
ID   Autophagosome.
AC   SL-0023
DE   The autophagosome is a double membrane vesicle involved in the
DE   degradation of long-lived proteins, unnecessary or damaged organelles
DE   as well as other cellular constituents such as lipids or
DE   carbohydrates. Crescent-shape isolation membranes or phagophores can
DE   sequester cytoplasm and organelles giving rise to autophagosomes. The
DE   outer membrane of the autophagosomes then fuse with vacuoles and/or
DE   lysosomes and the inner membrane vesicles (termed autophagic bodies)
DE   are released into the vacuole/lysosome lumen. These vesicles are then
DE   lysed and the contents are degraded by resident hydrolases.
SY   Autophagic vacuole.
SL   Cytoplasmic vesicle, autophagosome.
HI   Cytoplasmic vesicle.
GO   GO:0005776; autophagosome
//
ID   Autophagosome lumen.
AC   SL-0318
DE   The autophagosomal compartment bounded by the autophagosomal membrane.
SY   Autophagic vacuolar lumen; Autophagic vacuole lumen;
SY   Autophagosomal lumen.
SL   Cytoplasmic vesicle, autophagosome lumen.
HI   Cytoplasmic vesicle lumen.
HP   Autophagosome.
GO   GO:0034423; autophagosome lumen
//
ID   Autophagosome membrane.
AC   SL-0022
DE   The membrane surrounding the autophagosome.
SY   Autophagic vacuolar membrane; Autophagic vacuole membrane;
SY   Autophagosomal membrane.
SL   Cytoplasmic vesicle, autophagosome membrane.
HI   Cytoplasmic vesicle membrane.
HP   Autophagosome.
GO   GO:0000421; autophagosome membrane
//
ID   Axon.
AC   SL-0279
DE   The axon is the long process of a neuron that conducts nerve impulses,
DE   usually away from the cell body to the terminals and varicosities,
DE   which are sites of storage and release of neurotransmitter.
SY   Axon shaft.
SL   Cell projection, axon.
HI   Neuron projection.
GO   GO:0030424; axon
//
ID   Bacterial extracellular vesicle.
AC   SL-0489
DE   Small membrane vesicle (< 1 um) that buds off a prokaryotic cell's
DE   plasma membrane, able to carry proteins, phospholipids,
DE   lipopolysaccharides, nucleic acids, viruses, etc. Bacterial
DE   extracellular vesicles are important in intercellular communication
DE   and pathogenesis, and can exist within host cells.
SY   Bacterial membrane vesicle; Membrane vesicle; Microvesicle.
SL   Extracellular vesicle, bacterial extracellular vesicle.
HI   Extracellular vesicle.
GO   GO:0097691; bacterial extracellular vesicle
//
ID   Bacterial flagellum.
AC   SL-0307
DE   The flagellum of Bacteria is a long hair-like cell surface appendage.
DE   The flagellar apparatus consists of the flagellar filament made of
DE   polymerized flagellin (the propeller), the hook-like structure near
DE   the cell surface (the universal joint) and the basal body (the engine)
DE   which is a rod and a system of rings embedded in the cell envelope.
DE   The basal body and the hook anchor the whip-like filament to the cell
DE   surface. The flagellum is a rotating structure whose switches propels
DE   the cell through a liquid medium.
SY   Bacterial flagella; Bacterial flagellar apparatus.
SL   Bacterial flagellum.
KW   KW-0975
GO   GO:0009288; bacterial-type flagellum
//
ID   Bacterial flagellum basal body.
AC   SL-0142
DE   The basal body of a bacterial flagellum is a rod and a system of rings
DE   embedded in the cell envelope. Gram-negative flagella usually have an
DE   L ring in the plane of the lipopolysaccharide in the outer membrane, a
DE   periplasmic P ring in the plane of the peptidoglycan around the
DE   flagellar rod and a MS ring that is located within and above the
DE   cytoplasmic membrane. A C ring extends into the cytoplasm. The rod is
DE   a major component of the flagellar basal body and it spans the
DE   bacterial periplasm. The L and P rings are not found in Gram-positive
DE   bacteria.
SY   Bacterial flagellar basal body; Bacterial flagellar kinetosome;
SY   Bacterial flagellar motor.
SL   Bacterial flagellum basal body.
HP   Bacterial flagellum.
GO   GO:0009425; bacterial-type flagellum basal body
//
ID   Bacterial flagellum filament.
AC   SL-0358
DE   The bacterial flagellar filament is made of polymerized flagellin.
SY   Bacterial flagella filament; Bacterial flagellar filament.
SL   Bacterial flagellum filament.
HP   Bacterial flagellum.
GO   GO:0009420; bacterial-type flagellum filament
//
ID   Bacterial flagellum hook.
AC   SL-0357
DE   The hook of a bacterial flagellum connects the basal body and the
DE   filament and acts as a universal joint. This flexible hinge relays the
DE   energy generated by the motor into torque formation that is
DE   transferred onto the rigid filament.
SY   Bacterial flagella hook; Bacterial flagellar hook.
SL   Bacterial flagellum hook.
HP   Bacterial flagellum.
GO   GO:0009424; bacterial-type flagellum hook
//
ID   Bacterial microcompartment.
AC   SL-0544
DE   Bacterial microcompartments (BMC) are proteinaceous polyhedral shells
DE   that encapsulate enzymes. The selectively permeable organelles protect
DE   their contents from the cytoplasm and/or the cytoplasm from reactants
DE   in their interior. The best characterized BMC is the carboxysome,
DE   which encapsulates RuBisCO and carbonic anhydrase, and enhances
DE   autotrophic CO(2) fixation. Other characterized BMCs encapsulate
DE   enzymes involved in ethanolamine or propanediol degradation; both
DE   pathways make toxic intermediates. Artifical BMCs can be expressed and
DE   filled with cargo proteins for biotechnological uses. BMCs are found
DE   in many bacterial phyla; in most cases their cargo is unknown.
SY   Metabolosome; Polyhedral organelle.
SL   Bacterial microcompartment.
KW   KW-1283
//
ID   Barrier septum.
AC   SL-0454
DE   The barrier septum, is a septum which spans a cell and does not allow
DE   exchange of organelles or cytoplasm between compartments.
SL   Barrier septum.
HI   Cell septum.
GO   GO:0000935; division septum
//
ID   Basal cell membrane.
AC   SL-0024
DE   The basal cell membrane is the fraction of the plasma membrane at the
DE   basal side of the cell, which faces the underlying connective tissue.
SY   Basal plasma membrane.
SL   Basal cell membrane.
HP   Cell membrane.
GO   GO:0009925; basal plasma membrane
//
ID   Basement membrane.
AC   SL-0025
DE   The basement membrane is a highly specialized extracellular matrix
DE   structure undelying the basal surface of cells exhibiting polarity
DE   (epithelial, endothelial and mesothelial cells) and surrounding
DE   certain cell types such as muscle, adipose and Schwann cells.
SL   Secreted, extracellular space, extracellular matrix, basement membrane.
HI   Extracellular matrix.
KW   KW-0084
GO   GO:0005604; basement membrane
//
ID   Basolateral cell membrane.
AC   SL-0026
DE   The basolateral cell membrane is the fraction of the plasma membrane
DE   at the basolateral side of the cell, which faces adjacent cells and
DE   the underlying connective tissue.
SY   Basolateral plasma membrane.
SL   Basolateral cell membrane.
HP   Cell membrane.
GO   GO:0016323; basolateral plasma membrane
//
ID   Bleb.
AC   SL-0472
DE   These cellular membrane protrusions are the result of actomyosin
DE   contractions of the cortex, which cause either transient detachment of
DE   the cell membrane from the actin cortex or a rupture in the actin
DE   cortex. Then, cytosol streams out of the cell body and inflates the
DE   newly formed bleb. Once expansion slows, an actin cortex is
DE   reconstituted. Retraction is powered by myosin motor proteins.
DE   Blebbing is a common feature of cell physiology during cell movement,
DE   cytokinesis, cell spreading and apoptosis.
SL   Cell projection, bleb.
HI   Cell projection.
GO   GO:0032059; bleb
RX   PubMed=17318224; DOI=10.1038/nrm2122;
//
ID   Bud.
AC   SL-0027
DE   A growing bud is an asexual reproductive structure, as in yeast or a
DE   hydra, that consists of an outgrowth capable of developing into a new
DE   individual.
SY   Growing bud.
SL   Bud.
GO   GO:0005933; cellular bud
//
ID   Bud membrane.
AC   SL-0028
DE   The membrane surrounding a bud.
SY   Cellular bud membrane.
SL   Bud membrane.
HP   Bud.
HP   Cell membrane.
GO   GO:0033101; cellular bud membrane
//
ID   Bud neck.
AC   SL-0029
DE   The bud neck is a constriction between the mother and the daughter
DE   cell (bud) in an organism that reproduces by budding. This structure
DE   comprises the septin ring, an hourglass-shaped collar around the
DE   mother-bud neck, which splits into two rings flanking the division
DE   plane at cytokinesis and that acts as a diffusion barrier to maintain
DE   polarity factors in the bud and as a scaffold to recruit actomyosin
DE   contractile ring components.
SY   Cellular bud neck.
SL   Bud neck.
HP   Bud.
GO   GO:0005935; cellular bud neck
//
ID   Bud tip.
AC   SL-0030
DE   The bud tip is the distal tip of the bud opposite to the site of
DE   attachment to the mother cell.
SY   Cellular bud tip.
SL   Bud tip.
HP   Bud.
GO   GO:0005934; cellular bud tip
//
ID   Cajal body.
AC   SL-0031
DE   The nuclear Cajal bodies (CBs) are small subnuclear membraneless
DE   organelles present either free in the nucleoplasm and/or physically
DE   associated to specific regions of chromatin. CBs contain newly
DE   assembled small nuclear ribonucleoproteins (snRNPs) and small
DE   nucleolar ribonucleoproteins (snoRNPs) particles, which are involved
DE   in pre-mRNA splicing and in ribosomal RNA processing, respectively.
DE   Mammalian nucleus in interphase, show 2-6 CBs, as irregular, punctuate
DE   structures, which vary in size and shape and which are often
DE   juxtaposed to nucleoli. At the electronic-microscope level, they are
DE   composed of heterogeneous mixture of electro-dense particles with
DE   diameters ranging from 20-25 nm and are called coiled body. Structures
DE   similar to CBs have been identified in the amphibian oocyte nucleus
DE   (called sphere organelles) and in insect (called endobodies). CBs are
DE   motile and dynamic structures. Both their protein and RNA-protein
DE   components can cycle continuously between CBs and other nuclear
DE   locations depending on the transcriptional state of the cell.
SY   Cajal bodies; Coiled body; Endobodies; Nucleolar accessory bodies;
SY   Sphere organelles.
SL   Nucleus, Cajal body.
HI   Nuclear body.
HP   Nucleus.
GO   GO:0015030; Cajal body
//
ID   Calyx.
AC   SL-0032
DE   The calyx is a large cytoskeletal component of the perinuclear theca
DE   of the mammalian sperm head.
SY   Calyces; Cytoskeletal calyx.
SL   Cytoplasm, cytoskeleton, perinuclear theca, calyx.
HP   Perinuclear theca.
GO   GO:0033150; cytoskeletal calyx
//
ID   Capsule.
AC   SL-0033
DE   The capsule is a protective structure surrounding some bacteria or
DE   fungi. The bacterial capsule is a layer of material, usually
DE   polysaccharide, attached to the cell wall possibly via covalent
DE   attachments to either phospholipid or lipid-A molecules. It has
DE   several functions: promote bacterial adhesion to surfaces or
DE   interaction with other organisms; act as a permeability barrier, as a
DE   defense mechanism against phagocytosis and/or as a nutrient reserve.
DE   Among pathogens, capsule formation often correlates with
DE   pathogenicity. The fungal capsule is an extracellular layer which lies
DE   outside the cell wall and it is usually composed of polysaccharides.
DE   It protects the cell from different environmental dangers such as
DE   phagocytosis, dessication, etc.
SL   Secreted, capsule.
HP   Cell envelope.
HP   Secreted.
GO   GO:0042603; capsule
//
ID   Carboxysome.
AC   SL-0034
DE   Carboxysomes are bacterial microcompartments in which ribulose
DE   bisphosphate carboxylase (RuBisCO)-mediated CO(2) fixation occurs. The
DE   cytoplasmic polyhedral inclusion bodies are surrounded by a thin
DE   protein coat. They enhance autotrophic CO(2) fixation in air by
DE   increasing the CO(2) concentration around RuBisCO, thus reducing its
DE   reaction with O(2), a competing substrate. They contain carbonic
DE   anhydrase as part of the CO(2) concentration mechanism.
SL   Carboxysome.
HI   Bacterial microcompartment.
KW   KW-1282
GO   GO:0031470; carboxysome
//
ID   Caveola.
AC   SL-0035
DE   The caveola is a small (apparently) uncoated pit mostly found in the
DE   cell membrane of many highly differentiated mammalian cells, such as
DE   adipocytes, endothelial cells and muscle cells. These flask-shaped
DE   invaginations are defined by the presence of caveolins and contains a
DE   subset of lipid-raft components, including cholesterol and
DE   sphingolipids. Caveolae each comprise a caveolar bulb with a diameter
DE   of 60-80 nm, connected to an opening of fairly constant diameter.
DE   Caveolae might exists as single pits or can form a cluster of caveolae
DE   with non-caveolar membrane between the pits. In many tissues, and
DE   particularly in adipocytes, multiple caveolae are arranged around a
DE   central vacuolar domain. In developing muscle fibres, multiple
DE   caveolae are connected by a single neck to the cell membrane,
DE   producing large chains of interconnected caveolae. Another structural
DE   feature of caveolae in certain endothelia is the presence of a
DE   stomatal diaphragm, which consists of a central density and radial
DE   spikes, in the neck of the caveolae. Mature caveolae might be
DE   assembled in the Golgi apparatus. Caveolae can flatten out into the
DE   cell membrane, thereby loosing their caveolar identity.
SY   Caveolae; Membrane microdomain; Plasmalemmal vesicle.
SL   Membrane, caveola.
HP   Endomembrane system.
GO   GO:0005901; caveola
RX   PubMed=17318224; DOI=10.1038/nrm2122;
//
ID   Cell cortex.
AC   SL-0138
DE   The cell cortex is the cytoplasmic region under the cell membrane.
SL   Cytoplasm, cell cortex.
HP   Cytoplasm.
GO   GO:0005938; cell cortex
//
ID   Cell envelope.
AC   SL-0036
DE   The cell envelope comprises the cell membrane, the cell wall and an
DE   outer membrane if present. In bacteria with 1 membrane (Gram-positive)
DE   the cell envelope consists of the cytoplasmic membrane, cell wall and
DE   capsule. In bacteria with 2 membranes (Gram-negative) the envelope
DE   consists of the cytoplasmic membrane, cell wall, periplasmic space,
DE   outer membrane and capsule. The archaeal cell envelope generally
DE   consists of single membrane covered by a surface layer (S-layer).
DE   Ignicoccus species exceptionally have an outer membrane which encloses
DE   a large periplasmic space. Extreme thermophiles and acidophiles have
DE   tetraether type glycerophospholipids with C40 isoprenoid chains. The
DE   yeast cell envelope is a protecting capsule which consists of the
DE   cytoplasmic membrane, the periplasmic space, and the cell wall.
SY   Envelope.
SL   Cell envelope.
GO   GO:0031975; envelope
AN   Try to use a child/narrower/more specific term instead
WW   http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/ecce.htm
//
ID   Cell inner membrane.
AC   SL-0037
DE   The prokaryotic inner cell membrane is the selectively permeable
DE   membrane which separates the cytoplasm from the periplasm in
DE   prokaryotes with 2 membranes.
SY   Cytoplasmic membrane; Inner membrane; Plasma membrane.
SL   Cell inner membrane.
HI   Cell membrane.
KW   KW-0997
GO   GO:0005886; plasma membrane
//
ID   Cell junction.
AC   SL-0038
DE   The cell junction is a cell-cell or cell-extracellular matrix contact
DE   within a tissue of a multicellular organism, especially abundant in
DE   epithelia. In vertebrates, there are three major types of cell
DE   junctions: anchoring junctions (e.g. adherens junctions),
DE   communicating junctions (e.g. gap junctions) and occluding junctions
DE   (e.g. tight junctions).
SL   Cell junction.
KW   KW-0965
GO   GO:0030054; cell junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
WW   https://www.ncbi.nlm.nih.gov/books/NBK26857/
//
ID   Cell membrane.
AC   SL-0039
DE   The cell membrane is the selectively permeable membrane which
DE   separates the cytoplasm from its surroundings. Known as the cell inner
DE   membrane in prokaryotes with 2 membranes.
SY   Cytoplasmic membrane; Plasmalemma; Plasma membrane.
SL   Cell membrane.
HI   Membrane.
HP   Cell envelope.
HP   Endomembrane system.
KW   KW-1003
GO   GO:0005886; plasma membrane
//
ID   Cell outer membrane.
AC   SL-0040
DE   The prokaryotic outer cell membrane is the selectively permeable
DE   membrane which separates the prokaryotic periplasm from its cell
DE   surroundings. Traditionally only Gram-negative bacteria were thought
DE   of as having an outer membrane, but recent work has shown some
DE   Actinobacteria, including Mycobacterium tuberculosis, as well as at
DE   least 1 archaea (Ignicoccus hospitalis) have a cell outer membrane.
SY   Outer membrane.
SL   Cell outer membrane.
HI   Membrane.
KW   KW-0998
GO   GO:0009279; cell outer membrane
//
ID   Cell projection.
AC   SL-0280
DE   A cell projection is a cell protrusion such as pseudopodium,
DE   filopodium, lamellipodium, growth cone, flagellum, acrosome, axon, or
DE   bacterial comet tail. These membrane-cytoskeleton-coupled processes
DE   are involved in many biological functions, such as cell motility,
DE   cancer-cell invasion, endocytosis, phagocytosis, exocytosis, pathogen
DE   infection, neurite extension and cytokinesis.
SY   Cell protrusion.
SL   Cell projection.
KW   KW-0966
GO   GO:0042995; cell projection
//
ID   Cell septum.
AC   SL-0455
DE   A structure composed of peptidoglycan and often chitin in addition to
DE   other materials. It usually forms perpendicular to the long axis of a
DE   cell or hypha and grows centripetally from the cell wall to the center
DE   of the cell and often functions in the compartmentalization of a cell
DE   into two daughter cells.
SL   Cell septum.
GO   GO:0030428; cell septum
//
ID   Cell surface.
AC   SL-0310
DE   The outermost side of the cell.
SL   Cell surface.
GO   GO:0009986; cell surface
AN   Try to use a child/narrower/more specific term instead
//
ID   Cell tip.
AC   SL-0456
DE   The region at either end of the longest axis of a cylindrical or
DE   elongated cell, where polarized growth may occur.
SL   Cell tip.
GO   GO:0051286; cell tip
//
ID   Cell wall.
AC   SL-0041
DE   The complex and rigid layer surrounding the cell. Cell walls are found
DE   in bacteria, archaea, fungi, plants, and algae. The cell wall
DE   envelopes the inner or plasma membrane in all bacteria and is
DE   surrounded by the outer membrane in bacteria with 2 membranes (Gram-
DE   negative). Bacterial cell walls contain peptidoglycan while those of
DE   archaea are not made of peptidoglycan, but some archaea may contain
DE   pseudopeptidoglycan, which is composed of N-acetyltalosaminuronic
DE   acid, instead of N-acetyl muramic acid in peptidoglycan. The plant
DE   cell wall is made of fibrils of cellulose embedded in a matrix of
DE   several other kinds of polymers such as pectin and lignin. Algal cell
DE   walls are usually composed of cellulose, glycoproteins, sporopollenin,
DE   calcium and various polysaccharides such as manosyl, xylanes, alginic
DE   acid. Diatom cell walls (or frustules) contain silica. The cell wall
DE   plays a role in cell shape, cell stability and development, and
DE   protection against environmental dangers.
SL   Secreted, cell wall.
HP   Cell envelope.
HP   Secreted.
KW   KW-0134
GO   GO:0005618; cell wall
//
ID   Cellular chromatophore membrane.
AC   SL-0042
DE   The cellular chromatophore membrane is the plasma-membrane derived
DE   internal, photosynthetic membrane found in the cytoplasm in purple
DE   photosynthetic bacteria. They contain the reaction centers, antennae
DE   complexes, cytochrome bc1 complex and the F(0)F(1)-ATPase.
SY   Chromatophore membrane.
SL   Cellular chromatophore membrane.
HI   Membrane.
HP   Endomembrane system.
GO   GO:0042717; plasma membrane-derived chromatophore membrane
//
ID   Cellular thylakoid.
AC   SL-0043
DE   A bacterial thylakoid membrane usually formed by extensive
DE   invaginations of the cell inner (plasma) membrane. In cyanobacteria
DE   thylakoids house the photosynthetic machinery and pigments. In
DE   Synechocystis sp. strain PCC 6803 the thylakoid membranes are
DE   physically discontinuous from the plasma membrane, and thus represent
DE   bona fide intracellular organelles.
SY   Bacterial thylakoid.
SL   Cellular thylakoid.
HI   Thylakoid.
GO   GO:0030075; bacterial thylakoid
//
ID   Cellular thylakoid lumen.
AC   SL-0044
DE   The lumen of the cellular thylakoid.
SL   Cellular thylakoid lumen.
HP   Cellular thylakoid.
GO   GO:0031979; plasma membrane-derived thylakoid lumen
//
ID   Cellular thylakoid membrane.
AC   SL-0045
DE   The membrane of the cellular thylakoid.
SL   Cellular thylakoid membrane.
HI   Membrane.
HP   Cellular thylakoid.
HP   Endomembrane system.
GO   GO:0031676; plasma membrane-derived thylakoid membrane
//
ID   Centriolar satellite.
AC   SL-0485
DE   Centriolar satellites are nonmembranous, electron-dense and spherical
DE   cytoplasmic granules of about 70-100 nm in diameter, occurring around
DE   centrosomes in most vertebrate cell types. They contain a number of
DE   centrosomal proteins. Centriolar satellites have the ability to move
DE   along microtubules, toward their minus ends, i.e. toward centrosomes.
DE   Their number increase during interphase and decrease during mitosis.
SY   Massule; satellites.
SL   Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriolar satellite.
HP   Centrosome.
//
ID   Centriole.
AC   SL-0046
DE   The centriole is a barrel-shaped microtubule-based structure. A pair
DE   of centrioles, embedded in the so-called pericentriolar material,
DE   constitute the centrosome, a microtubule organizing center of an
DE   eukaryotic cell. Centrioles are barrel-shaped microtubule-based
DE   structures organized in a 9-fold radial symmetry. Centriolar
DE   microtubule arrays usually consist of triplet microtubules, although
DE   doublets or singlets are present in some species. Centrioles are
DE   structurally related to (and often interconvertible with) basal
DE   bodies, the organelles required for the assembly of a cilium or
DE   flagellum.
SL   Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole.
HP   Centrosome.
GO   GO:0005814; centriole
//
ID   Centromere.
AC   SL-0047
DE   The centromere is a region of replicated eukaryotic chromosomes where
DE   the two chromatids are joined together.
SY   Chromosome, pericentric region.
SL   Chromosome, centromere.
HP   Chromosome.
KW   KW-0137
GO   GO:0000775; chromosome, centromeric region
//
ID   Centrosome.
AC   SL-0048
DE   The centrosome is a microtubule organizing center (MTOC) responsible
DE   for the nucleation and organisation of  microtubules. It is composed
DE   of two orthogonally arranged centrioles, each one having a barrel
DE   shaped microtubule structure, and their surrounding pericentriolar
DE   material (PCM).
SL   Cytoplasm, cytoskeleton, microtubule organizing center, centrosome.
HP   Microtubule organizing center.
GO   GO:0005815; microtubule organizing center
//
ID   Chloroplast.
AC   SL-0049
DE   The most common form of plastid, the chloroplast is a photosynthetic
DE   organelle found in all photosynthetic eukaryotes except
DE   glaucocystophyte algae (where it is called a cyanelle) and Paulinella
DE   species (where it is called an organellar chromatophore). In green
DE   (photosynthetic) tissue they house the machinery necessary for pigment
DE   biosynthesis, amino acid synthesis, lipid metabolism etc, as well as
DE   the machinery for photosynthesis and CO(2) fixation. They are
DE   surrounded by between 2 and 4 membranes and contain thylakoids in
DE   green tissue.
SL   Plastid, chloroplast.
HI   Plastid.
KW   KW-0150
GO   GO:0009507; chloroplast
//
ID   Chloroplast envelope.
AC   SL-0050
DE   The envelope of a chloroplast comprises the inner and outer
DE   chloroplast membrane including the intermembrane space.
SY   Chloroplastic envelope.
SL   Plastid, chloroplast envelope.
HI   Plastid envelope.
HP   Chloroplast.
GO   GO:0009941; chloroplast envelope
//
ID   Chloroplast inner membrane.
AC   SL-0051
DE   The inner membrane of a chloroplast is the membrane which separates
DE   the chloroplast stroma from the intermembrane space.
SY   Chloroplastic inner membrane.
SL   Plastid, chloroplast inner membrane.
HI   Chloroplast membrane.
HI   Plastid inner membrane.
GO   GO:0009706; chloroplast inner membrane
//
ID   Chloroplast intermembrane space.
AC   SL-0052
DE   The intermembrane space between the inner and the outer chloroplast
DE   membranes.
SY   Chloroplastic intermembrane space.
SL   Plastid, chloroplast intermembrane space.
HI   Plastid intermembrane space.
HP   Chloroplast envelope.
GO   GO:0031972; chloroplast intermembrane space
//
ID   Chloroplast membrane.
AC   SL-0053
DE   The membrane surrounding a chloroplast. Also used when it is not clear
DE   in which chloroplast membrane (outer membrane, inner membrane or
DE   thylakoid) a protein is found.
SY   Chloroplastic membrane.
SL   Plastid, chloroplast membrane.
HI   Plastid membrane.
HP   Chloroplast envelope.
GO   GO:0031969; chloroplast membrane
//
ID   Chloroplast nucleoid.
AC   SL-0139
DE   The chloroplast nucleoid is the chloroplastic pseudocompartment formed
DE   by the chromatin-dense area. This region, which is functionally
DE   equivalent to the eukaryotic nucleus, is not surrounded by a membrane.
SY   Chloroplastic nucleoid.
SL   Plastid, chloroplast stroma, chloroplast nucleoid.
HP   Chloroplast stroma.
GO   GO:0042644; chloroplast nucleoid
//
ID   Chloroplast outer membrane.
AC   SL-0054
DE   The outer membrane of a chloroplast is the chloroplast membrane facing
DE   the cytoplasm.
SY   Chloroplastic outer membrane.
SL   Plastid, chloroplast outer membrane.
HI   Chloroplast membrane.
HI   Plastid outer membrane.
GO   GO:0009707; chloroplast outer membrane
//
ID   Chloroplast stroma.
AC   SL-0055
DE   The internal space enclosed by the chloroplast double membrane but
DE   excluding the thylakoid space. This space, filled with a colorless
DE   hydrophilic matrix, contains DNA, ribosomes and some temporary
DE   products of photosynthesis.
SY   Chloroplastic stroma.
SL   Plastid, chloroplast stroma.
HI   Plastid stroma.
HP   Chloroplast.
GO   GO:0009570; chloroplast stroma
//
ID   Chloroplast thylakoid.
AC   SL-0056
DE   The thylakoid of a chloroplast is an internal system of interconnected
DE   membranes, that carry out the light reactions of photosynthesis. They
DE   are arranged into stacked and unstacked regions called grana and
DE   stroma thylakoids, respectively, that are differentially enriched in
DE   photosystem I and II complexes. Although extensive, the thylakoid
DE   network in an individual chloroplast is thought to comprise a single
DE   lumenal compartment.
SL   Plastid, chloroplast thylakoid.
HI   Plastid thylakoid.
HP   Chloroplast.
GO   GO:0009534; chloroplast thylakoid
//
ID   Chloroplast thylakoid lumen.
AC   SL-0057
DE   The chloroplast thylakoid lumen is the chloroplast compartment bounded
DE   by the thylakoid membranes.
SL   Plastid, chloroplast thylakoid lumen.
HI   Plastid thylakoid lumen.
HP   Chloroplast thylakoid.
GO   GO:0009543; chloroplast thylakoid lumen
//
ID   Chloroplast thylakoid membrane.
AC   SL-0058
DE   The thylakoid membranes of a chloroplast is an internal system of
DE   interconnected membranes, that carry out the light reactions of
DE   photosynthesis. They are arranged into stacked and unstacked regions
DE   called grana and stroma thylakoids, respectively, that are
DE   differentially enriched in photosystem I and II complexes. Although
DE   extensive, the thylakoid network in an individual chloroplast is
DE   thought to comprise a single lumenal compartment.
SL   Plastid, chloroplast thylakoid membrane.
HI   Plastid thylakoid membrane.
HP   Chloroplast thylakoid.
GO   GO:0009535; chloroplast thylakoid membrane
//
ID   Chlorosome.
AC   SL-0059
DE   The chlorosome is a photosynthetic light-harvesting complex found in
DE   anoxygenic green bacteria. Chlorosomes are flattened ellipsoidal
DE   organelles appressed to the cytoplasmic face of the cell membrane.
DE   They typically contain highly aggregated bacteriochlorophyll c, d, or
DE   e (Bchl), a small amount of Bchl a, carotenoids, quinones, and
DE   occasionally wax esters. The chlorosome envelope of green sulfur
DE   bacteria is an asymmetric membrane containing galactolipids with the
DE   galactosyl moieties exposed on the outer surface. The farnesyl tails
DE   of the BChl molecules within the chlorosome probably comprise the
DE   inner leaflet of this membrane.
SL   Chlorosome.
KW   KW-0151
GO   GO:0046858; chlorosome
RX   PubMed=16866355; DOI=10.1021/bi060776y;
//
ID   Chlorosome envelope.
AC   SL-0060
DE   The chlorosome envelope of green sulfur bacteria is an asymmetric
DE   membrane containing galactolipids with the galactosyl moieties exposed
DE   on the outer surface. The farnesyl tails of the BChl c molecules
DE   within the chlorosome probably comprise the inner leaflet of this
DE   membrane.
SY   Chlorosomal envelope.
SL   Chlorosome, chlorosome envelope.
HP   Chlorosome.
GO   GO:0033105; chlorosome envelope
//
ID   Chromaffin granule.
AC   SL-0061
DE   A chromaffin granule is a specialized secretory vesicle characteristic
DE   of chromaffin cells.
SL   Cytoplasmic vesicle, secretory vesicle, chromaffin granule.
HI   Secretory vesicle.
GO   GO:0042583; chromaffin granule
//
ID   Chromaffin granule lumen.
AC   SL-0349
DE   The chromaffin granule comparment bounded by the chromaffin granule
DE   membrane.
SY   Chromaffin granular lumen.
SL   Cytoplasmic vesicle, secretory vesicle, chromaffin granule lumen.
HI   Secretory vesicle lumen.
HP   Chromaffin granule.
GO   GO:0034466; chromaffin granule lumen
//
ID   Chromaffin granule membrane.
AC   SL-0062
DE   The chromaffin granule membrane is the membrane surrounding a
DE   chromaffin granule, a specialized secretory vesicle characteristic of
DE   chromaffin cells.
SY   Chromaffin granular membrane.
SL   Cytoplasmic vesicle, secretory vesicle, chromaffin granule membrane.
HI   Secretory vesicle membrane.
HP   Chromaffin granule.
GO   GO:0042584; chromaffin granule membrane
//
ID   Chromoplast.
AC   SL-0063
DE   A chromoplast is a plastid containing pigments other than chlorophyll.
DE   Found in flower, petals and fruit.
SL   Plastid, chromoplast.
HI   Plastid.
GO   GO:0009509; chromoplast
//
ID   Chromoplast membrane.
AC   SL-0064
DE   The membrane surrounding the chromoplast. Also used when it is not
DE   clear in which chromoplast membrane (outer membrane, inner membrane or
DE   thylakoid) a protein is found.
SY   Chromoplastic membrane.
SL   Plastid, chromoplast membrane.
HI   Plastid membrane.
HP   Chromoplast.
GO   GO:0046862; chromoplast membrane
//
ID   Chromoplast stroma.
AC   SL-0065
DE   The chromoplast stroma is the space enclosed by the chromoplast double
DE   membrane but excluding the photosynthetic material. The chromoplast is
DE   a plastid containing pigments other than chlorophyll.
SY   Chromoplastic stroma.
SL   Plastid, chromoplast stroma.
HP   Chromoplast.
GO   GO:0009575; chromoplast stroma
//
ID   Chromosome.
AC   SL-0468
DE   An organized structure composed of a single very long molecule of
DE   coiled DNA and associated proteins (e.g. histones) that carries
DE   hereditary information.
SY   Chromoplastic stroma.
SL   Chromosome.
KW   KW-0158
GO   GO:0005694; chromosome
//
ID   Cilium.
AC   SL-0066
DE   The cilium is a cell surface projection found at the surface of a
DE   large proportion of eukaryotic cells. The two basic types of cilia,
DE   motile (alternatively named flagella) and non-motile, collectively
DE   perform a wide variety of functions broadly encompassing cell/fluid
DE   movement and sensory perception. Their most prominent structural
DE   component is the axoneme which consists of nine doublet microtubules,
DE   with all motile cilia - except those at the embryonic node
DE   - containing an additional central pair of microtubules. The axonemal
DE   microtubules of all cilia nucleate and extend from a basal body, a
DE   centriolar structure most often composed of a radial array of nine
DE   triplet microtubules. In most cells, basal bodies associate with cell
DE   membranes and cilia are assembled as 'extracellular' membrane-enclosed
DE   compartments.
SY   Cilia.
SL   Cell projection, cilium.
HI   Cell projection.
GO   GO:0005929; cilium
//
ID   Cilium axoneme.
AC   SL-0304
DE   The cilium axoneme is the most prominent structural component of the
DE   cilium. It consists of nine doublet microtubules, with all motile
DE   cilia - except those at the embryonic node - containing an additional
DE   central pair of microtubules. The axonemal microtubules of all cilia
DE   nucleate and extend from a basal body, a centriolar structure most
DE   often composed of a radial array of nine triplet microtubules. In most
DE   cells, basal bodies associate with cell membranes and cilia are
DE   assembled as 'extracellular' membrane-enclosed compartments.
SY   Ciliary axoneme.
SL   Cytoplasm, cytoskeleton, cilium axoneme.
HP   Cilium.
HP   Cytoskeleton.
//
ID   Cilium basal body.
AC   SL-0087
DE   The basal body is a barrel-shaped microtubule-based structure required
DE   for the formation of cilia. Basal bodies, structuraly related to and
DE   often interconvertible with centrioles, serves as a nucleation site
DE   for axoneme growth.
SY   Ciliary basal body; Ciliary kinetosome; Cilium kinetosome.
SL   Cytoplasm, cytoskeleton, cilium basal body.
HP   Cilium.
HP   Cytoskeleton.
//
ID   Cilium membrane.
AC   SL-0305
DE   The portion of the cell membrane surrounding the cilium.
SY   Ciliary membrane.
SL   Cell projection, cilium membrane.
HP   Cell membrane.
HP   Cilium.
GO   GO:0060170; ciliary membrane
//
ID   cis-Golgi network.
AC   SL-0067
DE   The cis-Golgi network is an extensive tubulovesicular network bound to
DE   the cis face of the Golgi stack and which function is to receive
DE   process the biosynthetic output from the ER.
SY   CGN; cis-Golgi; cis-Golgi complex; Golgi cis-face.
SL   Golgi apparatus, cis-Golgi network.
HP   Golgi apparatus.
GO   GO:0005801; cis-Golgi network
AN   The CGN is not the cis cisternae of the Golgi stack. Compartment
AN   specific marker: GOLGA2/GM130.
//
ID   cis-Golgi network membrane.
AC   SL-0068
DE   The lipid bilayer surrounding any of the compartments that make up the
DE   cis-Golgi network.
SY   CGN membrane; cis-Golgi complex membrane; cis-Golgi membrane;
SY   Golgi cis-face membrane.
SL   Golgi apparatus, cis-Golgi network membrane.
HI   Golgi apparatus membrane.
HP   cis-Golgi network.
GO   GO:0033106; cis-Golgi network membrane
//
ID   Clathrin-coated pit.
AC   SL-0069
DE   Coated pits are regions of the cell membrane specialized in receptor-
DE   mediated endocytosis. Their cytoplasmic surface is coated with a
DE   bristlelike structure made of clathrin. During the first steps of
DE   endocytosis, clathrin-coated pits are internalized to form clathrin-
DE   coated vesicles which transport proteins from organelle to organelle.
SL   Membrane, clathrin-coated pit.
HI   Coated pit.
GO   GO:0005905; clathrin-coated pit
//
ID   Clathrin-coated vesicle.
AC   SL-0070
DE   Clathrin coated vesicles (CCVs) mediate the vesicular transport of
DE   cargo such as proteins between organelles in the post-Golgi network
DE   connecting the trans-Golgi network, endosomes, lysosomes and the cell
DE   membrane. CCVs that bud from the cell membrane reveal a striking
DE   polyhedral pattern reminiscent of a fullerene which arises from the
DE   outermost protein in the coat, clathrin. Clathrin assembles from
DE   three-legged individual components called triskelions to form a
DE   polygonal lattice around the vesicle. Clathrin is a large
DE   heterohexameric protein complex composed of three heavy chains and
DE   three light chains. Clathrin molecules self-assemble together to make
DE   a spherical clathrin lattice structure, a polyhedron made of regular
DE   pentagons and hexagons. The clathrin lattice serves as a mechanical
DE   scaffold but is itself unable to bind directly to membrane components.
DE   The connection of the clathrin scaffold to the membrane is mediated by
DE   clathrin adaptors, which can bind directly to both the clathrin
DE   lattice and to the lipid and protein components of membranes.
DE   Clathrin-associated adaptor protein (AP) complexes are a
DE   stoichiometric coat component of CCVs alongside clathrin itself, and
DE   are considered a major clathrin adaptor contributing the CCV
DE   formation.
SY   CCV.
SL   Cytoplasmic vesicle, clathrin-coated vesicle.
HI   Cytoplasmic vesicle.
GO   GO:0030136; clathrin-coated vesicle
//
ID   Clathrin-coated vesicle lumen.
AC   SL-0319
DE   The clathrin-coated vesicle compartment bounded by the clathrin-coated
DE   vesicle membrane.
SY   Clathrin-coated vesicular lumen.
SL   Cytoplasmic vesicle, clathrin-coated vesicle lumen.
HI   Cytoplasmic vesicle lumen.
HP   Clathrin-coated vesicle.
//
ID   Clathrin-coated vesicle membrane.
AC   SL-0071
DE   The membrane surrounding a clathrin-coated vesicle (CCV). CCVs mediate
DE   the vesicular transport of cargo such as proteins between organelles
DE   in the post-Golgi network connecting the trans-Golgi network,
DE   endosomes, lysosomes and the cell membrane. CCVs that bud from the
DE   cell membrane reveal a striking polyhedral pattern reminiscent of a
DE   fullerene which arises from the outermost protein in the coat,
DE   clathrin. Clathrin assembles from three-legged individual components
DE   called triskelions to form a polygonal lattice around the vesicle.
DE   Clathrin is a large heterohexameric protein complex composed of three
DE   heavy chains and three light chains. Clathrin molecules self-assemble
DE   together to make a spherical clathrin lattice structure, a polyhedron
DE   made of regular pentagons and hexagons. The clathrin lattice serves as
DE   a mechanical scaffold but is itself unable to bind directly to
DE   membrane components. The connection of the clathrin scaffold to the
DE   membrane is mediated by clathrin adaptors, which can bind directly to
DE   both the clathrin lattice and to the lipid and protein components of
DE   membranes. Clathrin-associated adaptor protein (AP) complexes are a
DE   stoichiometric coat component of CCVs alongside clathrin itself, and
DE   are considered a major clathrin adaptor contributing the CCV
DE   formation.
SY   Clathrin-coated vesicular membrane.
SL   Cytoplasmic vesicle, clathrin-coated vesicle membrane.
HI   Cytoplasmic vesicle membrane.
HP   Clathrin-coated vesicle.
GO   GO:0030665; clathrin-coated vesicle membrane
//
ID   Cleavage furrow.
AC   SL-0467
DE   In fungal, amoeboid and animal cells, during the cytokinesis at the
DE   end of cell division, a cleavage furrow forms in the plasma membrane.
DE   A contractile ring containing actin and myosin is assembled at the
DE   selected site of the future cleavage furrow. Ring contraction produces
DE   the force to constrict the cleavage furrow and the daughter cells
DE   separate by membrane fusion.
SL   Cleavage furrow.
GO   GO:0032154; cleavage furrow
//
ID   Coated pit.
AC   SL-0072
DE   Coated pits are regions of the donor membrane where the assembly of
DE   the vesicle coat take place. The coat assembles from soluble protomers
DE   such as coat protein complex-I and coat protein complex-II. The
DE   components of the coat often define the intracellular sorting station,
DE   and contribute to both membrane deformation and local movement of the
DE   resulting transport intermediate following scission. During the first
DE   steps of the vesicle-mediated membrane transport, coated pits are
DE   internalized to form coated vesicles which transport proteins between
DE   distinct membrane-bound organelles.
SL   Membrane, coated pit.
HP   Endomembrane system.
KW   KW-0168
//
ID   Contractile vacuole.
AC   SL-0073
DE   A contractile vacuole (CV) complex is a membrane-bound osmoregulatory
DE   organelle of fresh water and soil amoebae and protozoa which
DE   segregates excess cytosolic water, acquired osmotically, and expel it
DE   to the cell exterior, so that the cytosolic osmolarity is kept
DE   constant under a given osmotic condition. Depending on the organism,
DE   the CV complex (CVC) shows different degrees of specialization of its
DE   tubular and vesicular elements. In the most elaborate CVCs of certain
DE   ciliates, e.g. Paramecium, a central vacuole, the contractile vacuole
DE   or cisterna, is surrounded by radially oriented ampullae or radial
DE   arms. These ampullae are connected to a network of channels. Excess
DE   cytosolic water, acquired osmotically, is segregated by the radial
DE   arms and enters the vacuole, so that the vacuole swells (the fluid-
DE   filling phase). The vacuole then rounds (the rounding phase) and the
DE   radial arms sever from the vacuole. The vacuole membrane then fuses
DE   with the plasma membrane at the pore region and the pore opens. The
DE   vacuole shrinks as its fluid is discharged through the pore (the
DE   fluid-discharging phase). The pore closes when the fluid has been
DE   discharged. The radial arms then reattach to the vacuole, so that the
DE   vacuole swells again as the fluid enters from the arms (the next
DE   fluid-filling phase).
SY   Contracile vacuole complex; CV; CVC.
SL   Contractile vacuole.
HI   Vacuole.
GO   GO:0000331; contractile vacuole
//
ID   Contractile vacuole lumen.
AC   SL-0320
DE   The contractile vacuole compartment bounded by the contractile vacuole
DE   membrane.
SY   Contractile vacuolar lumen.
SL   Contractile vacuole lumen.
HI   Vacuole lumen.
HP   Contractile vacuole.
//
ID   Contractile vacuole membrane.
AC   SL-0074
DE   The membrane surrounding a contractile vacuole. A contractile vacuole
DE   (CV) complex is a membrane-bound osmoregulatory organelle of fresh
DE   water and soil amoebae and protozoa which segregates excess cytosolic
DE   water, acquired osmotically, and expel it to the cell exterior, so
DE   that the cytosolic osmolarity is kept constant under a given osmotic
DE   condition.
SY   Contractile vacuolar membrane.
SL   Contractile vacuole membrane.
HI   Vacuole membrane.
HP   Contractile vacuole.
GO   GO:0031164; contractile vacuolar membrane
//
ID   COPI-coated vesicle.
AC   SL-0075
DE   COPI-coated vesicles mediate the vesicular transport of cargo such as
DE   proteins. COPI-coated vesicles are believed to bud from the cis-
DE   cisternae of the Golgi apparatus, mediate traffic from the cis-Golgi
DE   back to the ER (retrograde), and govern the flow pattern of materials
DE   within the Golgi stack. COPI is composed of the coatomer, which is a
DE   seven-subunit protein complex that participates in the formation of
DE   Golgi-derived coated vesicles. Evidence has also been presented for
DE   anterograde intra-Golgi transport mediated by COPI in yeast and
DE   mammals.
SY   Coat protein complex I.
SL   Cytoplasmic vesicle, COPI-coated vesicle.
HI   Cytoplasmic vesicle.
GO   GO:0030137; COPI-coated vesicle
//
ID   COPI-coated vesicle lumen.
AC   SL-0321
DE   The COPI-coated vesicle compartment bounded by the COPI-coated vesicle
DE   membrane.
SL   Cytoplasmic vesicle, COPI-coated vesicle lumen.
HI   Cytoplasmic vesicle lumen.
HP   COPI-coated vesicle.
//
ID   COPI-coated vesicle membrane.
AC   SL-0076
DE   The membrane surrounding a COPI-coated vesicle. COPI-coated vesicles
DE   mediate the vesicular transport of cargo such as proteins. COPI-coated
DE   vesicles are believed to bud from the cis-cisternae of the Golgi
DE   apparatus, mediate traffic from the cis-Golgi back to the ER
DE   (retrograde), and govern the flow pattern of materials within the
DE   Golgi stack. COPI is composed of the coatomer, which is a seven-
DE   subunit protein complex that participates in the formation of Golgi-
DE   derived coated vesicles. Evidence has also been presented for
DE   anterograde intra-Golgi transport mediated by COPI in yeast and
DE   mammals.
SL   Cytoplasmic vesicle, COPI-coated vesicle membrane.
HI   Cytoplasmic vesicle membrane.
HP   COPI-coated vesicle.
GO   GO:0030663; COPI-coated vesicle membrane
//
ID   COPII-coated vesicle.
AC   SL-0077
DE   COPII-coated vesicles mediate the vesicular transport of cargo such as
DE   proteins. COPII-coated vesicles are believed to bud from the
DE   endoplasmic reticulum be involved in the anterograde transport between
DE   the ER to Golgi and travel toward the Endoplasmic reticulum-Golgi
DE   intermediate compartment, where they fuse and release their contents
DE   (anterograde transport). The COPII coat has five main functional
DE   components that are highly conserved in all eukaryotic cells.
SY   Coat protein complexes II; ER to Golgi transport vesicle.
SL   Cytoplasmic vesicle, COPII-coated vesicle.
HI   Cytoplasmic vesicle.
GO   GO:0030134; COPII-coated ER to Golgi transport vesicle
//
ID   COPII-coated vesicle lumen.
AC   SL-0322
DE   The COPII-coated vesicle compartment bounded by the COPII-coated
DE   vesicle membrane.
SY   Coat protein complexes II lumen; ER to Golgi transport vesicle lumen.
SL   Cytoplasmic vesicle, COPII-coated vesicle lumen.
HI   Cytoplasmic vesicle lumen.
HP   COPII-coated vesicle.
//
ID   COPII-coated vesicle membrane.
AC   SL-0078
DE   The membrane surrounding a COPII-coated vesicle. COPII-coated vesicles
DE   mediate the vesicular transport of cargo such as proteins. COPII-
DE   coated vesicles are believed to bud from the endoplasmic reticulum be
DE   involved in the anterograde transport between the ER to Golgi and
DE   travel toward the Endoplasmic reticulum-Golgi intermediate
DE   compartment, where they fuse and release their contents (anterograde
DE   transport). The COPII coat has five main functional components that
DE   are highly conserved in all eukaryotic cells.
SY   Coat protein complexes II membrane;
SY   ER to Golgi transport vesicle membrane.
SL   Cytoplasmic vesicle, COPII-coated vesicle membrane.
HI   Cytoplasmic vesicle membrane.
HP   COPII-coated vesicle.
GO   GO:0012507; ER to Golgi transport vesicle membrane
//
ID   Cornified envelope.
AC   SL-0079
DE   The cornified envelope is a structure which is formed beneath the
DE   plasma membrane in terminally differentiating stratified squamous
DE   epithelia. It provides a vital physical barrier to these tissues in
DE   mammals and consists of a 10 nm thick layer of highly crosslinked
DE   insoluble proteins. In the specialized case of the epidermis, a 5 nm
DE   thick layer of ceramide lipids is covalently bound to the proteins.
DE   These organize extracellular lipids into orderly lamellae and,
DE   together, the cell envelope and extracellular lipids are essential for
DE   effective physical and water barrier function in the skin.
SL   Cornified envelope.
GO   GO:0001533; cornified envelope
//
ID   Cortical granule.
AC   SL-0541
DE   Cortical granules are secretory organelles located under the cell
DE   membrane of unfertilized oocytes. Following fertilization, cortical
DE   granules fuse with the oocyte's cell membrane and release their
DE   contents into the extracellular matrix. This exocytosis, known as the
DE   cortical reaction, is involved in the prevention of polyspermy.
DE   Cortical granules are found in all mammals and many other vertebrates,
DE   as well as some invertebrates.
SY   Cortical vesicle.
SL   Cytoplasmic vesicle, secretory vesicle, Cortical granule.
HI   Secretory vesicle.
GO   GO:0060473; cortical granule
//
ID   Cvt vesicle.
AC   SL-0080
DE   A cvt vesicle is a double membrane-layered vesicle implicated in the
DE   cytoplasm to vacuole targeting pathway.
SL   Cytoplasmic vesicle, cvt vesicle.
HI   Cytoplasmic vesicle.
GO   GO:0033107; Cvt vesicle
//
ID   Cvt vesicle lumen.
AC   SL-0323
DE   The cvt vesicle compartment bounded by the cvt vesicle membrane.
SL   Cytoplasmic vesicle, cvt vesicle lumen.
HI   Cytoplasmic vesicle lumen.
HP   Cvt vesicle.
//
ID   Cvt vesicle membrane.
AC   SL-0081
DE   The membrane surrounding a cvt vesicle. A cvt vesicle is a double
DE   membrane-layered vesicle implicated in the cytoplasm to vacuole
DE   targeting pathway.
SL   Cytoplasmic vesicle, cvt vesicle membrane.
HI   Cytoplasmic vesicle membrane.
HP   Cvt vesicle.
GO   GO:0033110; Cvt vesicle membrane
//
ID   Cyanelle.
AC   SL-0082
DE   A cyanelle is a photosynthetic organelle of glaucocystophyte algae.
DE   Cyanelles are surrounded by a double membrane and, in between, a
DE   peptidoglycan wall. Thylakoid membrane architecture is cyanobacteria-
DE   like. Historically, the term cyanelle is derived from a classification
DE   as endosymbiotic cyanobacteria, and thus is not fully correct.
SY   Cyanoplast; Muroplast.
SL   Plastid, cyanelle.
HI   Plastid.
KW   KW-0194
GO   GO:0009842; cyanelle
//
ID   Cyanelle envelope.
AC   SL-0479
DE   The envelope of a cyanelle comprises the inner and outer cyanelle
DE   membrane including the intermembrane space and the vestigal
DE   peptidoglycan layer.
SL   Plastid, cyanelle envelope.
HI   Plastid envelope.
HP   Cyanelle.
GO   GO:0033112; cyanelle envelope
//
ID   Cyanelle inner membrane.
AC   SL-0480
DE   The inner membrane of a cyanelle is the membrane which separates the
DE   cyanelle stroma from the intermembrane space.
SL   Plastid, cyanelle inner membrane.
HI   Cyanelle membrane.
HI   Plastid inner membrane.
HP   Cyanelle envelope.
GO   GO:0036012; cyanelle inner membrane
//
ID   Cyanelle intermembrane space.
AC   SL-0481
DE   The intermembrane space between the inner and the outer cyanelle
DE   membranes, it includes the vestigial peptidoglycan layer.
SY   Cyanelle periplasm.
SL   Plastid, cyanelle intermembrane space.
HI   Plastid intermembrane space.
HP   Cyanelle envelope.
GO   GO:0036014; cyanelle intermembrane space
//
ID   Cyanelle membrane.
AC   SL-0083
DE   The membrane surrounding a cyanelle, a photosynthetic organelle of
DE   glaucocystophyte algae. Also used when it is not clear in which
DE   cyanelle membrane (outer membrane, inner membrane or thylakoid) a
DE   protein is found.
SL   Plastid, cyanelle membrane.
HI   Plastid membrane.
HP   Cyanelle.
GO   GO:0033113; cyanelle membrane
//
ID   Cyanelle outer membrane.
AC   SL-0482
DE   The outer membrane of a cyanelle is the cyanelle membrane facing the
DE   cytoplasm.
SL   Plastid, cyanelle outer membrane.
HI   Cyanelle membrane.
HI   Plastid outer membrane.
HP   Cyanelle envelope.
GO   GO:0036013; cyanelle outer membrane
//
ID   Cyanelle stroma.
AC   SL-0350
DE   The internal space enclosed by the cyanelle double membrane but
DE   excluding the thylakoid space. This space, filled with a colorless
DE   hydrophilic matrix, contains DNA, ribosomes and some temporary
DE   products of photosynthesis.
SL   Plastid, cyanelle stroma.
HI   Plastid stroma.
HP   Cyanelle.
GO   GO:0034060; cyanelle stroma
//
ID   Cyanelle thylakoid.
AC   SL-0277
DE   The cyanelle thylakoid is an internal system of interconnected
DE   photosynthetic membranes resembling that of cyanobacteria found in the
DE   cyanelles of certain algae.
SL   Plastid, cyanelle thylakoid.
HI   Plastid thylakoid.
HP   Cyanelle.
GO   GO:0009843; cyanelle thylakoid
//
ID   Cyanelle thylakoid lumen.
AC   SL-0084
DE   The cyanelle thylakoid lumen is the cyanelle compartment bounded by
DE   the thylakoid membranes.
SL   Plastid, cyanelle thylakoid lumen.
HI   Plastid thylakoid lumen.
HP   Cyanelle thylakoid.
GO   GO:0033114; cyanelle thylakoid lumen
//
ID   Cyanelle thylakoid membrane.
AC   SL-0085
DE   The lipid bilayer membrane of any thylakoid within a cyanelle, a
DE   photosynthetic organelle of glaucocystophyte algae.
SL   Plastid, cyanelle thylakoid membrane.
HI   Plastid thylakoid membrane.
HP   Cyanelle thylakoid.
GO   GO:0033115; cyanelle thylakoid membrane
//
ID   Cytolytic granule.
AC   SL-0543
DE   A specialized secretory lysosome that is present in cells with
DE   cytolytic capability such as cytotoxic T lymphocytes and natural
DE   killer cells. Cytolytic granules mediate the storage and regulated
DE   excretion of lytic molecules for killing of target cells.
SY   Lytic granule, cytotoxic granule.
SL   Cytolytic granule.
HP   Lysosome.
GO   GO:0044194; cytolytic granule
//
ID   Cytolytic granule lumen.
AC   SL-0546
DE   The cytolytic granule comparment bounded by the cytolytic granule
DE   membrane.
SL   Cytolytic granule lumen.
HI   Lysosome lumen.
HP   Cytolytic granule.
//
ID   Cytolytic granule membrane.
AC   SL-0547
DE   The cytolytic granule membrane is the membrane surrounding a cytolytic
DE   granule.
SL   Cytolytic granule membrane.
HI   Lysosome membrane.
HP   Cytolytic granule.
//
ID   Cytoplasm.
AC   SL-0086
DE   The cytoplasm is the content of a cell within the plasma membrane and,
DE   in eukaryotics cells, surrounding the nucleus. This three-dimensional,
DE   jelly-like lattice interconnects and supports the other solid
DE   structures. The cytosol (the soluble portion of the cytoplasm outside
DE   the organelles) is mostly composed of water and many low molecular
DE   weight compounds. In eukaryotes, the cytoplasm also contains a network
DE   of cytoplasmic filaments (cytoskeleton).
SL   Cytoplasm.
KW   KW-0963
GO   GO:0005737; cytoplasm
//
ID   Cytoplasmic granule.
AC   SL-0281
DE   Protein found in or associated with cytoplasmic granules.
SL   Cytoplasmic granule.
//
ID   Cytoplasmic granule lumen.
AC   SL-0324
DE   The cytoplasmic granule compartment bounded by the cytoplasmic granule
DE   membrane.
SL   Cytoplasmic granule lumen.
HP   Cytoplasmic granule.
//
ID   Cytoplasmic granule membrane.
AC   SL-0282
DE   The membrane surrounding a cytoplasmic granule.
SL   Cytoplasmic granule membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Cytoplasmic granule.
//
ID   Cytoplasmic ribonucleoprotein granule.
AC   SL-0495
DE   Cytoplasmic ribonucleoprotein granule is a collective term for
DE   distinct protein and RNA foci inside the cytoplasm, including
DE   processing bodies (P-bodies), stress granules, neuronal
DE   ribonucleoprotein granule (neuronal transport granule) and germ
DE   granules (germline granules).
SY   Cytoplasmic mRNP granule; Cytoplasmic mRNP granules; mRNP granule;
SY   mRNP granules.
SL   Cytoplasm, Cytoplasmic ribonucleoprotein granule.
HP   Cytoplasm.
GO   GO:0036464; cytoplasmic ribonucleoprotein granule
AN   The synonym "cytoplasmic body/bodies" is also used to indicate
AN   cytoplasmic speckles or foci. In this case, the location "Cytoplasmic
AN   ribonucleoprotein granule" does not apply.
RX   PubMed=25531407; DOI=10.4161/15476286.2014.972208;
//
IO   Cytoplasmic side.
AC   SL-9910
DE   Protein found mostly on the cytoplasmic side of the membrane.
SL   Cytoplasmic side.
//
ID   Cytoplasmic vesicle.
AC   SL-0088
DE   The cytoplasmic vesicles mediate vesicular transport among the
DE   organelles of secretory and endocytic systems. These transport
DE   vesicles are classified by the identity of the protein coat used in
DE   their formation and also by the cargo they contain, e.g. clathrin-,
DE   COPI-, and COPII-coated vesicles, synaptic vesicles, secretory
DE   vesicles, phagosomes, etc.
SL   Cytoplasmic vesicle.
HI   Vesicle.
KW   KW-0968
//
ID   Cytoplasmic vesicle lumen.
AC   SL-0325
DE   The cytoplasmic vesicle compartment bounded by the cytoplasmic vesicle
DE   membrane.
SL   Cytoplasmic vesicle lumen.
HP   Cytoplasmic vesicle.
GO   GO:0060205; cytoplasmic vesicle lumen
//
ID   Cytoplasmic vesicle membrane.
AC   SL-0089
DE   The membrane surrounding a cytoplasmic vesicle. The cytoplasmic
DE   vesicles mediate vesicular transport among the organelles of secretory
DE   and endocytic systems.
SL   Cytoplasmic vesicle membrane.
HI   Membrane.
HP   Cytoplasmic vesicle.
HP   Endomembrane system.
GO   GO:0030659; cytoplasmic vesicle membrane
//
ID   Cytoskeleton.
AC   SL-0090
DE   The cytoskeleton is a dynamic three-dimensional filamentous structure
DE   in the cytoplasm. Its roles include maintenance of cell shape, cell
DE   movement (in eukaryotes), cytokinesis, and the organization of
DE   organelles or organelle-like structures within the cell. The
DE   cytoskeleton includes microfilaments (actin-like proteins),
DE   microtubules (tubulin-like proteins), the intermediate filaments
DE   (mostly in eukaryotes) and the MinD-ParA proteins, which appear to be
DE   unique to prokaryotes.
SL   Cytoplasm, cytoskeleton.
HP   Cytoplasm.
KW   KW-0206
GO   GO:0005856; cytoskeleton
//
ID   Cytosol.
AC   SL-0091
DE   The cytosol is the unstructured aqueous phase of the cytoplasm
DE   excluding organelles, membranes, and insoluble cytoskeletal
DE   components.
SL   Cytoplasm, cytosol.
HP   Cytoplasm.
GO   GO:0005829; cytosol
//
ID   Dendrite.
AC   SL-0283
DE   The dendrite is a short and typically branched process extending from
DE   the cell body of a neuron that receives and integrates signals coming
DE   from axons of other neurons, and conveys the resulting signal to the
DE   body of the cell.
SL   Cell projection, dendrite.
HI   Neuron projection.
GO   GO:0030425; dendrite
//
ID   Dendritic spine.
AC   SL-0284
DE   A dendritic spine is a small, club-like cell protrusion from neuronal
DE   dendrites that form the postsynaptic component of most excitatory
DE   synapses in the brain. Spines are complex, dynamic structures that
DE   contain a dense array of cytoskeletal, transmembrane, and scaffolding
DE   molecules. Despite their modest size, most spines contain at least
DE   some form of smooth endoplasmic reticulum, which in the largest spines
DE   takes the form of a specialized organelle called the "spine
DE   apparatus". These cell protrusions play a critical role in synaptic
DE   transmission and plasticity.
SY   Postsynaptic dendritic spine; Spine.
SL   Cell projection, dendritic spine.
HI   Postsynapse.
HP   Neuron projection.
GO   GO:0043197; dendritic spine
RX   PubMed=16443821; DOI=10.1152/physiol.00042.2005;
//
ID   Dendritic spine membrane.
AC   SL-0285
DE   The portion of the cell membrane surrounding the dendritic spine, a
DE   small, club-like cell protrusion from neuronal dendrites that form the
DE   postsynaptic component of most excitatory synapses in the brain.
SL   Cell projection, dendritic spine membrane.
HI   Postsynaptic cell membrane.
HP   Dendritic spine.
GO   GO:0032591; dendritic spine membrane
//
ID   Desmosome.
AC   SL-0092
DE   A desmosome (DS) is a button-like adhesion complex that stabilizes
DE   epithelial sheets by anchoring the intermediate filament cytoskeleton
DE   to the cell junction. Desmosomes are found particularly in tissues
DE   subjected to mechanical stress.
SY   DS; Macula adherens.
SL   Cell junction, desmosome.
HI   Cell junction.
GO   GO:0030057; desmosome
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
WW   http://celljunctions.med.nyu.edu/desmosomes/desframe.html
//
ID   Dynein axonemal particle.
AC   SL-0542
DE   Dynein axonemal particles are ciliated cell-specific cytoplasmic
DE   membrane-less organelles, where dynein axonemal assembly factors
DE   (DNAAFs) and chaperones flux through rapidly while dynein subunits are
DE   stably retained. May act in storage or assembly of axonemal dyneins
DE   for rapid deployment to cilia.
SY   DynAP.
SL   Dynein axonemal particle.
HP   Cytoplasm.
GO   GO:0120293; dynein axonemal particle
RX   PubMed=33263282; DOI=10.7554/elife.38497;
//
ID   Early endosome.
AC   SL-0094
DE   Early endosomes form a tubulovesicular network spread throughout the
DE   cortical cytoplasm of the cell. Early endosomes are the primary
DE   sorting station in the endocytic pathway from which endocytosed
DE   molecules can be recycled back to the cell membrane or targeted to
DE   degradation in the lysosomes. Loaded by endocytosed molecules in 1 to
DE   4 minutes, their acidic luminal pH around 6.0 allows ligand release
DE   from recycling receptors.
SL   Early endosome.
HP   Endosome.
GO   GO:0005769; early endosome
AN   Compartment specific marker: EEA1; Rab5; Rab4.
//
ID   Early endosome lumen.
AC   SL-0337
DE   The early endosomal compartment bounded by the membrane of early
DE   endosomes, which form a tubulovesicular network spread throughout the
DE   cortical cytoplasm of the cell.
SY   Early endosomal lumen.
SL   Early endosome lumen.
HI   Endosome lumen.
HP   Early endosome.
GO   GO:0031905; early endosome lumen
//
ID   Early endosome membrane.
AC   SL-0093
DE   The membrane surrounding the early endosomes, which form a
DE   tubulovesicular network spread throughout the cortical cytoplasm of
DE   the cell.
SY   Early endosomal membrane.
SL   Early endosome membrane.
HI   Endosome membrane.
HP   Early endosome.
GO   GO:0031901; early endosome membrane
//
ID   Encapsulin nanocompartment.
AC   SL-0550
DE   Proteinaceous polyhedral shells that encapsulate enzymes. The
DE   selectively permeable organelles protect their contents from their
DE   surrounding milieu and/or the milieu from reactants in their interior.
DE   The self-assembling, 25-42 nm nanocompartment shell, unlike larger
DE   bacterial microcompartments, is made of only 1 protein, and has only a
DE   few proteins inside. Shells 25 nm in diameter are made of 60 monomers,
DE   shells 32 nm are made of 180 monomers, while shells 42 nm in diameter
DE   are made of 240 monomers with T=1, T=3 or T=4 icosahedral symmetry
DE   respectively. The shell protein has an HK97-like fold and probably
DE   evolved from a viral protein. Artificial encapsulin nanocompartments
DE   can be expressed and filled with cargo proteins for biotechnological
DE   uses. They are found in many bacterial and a few archaeal phyla. In
DE   anammox bacteria they may be located inside the anammoxosome.
SL   Encapsulin nanocompartment.
KW   KW-1284
//
ID   Endomembrane system.
AC   SL-0147
DE   A collection of membranous structures involved in transport within the
DE   cell. The main components of the endomembrane system are endoplasmic
DE   reticulum, Golgi apparatus, vesicles and cell membrane and nuclear
DE   envelope. The endomembrane system does not include the membranes of
DE   mitochondria or plastids.
SY   Endomembrane.
SL   Endomembrane system.
HI   Membrane.
GO   GO:0012505; endomembrane system
AN   Try to use a child/narrower/more specific term instead
//
ID   Endoplasmic reticulum.
AC   SL-0095
DE   The endoplasmic reticulum (ER) is an extensive network of membrane
DE   tubules, vesicles and flattened cisternae (sac-like structures) found
DE   throughout the eukaryotic cell, especially those responsible for the
DE   production of hormones and other secretory products. The membrane is a
DE   continuation of the outer nuclear membrane, it encloses the cytosol
DE   cisternal spaces (or internal lumen), which are continuous with the
DE   nuclear periplasmic space. The ER sustains many general functions,
DE   including protein synthesis, protein modification, protein folding,
DE   insertion of membrane proteins, sequestration of calcium, production
DE   of phospholipids and steroids and transport of proteins destined for
DE   membranes and secretion.
SL   Endoplasmic reticulum.
KW   KW-0256
GO   GO:0005783; endoplasmic reticulum
AN   Compartment specific marker: PDI; calreticulin; calnexin.
//
ID   Endoplasmic reticulum lumen.
AC   SL-0096
DE   The lumen of the endoplasmic reticulum (ER) is the area enclosed by
DE   the endoplasmic reticulum membrane, an extensive network of membrane
DE   tubules, vesicles and flattened cisternae (sac-like structures) found
DE   throughout the eukaryotic cell, especially those responsible for the
DE   production of hormones and other secretory products.
SL   Endoplasmic reticulum lumen.
HP   Endoplasmic reticulum.
GO   GO:0005788; endoplasmic reticulum lumen
//
ID   Endoplasmic reticulum membrane.
AC   SL-0097
DE   The membrane surrounding the endoplasmic reticulum (ER). The
DE   endoplasmic reticulum is an extensive network of membrane tubules,
DE   vesicles and flattened cisternae (sac-like structures) found
DE   throughout the eukaryotic cell, especially those responsible for the
DE   production of hormones and other secretory products.
SL   Endoplasmic reticulum membrane.
HI   Membrane.
HP   Endoplasmic reticulum.
HP   Endomembrane system.
GO   GO:0005789; endoplasmic reticulum membrane
//
ID   Endoplasmic reticulum-Golgi intermediate compartment.
AC   SL-0098
DE   The ER-Golgi intermediate compartment is a collection of
DE   tubulovesicular membrane clusters in the vicinity of ER exit sites.
DE   The ERGIC mediates transport between the endoplasmic reticulum and the
DE   Golgi and is the first anterograde/retrograde sorting station in the
DE   secretory pathway. ERGIC has not been observed in yeast and plants.
SY   ERGIC; ER-Golgi intermediate compartment; IC;
SY   Intermediate compartment; Vesiculo-tubular cluster; VTC.
SL   Endoplasmic reticulum-Golgi intermediate compartment.
GO   GO:0005793; endoplasmic reticulum-Golgi intermediate compartment
AN   Compartment specific marker: LMAN1/ERGIC-53 (Also called P-58).
//
ID   Endoplasmic reticulum-Golgi intermediate compartment lumen.
AC   SL-0326
DE   The ERGIC compartment bounded by the ERGIC membrane.
SY   ERGIC lumen; ER-Golgi intermediate compartment lumen; IC lumen;
SY   Intermediate compartment lumen; Vesiculo-tubular cluster lumen;
SY   VTC lumen.
SL   Endoplasmic reticulum-Golgi intermediate compartment lumen.
HP   Endoplasmic reticulum-Golgi intermediate compartment.
//
ID   Endoplasmic reticulum-Golgi intermediate compartment membrane.
AC   SL-0099
DE   The membrane surrounding the ER-Golgi intermediate compartment, which
DE   is a collection of tubulovesicular membrane clusters in the vicinity
DE   of ER exit sites.
SY   ERGIC membrane; ER-Golgi intermediate compartment membrane;
SY   IC membrane; Intermediate compartment membrane;
SY   Vesiculo-tubular cluster membrane; VTC membrane.
SL   Endoplasmic reticulum-Golgi intermediate compartment membrane.
HI   Membrane.
HP   Endoplasmic reticulum-Golgi intermediate compartment.
HP   Endomembrane system.
GO   GO:0033116; endoplasmic reticulum-Golgi intermediate compartment membrane
//
ID   Endosome.
AC   SL-0101
DE   Endosomes are highly dynamic membrane systems involved in transport
DE   within the cell, they receive endocytosed cell membrane molecules and
DE   sort them for either degradation or recycling back to the cell
DE   surface. They also receive newly synthesised proteins destined for
DE   vacuolar/lysosomal compartments. In certain cell types, endosomal
DE   multivesicular bodies may fuse with the cell surface in an exocytic
DE   manner. These released vesicles are called exosomes.
SL   Endosome.
KW   KW-0967
GO   GO:0005768; endosome
//
ID   Endosome lumen.
AC   SL-0327
DE   The endosomal compartment bounded by the endosomal membrane.
SY   Endosomal lumen.
SL   Endosome lumen.
HP   Endosome.
GO   GO:0031904; endosome lumen
//
ID   Endosome membrane.
AC   SL-0100
DE   The membrane surrounding the endosome. Endosomes are highly dynamic
DE   membrane systems involved in transport within the cell, they receive
DE   endocytosed cell membrane molecules and sort them for either
DE   degradation or recycling back to the cell surface.
SY   Endosomal membrane.
SL   Endosome membrane.
HI   Membrane.
HP   Endosome.
HP   Endomembrane system.
GO   GO:0010008; endosome membrane
//
ID   Esterosome.
AC   SL-0109
DE   The esterosome is a crystalline inclusion body. This vesicle is filled
DE   with crystals of proteins showing sequence similarities with various
DE   esterases. The enclosing membrane has the characteristics of RER.
SL   Cytoplasmic vesicle, esterosome.
HI   Cytoplasmic vesicle.
GO   GO:0033117; esterosome
//
ID   Esterosome lumen.
AC   SL-0328
DE   The esterosomal compartment bounded by the esterosomal membrane.
SY   Esterosomal lumen.
SL   Cytoplasmic vesicle, esterosome lumen.
HI   Cytoplasmic vesicle lumen.
HP   Esterosome.
GO   GO:0034467; esterosome lumen
//
ID   Esterosome membrane.
AC   SL-0108
DE   The membrane surrounding the esterosome, a crystalline inclusion body
DE   is a vesicle filled with crystals of proteins showing sequence
DE   similarities with various esterases.
SY   Esterosomal membrane.
SL   Cytoplasmic vesicle, esterosome membrane.
HI   Cytoplasmic vesicle membrane.
HP   Esterosome.
HP   Endomembrane system.
GO   GO:0033118; esterosome membrane
//
ID   Etioplast.
AC   SL-0110
DE   The etioplast is a plastid found in plants grown in the dark.
SL   Plastid, etioplast.
HI   Plastid.
GO   GO:0009513; etioplast
//
ID   Etioplast membrane.
AC   SL-0329
DE   The membrane surrounding the etioplast, a plastid found in plants
DE   grown in the dark. Also used when it is not clear in which etioplast
DE   membrane a protein is found.
SL   Plastid, etioplast membrane.
HI   Plastid membrane.
HP   Etioplast.
GO   GO:0034426; etioplast membrane
//
ID   Etioplast stroma.
AC   SL-0330
DE   The etioplast stroma is the space enclosed by the double membrane of
DE   an etioplast but excluding the prothylakoid space. It contains the
DE   etioplast DNA.
SL   Plastid, etioplast stroma.
HI   Plastid stroma.
HP   Etioplast.
GO   GO:0009578; etioplast stroma
//
ID   Extracellular exosome.
AC   SL-0466
DE   Exosomes are 30-120 nm microvesicles of endocytic origin secreted by
DE   most cell types and found in abundance in body fluids, including
DE   blood, saliva, urine, and breast milk. They contain various molecular
DE   constituents of their cell of origin, including proteins and nucleic
DE   acids, and carry this cargo between diverse locations in the body.
DE   These microvesicles form by budding into the lumen of the
DE   multivesicular bodies (MVBs) and are released to extracellular fluids
DE   by fusion of MVBs with the plasma membrane.
SY   Extracellular vesicular exosome.
SL   Secreted, extracellular exosome.
HP   Secreted.
WW   http://exocarta.ludwig.edu.au/
//
ID   Extracellular matrix.
AC   SL-0111
DE   The extracellular matrix (ECM) is a vague term used to refer to all
DE   the material surrounding cells in a multicellular organism, except
DE   circulating fluids such as blood or lymph. In some cases, the ECM
DE   accounts for more of the organism's bulk than its cells. In plants,
DE   arthropods and fungi the ECM is primarily composed of nonliving
DE   material such as cellulose or chitin. In vertebrates the ECM consists
DE   of a complex network including the basement membrane, collage,
DE   elastin, proteoglycans and hyaluronan.
SY   Proteinaceous extracellular matrix.
SL   Secreted, extracellular space, extracellular matrix.
HP   Extracellular space.
KW   KW-0272
//
IO   Extracellular side.
AC   SL-9911
DE   Protein found mostly on the extracellular side of the membrane.
SL   Extracellular side.
//
ID   Extracellular space.
AC   SL-0112
DE   The extracellular space is the space outside of the cell membrane but
DE   part of a multicellular organism. The term is typically used for a
DE   secreted protein that remains associated with the cell, e.g. as part
DE   of the extracellular matrix. It is not used for a protein that is
DE   secreted into the blood stream (or other body fluids) of eukaryotic,
DE   multicellular organisms, such as insulin or fibroblast growth factors.
SY   Intercellular space.
SL   Secreted, extracellular space.
HP   Secreted.
GO   GO:0005615; extracellular space
//
ID   Extracellular vesicle.
AC   SL-0499
DE   Extracellular vesicles are vesicles that have been released by cells.
SY   Microparticle.
SL   Extracellular vesicle.
HI   Vesicle.
RX   PubMed=24769233; DOI=10.1016/j.jprot.2014.04.028;
//
ID   Extracellular vesicle membrane.
AC   SL-0500
DE   The membrane surrounding an extracellular vesicle.
SL   Extracellular vesicle membrane.
HI   Membrane.
HP   Extracellular vesicle.
//
IO   Extravirionic side.
AC   SL-9918
DE   Protein found mostly on the extracellular side of the virion membrane.
SL   Extravirionic side.
//
ID   Filopodium.
AC   SL-0286
DE   The filopodium is a thin, tubular, finger-like cell protrusion filled
DE   with straight bundled, crosslinked actin filaments having their barbed
DE   ends directed towards the cell membrane. Filopodium are observed at
DE   the advancing front of the migrating cell and are implicated in cell
DE   motility as well as in cell-substrate adhesion. Filopodia explore the
DE   environment and form nascent adhesive structures in response to
DE   external signaling cues. These long and highly dynamic protrusions,
DE   which can extend and retract, are involved in mesenchymal migration.
DE   They are observed in many cell types, such as amoebae, keratinocytes,
DE   fibroblasts and in neurite growth cones.
SY   Filopodia; Microspike.
SL   Cell projection, filopodium.
HI   Cell projection.
GO   GO:0030175; filopodium
//
ID   Filopodium membrane.
AC   SL-0287
DE   The portion of the cell membrane surrounding the filopodium. The
DE   filopodium is a thin, tubular, finger-like cell protrusion filled with
DE   straight bundled, crosslinked actin filaments having their barbed ends
DE   directed towards the cell membrane.
SY   Filopodia membrane; Microspike membrane.
SL   Cell projection, filopodium membrane.
HP   Cell membrane.
HP   Filopodium.
GO   GO:0031527; filopodium membrane
//
ID   Filopodium tip.
AC   SL-0470
DE   The end of the filopodium distal to the body of the cell. The
DE   filopodium is a thin, tubular, finger-like cell protrusion filled with
DE   straight bundled, crosslinked actin filaments having their barbed ends
DE   directed towards the cell membrane.
SY   Filopodia tip; Microspike tip.
SL   Cell projection, filopodium tip.
HP   Filopodium.
GO   GO:0032433; filopodium tip
//
ID   Fimbrium.
AC   SL-0113
DE   A fimbrium or pilus is a hair-like, non-flagellar, polymeric
DE   filamentous appendage that extend from the bacterial or archaeal cell
DE   surface, such as type 1 pili, P-pili, type IV pili or curli. Pili
DE   perform a variety of functions, including surface adhesion, motility,
DE   cell-cell interactions, biofilm formation, conjugation, DNA uptake,
DE   and twitching motility.
SY   Fimbria; Pili; Pilus.
SL   Fimbrium.
KW   KW-0281
GO   GO:0009289; pilus
//
ID   Flagellar pocket.
AC   SL-0116
DE   The flagellar pocket is a structure found in trypanosomes. The
DE   flagellar pocket is formed by an invagination in the plasma membrane
DE   where the flagellum emerges from the cell body. This pocket provides
DE   the portal through which most of the dynamic interactions with the
DE   host occur.
SL   Flagellar pocket.
GO   GO:0020016; ciliary pocket
//
ID   Flagellum.
AC   SL-0117
DE   The flagellum is a long whip-like or feathery structure which propels
DE   the cell through a liquid medium. This motile cilium is produced by
DE   the unicellular eukaryotes, and by the motile male gametes of many
DE   eukaryotic organisms. The flagella commonly have a characteristic
DE   axial '9+2' microtubular array (axoneme) and bends are generated along
DE   the length of the flagellum by restricted sliding of the nine outer
DE   doublets.
SY   Flagella; Motile cilia; Motile cilium; Undulipodia; Undulipodium.
SL   Cell projection, cilium, flagellum.
HI   Cilium.
KW   KW-0282
GO   GO:0031514; motile cilium
WW   http://www.ciliome.com
//
ID   Flagellum axoneme.
AC   SL-0114
DE   The flagellum axoneme is the most prominent structural component of
DE   the flagellum, which is a long whip-like or feathery structure which
DE   propels the cell through a liquid medium. The flagellum axoneme
DE   consists of a characteristic axial '9+2' microtubular array.
SY   Flagellar axoneme.
SL   Cytoplasm, cytoskeleton, flagellum axoneme.
HI   Cilium axoneme.
HP   Flagellum.
//
ID   Flagellum basal body.
AC   SL-0308
DE   The basal body is a barrel-shaped microtubule-based structure required
DE   for the formation of flagella. Basal bodies, structuraly related to
DE   and often interconvertible with centrioles, serves as a nucleation
DE   site for axoneme growth.
SY   Flagellar basal body; Flagellar kinetosome; Flagellum kinetosome.
SL   Cytoplasm, cytoskeleton, flagellum basal body.
HI   Cilium basal body.
HP   Flagellum.
//
ID   Flagellum membrane.
AC   SL-0115
DE   The portion of the cell membrane surrounding the flagellum, a long
DE   whip-like or feathery structure which propels the cell through a
DE   liquid medium.
SY   Flagellar membrane.
SL   Cell projection, cilium, flagellum membrane.
HI   Cilium membrane.
HP   Flagellum.
//
ID   Focal adhesion.
AC   SL-0118
DE   Focal adhesions are sites of tightest adhesion made to the underlying
DE   extracellular matrix by cells in culture. They serve a structural
DE   role, linking the ECM on the outside to the actin cytoskeleton on the
DE   inside. In addition, they are sites of signal transduction, initiating
DE   signaling pathways in response to adhesion. Focal adhesions are formed
DE   around a transmembrane core of an alpha-beta integrin heterodimer,
DE   which binds to a component of the extracellular matrix on its
DE   extracellular region, constitutes the site of anchorage of the actin
DE   cytoskeleton to the cytoplasmic side of the membrane, and mediates
DE   various intracellular signaling pathways.
SL   Cell junction, focal adhesion.
HI   Cell junction.
GO   GO:0005925; focal adhesion
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
WW   http://www-cellbio.med.unc.edu/grad/depttest/burridge.htm
//
ID   Forespore.
AC   SL-0119
DE   Sporulation leads to the formation of an asymmetrically positioned
DE   division septum (the polar septum) which divides the developing cell
DE   into two adjacent, but unequal-sized compartments called the forespore
DE   (the smaller cell) and the mother cell.
SY   Prespore.
SL   Forespore.
GO   GO:0042763; intracellular immature spore
RX   PubMed=15753026; DOI=10.1016/j.cub.2005.02.041;
//
ID   Forespore inner membrane.
AC   SL-0120
DE   The inner membrane of the smaller compartment, the forespore, of a
DE   sporulating cell.
SY   Prespore inner membrane.
SL   Forespore inner membrane.
HI   Forespore membrane.
HP   Forespore.
//
ID   Forespore intermembrane space.
AC   SL-0121
DE   The intermembrane space between the inner and outer forespore
DE   membranes.
SY   Prespore intermembrane space.
SL   Forespore intermembrane space.
HP   Forespore.
//
ID   Forespore membrane.
AC   SL-0122
DE   The membrane surrounding a forespore. This term is used when it is not
DE   known if the protein is found in or associated with the inner or outer
DE   forespore membrane.
SY   Prespore membrane.
SL   Forespore membrane.
HI   Membrane.
HP   Forespore.
//
ID   Forespore outer membrane.
AC   SL-0123
DE   The outer membrane of the smaller compartment, the forespore, of a
DE   sporulating cell.
SY   Prespore outer membrane.
SL   Forespore outer membrane.
HI   Forespore membrane.
HP   Forespore.
//
ID   Gap junction.
AC   SL-0124
DE   A gap junction (GJ) is a communicating junction between certain cell
DE   types that allows the passive passage of ions and small molecules
DE   providing a direct pathway for electrical and metabolic signaling. In
DE   vertebrates GJs are patches of channels, each cell membrane contains a
DE   'hemichannel', so that each GJ channel is composed of two hemichannels
DE   (connexons), which in turn are composed of six membrane proteins
DE   (connexins (Cxs)). In invertebrates, GJ channels are formed by another
DE   large family of integral membrane proteins, the innexins. GJ exists in
DE   all metazoans (multi-cellular organisms) and in almost all cell types
DE   in these organisms.
SY   Connexons.
SL   Cell junction, gap junction.
HI   Cell junction.
KW   KW-0303
GO   GO:0005921; gap junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
//
ID   Gas vesicle.
AC   SL-0125
DE   Gas vesicles are rigid hollow structures found in five phyla of the
DE   Bacteria and two groups of the Archaea, but mostly restricted to
DE   planktonic microorganisms, in which they provide buoyancy. By
DE   regulating their relative gas vesicle content, aquatic microbes are
DE   able to perform vertical migrations. The gas vesicle is impermeable to
DE   liquid water, but is highly permeable to gases and is normally filled
DE   with air. Two proteins have been shown to be present in the gas
DE   vesicle: GVPa, which makes the ribs that form the structure, and GVPc,
DE   which binds to the outside of the ribs and stiffens the structure
DE   against collapse.
SL   Vacuole, gas vesicle.
HI   Vacuole.
KW   KW-0304
GO   GO:0031411; gas vesicle
//
ID   Gas vesicle lumen.
AC   SL-0331
DE   The gas vesicle compartment bounded by the membrane of a gas vesicle.
SL   Vacuole, gas vesicle lumen.
HI   Vacuole lumen.
HP   Gas vesicle.
//
ID   Gas vesicle membrane.
AC   SL-0126
DE   The membrane surrounding a gas vesicle.
SY   Gas vesicle shell.
SL   Vacuole, gas vesicle membrane.
HI   Vacuole membrane.
HP   Gas vesicle.
GO   GO:0033172; gas vesicle shell
//
ID   Gem.
AC   SL-0127
DE   Gems are nuclear bodies, often found paired or juxtaposed to Cajal
DE   bodies, called gems for "gemini of CBs". It is not clear if Cajal
DE   bodes and gems are distinct nuclear bodies or if they should be
DE   considered as two manifestations of the same structure.
SL   Nucleus, gem.
HI   Nuclear body.
HP   Nucleus.
GO   GO:0097504; Gemini of coiled bodies
//
ID   Glycosome.
AC   SL-0129
DE   The glycosome is a specialized peroxisome found in all members of the
DE   protist order Kinetoplastida examined. Nine enzymes involved in
DE   glucose and glycerol metabolism are associated with these organelles.
DE   These enzymes are involved in pathways which, in other organisms, are
DE   usually located in the cytosol.
SL   Glycosome.
HI   Peroxisome.
KW   KW-0327
GO   GO:0020015; glycosome
//
ID   Glycosome matrix.
AC   SL-0332
DE   The glycosomal compartment bounded by the membrane of the glycosome, a
DE   specialized peroxisome found in all members of the protist order
DE   Kinetoplastida examined.
SY   Glycosomal lumen; Glycosomal matrix; Glycosome lumen.
SL   Glycosome matrix.
HI   Peroxisome matrix.
HP   Glycosome.
GO   GO:0034468; glycosome lumen
//
ID   Glycosome membrane.
AC   SL-0128
DE   The membrane surrounding the the glycosome, a specialized peroxisome
DE   found in all members of the protist order Kinetoplastida examined.
SY   Glycosomal membrane.
SL   Glycosome membrane.
HI   Peroxisome membrane.
HP   Glycosome.
HP   Endomembrane system.
GO   GO:0046860; glycosome membrane
//
ID   Glyoxysome.
AC   SL-0131
DE   The glyoxysome is a plant peroxisome, especially found in germinating
DE   seeds, involved in the breakdown and conversion of fatty acids to
DE   acetyl-CoA for the glyoxylate bypass. Since it is also rich in
DE   catalase, the glyoxysome may be related to the microbodies or
DE   peroxisomes or derived from them.
SL   Glyoxysome.
HI   Peroxisome.
KW   KW-0330
GO   GO:0009514; glyoxysome
//
ID   Glyoxysome matrix.
AC   SL-0333
DE   The glyoxysomal compartment bounded by the membrane of the glyoxysome,
DE   a plant peroxisome, especially found in germinating seeds, involved in
DE   the breakdown and conversion of fatty acids to acetyl-CoA for the
DE   glyoxylate bypass.
SY   Glyoxysomal lumen; Glyoxysomal matrix; Glyoxysome lumen.
SL   Glyoxysome matrix.
HI   Peroxisome matrix.
HP   Glyoxysome.
GO   GO:0031908; glyoxysomal lumen
//
ID   Glyoxysome membrane.
AC   SL-0130
DE   The membrane surrounding the glyoxysome, a plant peroxisome,
DE   especially found in germinating seeds, involved in the breakdown and
DE   conversion of fatty acids to acetyl-CoA for the glyoxylate bypass.
SY   Glyoxysomal membrane.
SL   Glyoxysome membrane.
HI   Peroxisome membrane.
HP   Glyoxysome.
HP   Endomembrane system.
GO   GO:0046861; glyoxysomal membrane
//
ID   Golgi apparatus.
AC   SL-0132
DE   The Golgi apparatus is a series of flattened, cisternal membranes and
DE   similar vesicles usually arranged in close apposition to each other to
DE   form stacks. In mammalian cells, the Golgi apparatus is juxtanuclear,
DE   often pericentriolar. The stacks are connected laterally by tubules to
DE   create a perinuclear ribbon structure, the 'Golgi ribbon'. In plants
DE   and lower animal cells, the Golgi exists as many copies of discrete
DE   stacks dispersed throughout the cytoplasm. The Golgi is a polarized
DE   structure with, in most higher eukaryotic cells, a cis-face associated
DE   with a tubular reticular network of membranes facing the endoplasmic
DE   reticulum, the cis-Golgi network (CGN), a medial area of disk-shaped
DE   flattened cisternae, and a trans-face associated with another tubular
DE   reticular membrane network, the trans-Golgi network (TGN) directed
DE   toward the plasma membrane and compartments of the endocytic pathway.
DE   The Golgi apparatus receives the entire output of de novo synthesized
DE   polypeptides from the ER, and functions to posttranslationally process
DE   and sort them within vesicles destined to their proper final
DE   destination (e.g. plasma membrane, endosomes, lysosomes).
SY   Apparatus golgiensis; Complexus golgiensis; Golgi; Golgi complex.
SL   Golgi apparatus.
KW   KW-0333
GO   GO:0005794; Golgi apparatus
AN   Compartment specific marker: GolgB1/Giantin.
//
ID   Golgi apparatus lumen.
AC   SL-0133
DE   The Golgi lumen consist of the cisternal spaces (or internal lumen) of
DE   the Golgi apparatus.
SY   Apparatus golgiensis lumen; Complexus golgiensis lumen;
SY   Golgi complex lumen; Golgi lumen.
SL   Golgi apparatus lumen.
HP   Golgi apparatus.
GO   GO:0005796; Golgi lumen
//
ID   Golgi apparatus membrane.
AC   SL-0134
DE   The membrane surrounding the Golgi apparatus.
SY   Apparatus golgiensis membrane; Complexus golgiensis membrane;
SY   Golgi complex membrane; Golgi membrane.
SL   Golgi apparatus membrane.
HI   Membrane.
HP   Golgi apparatus.
HP   Endomembrane system.
GO   GO:0000139; Golgi membrane
//
ID   Golgi outpost.
AC   SL-0521
DE   Golgi outpost is an organelle that shares common markers with the
DE   perinuclear Golgi body, but is typically much smaller in size and
DE   located far from the nucleus or cell body. Golgi outposts can function
DE   as acentrosomal microtubule-organizing centers (MTOCs) and play
DE   specialized roles in building the cytoarchitecture of neuronal
DE   dendrites, muscle cells, and oligodendrocytes.
SY   Golgi elements; Golgi vesicles; Mini Golgi;
SY   Postsynaptic Golgi apparatus; Satellite Golgi.
SL   Golgi outpost.
HI   Golgi apparatus.
AN   PubMed=32863092
//
ID   Golgi stack.
AC   SL-0135
DE   The Golgi stack consist of a series of flattened curved and parallel
DE   series saccules, called cisternae or dictyosomes, that form the
DE   central portion of the Golgi complex. The stack usually comprises cis,
DE   medial, and trans cisternae; the cis- and trans-Golgi networks are not
DE   considered part of the stack.
SY   Dictyosome; Golgi bodies; Golgi body.
SL   Golgi apparatus, Golgi stack.
HP   Golgi apparatus.
GO   GO:0005795; Golgi stack
AN   Compartment specific marker: Mannosidase II.
//
ID   Golgi stack lumen.
AC   SL-0334
DE   The Golgi stack compartment bounded by the membrane of the Golgi
DE   stack.
SY   Dictyosome lumen; Golgi bodies lumen; Golgi body lumen.
SL   Golgi apparatus, Golgi stack lumen.
HI   Golgi apparatus lumen.
HP   Golgi stack.
GO   GO:0034469; Golgi stack lumen
//
ID   Golgi stack membrane.
AC   SL-0136
DE   The membrane surrounding the Golgi stack.
SY   Dictyosome membrane; Golgi bodies membrane; Golgi body membrane;
SY   Golgi cisterna membrane.
SL   Golgi apparatus, Golgi stack membrane.
HI   Golgi apparatus membrane.
HP   Golgi stack.
GO   GO:0032580; Golgi cisterna membrane
//
IT   GPI-anchor.
AC   SL-9902
DE   Protein bound to the lipid bilayer of a membrane through a GPI-anchor
DE   (glycosylphosphatidylinositol anchor), a complex oligoglycan linked to
DE   a phosphatidylinositol group, resulting in the attachment of the C-
DE   terminus of the protein to the membrane.
SY   Glycosylphosphatidylinositol anchor;
SY   Glycosylphospholipidinositol anchor.
SL   Lipid-anchor, GPI-anchor.
HI   Lipid-anchor.
KW   KW-0336
//
IT   GPI-like-anchor.
AC   SL-9920
DE   Protein bound to the lipid bilayer of a membrane through a GPI-like-
DE   anchor, a complex oligoglycan linked to a sphingolipidinositol group,
DE   resulting in the attachment of the C-terminus of the protein to the
DE   membrane.
SY   Glycosylphospholipidinositol anchor;
SY   Glycosylsphingolipidinositol anchor.
SL   Lipid-anchor, GPI-like-anchor.
HI   Lipid-anchor.
KW   KW-0336
//
ID   Growth cone.
AC   SL-0288
DE   The growth cone is a dynamic cell protrusion at the tip of the
DE   extending axon or dendrite. Neuron extends a specialized structure,
DE   the growth cone, to find targets in the wiring of the nervous system.
DE   The growth cone explores its environment by extending dynamic
DE   filopodia. Growth cone is composed of an ensemble of protruding and
DE   retracting veils (lamellipodia), net growth cone advance may be
DE   considered the vector sum of all veil's motility behavior in response
DE   to their local environments. Filopodia play a key role in delimiting
DE   veils and serving to nucleate the formation of new veils.
SL   Cell projection, growth cone.
HI   Neuron projection.
GO   GO:0030426; growth cone
RX   PubMed=17327278; DOI=10.1242/jcs.03384;
//
ID   Growth cone membrane.
AC   SL-0289
DE   The portion of the cell membrane surrounding a growth cone.
SL   Cell projection, growth cone membrane.
HP   Cell membrane.
HP   Growth cone.
GO   GO:0032584; growth cone membrane
//
ID   H zone.
AC   SL-0477
DE   The A band of a sarcomer is bisected by a paler zone, the H zone,
DE   where the thick and the thin filaments do not overlap. At the center
DE   of the H zone is the M line.
SY   H band; H-band; H disc; H disk.
SL   Cytoplasm, myofibril, sarcomere, H zone.
HP   A band.
GO   GO:0031673; H zone
//
ID   Hemidesmosome.
AC   SL-0137
DE   The hemidesmosome is an integrin-containing adhesive junction located
DE   along the basal layer of cells where they abut the basement membrane
DE   zone. As the name implies, only half the desmosome is present; only
DE   one cell is participating, the second cell being represented by the
DE   basement membrane.
SL   Cell junction, hemidesmosome.
HI   Cell junction.
GO   GO:0030056; hemidesmosome
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
WW   http://celljunctions.med.nyu.edu/hemidesmosomes/hemimain.html
//
ID   Host.
AC   SL-0431
DE   The host is any organism in which another organism, or symbiont,
DE   spends part or all of its life cycle. Most animals and plants live
DE   symbiotically with microorganisms. The larger organism is called the
DE   host and smaller organism the symbiont. When the interactions between
DE   the symbiont and the host benefits both partners, the symbiotic
DE   interaction is called mutualism. When there is a negative effect on
DE   one of the partners, it is called a parasitic symbiosis and if there
DE   is no beneficial or negative effect it is a commensal symbiosis. These
DE   clear-cut definitions are not always easy to apply in nature. Take the
DE   bacterium Pseudomonas aeruginosa for example. This bacterium can be
DE   found on the skin of humans and not cause disease, perhaps we would
DE   call it a commensial, but if the person has a severe burn P.
DE   aeruginosa can cause an infection and becomes a pathogen (a medicinal
DE   term for parasitism). This type of organism is called an opportunistic
DE   pathogen. Whether an association is a mutualist, commensal or
DE   parasitic depends on the relative "strengths" of the partners and the
DE   balance of power can change over time.
SL   Host.
GO   GO:0018995; host cellular component
WW   http://web.uconn.edu/mcbstaff/graf/GenSym/GenSym.htm
//
ID   Host apical cell membrane.
AC   SL-0372
DE   The fraction of the host cell membrane at the apical end of the host
DE   cell, which faces the outside world or the lumen of the host cavity.
SY   Host apical plasma membrane.
SL   Host apical cell membrane.
HP   Host cell membrane.
GO   GO:0020002; host cell plasma membrane
//
ID   Host basolateral cell membrane.
AC   SL-0459
DE   The fraction of the host cell membrane at the basolateral side of the
DE   cell, which faces adjacent host cells and the underlying host
DE   connective tissue.
SY   Host basolateral plasma membrane.
SL   Host basolateral cell membrane.
HP   Host cell membrane.
//
ID   Host caveola.
AC   SL-0428
DE   The host caveola is a small (apparently) uncoated pit found mostly in
DE   the host cell membrane of many highly differentiated mammalian cells,
DE   such as adipocytes, endothelial cells and muscle cells. These flask-
DE   shaped invaginations are defined by the presence of caveolins and
DE   contains a subset of lipid-raft components, including cholesterol and
DE   sphingolipids.
SY   Host caveolae; Host membrane microdomain; Host plasmalemmal vesicle.
SL   Host membrane, host caveola.
HP   Host endomembrane system.
GO   GO:0044155; host caveola
//
ID   Host cell.
AC   SL-0427
DE   A cell within a host organism including the host cell membrane and any
DE   external encapsulating structures such as the host cell wall and cell
DE   envelope.
SL   Host cell.
GO   GO:0043657; host cell
//
ID   Host cell envelope.
AC   SL-0421
DE   The host cell envelope comprises the cell membrane, the cell wall and
DE   an outer membrane if present. The Gram-positive bacteria host cell
DE   envelope consists of the cytoplasmic membrane, cell wall and capsule.
DE   The Gram-negative host envelope consists of the cytoplasmic membrane,
DE   cell wall, periplasmic space, outer membrane and capsule. The archaeal
DE   cell host envelope consists generally of single typical bilayer
DE   membrane covered by a surface layer (S-layer). Ignicoccus host species
DE   exceptionally have an outer membrane which encloses a large
DE   periplasmic space. Extreme host thermophiles and acidophiles have
DE   tetraether type glycerophospholipids with C40 isoprenoid chains. The
DE   yeast host cell envelope is a protecting capsule which consists of the
DE   cytoplasmic membrane, the periplasmic space, and the cell wall.
SY   Host envelope.
SL   Host cell envelope.
HP   Host cell.
GO   GO:0044230; host cell envelope
//
ID   Host cell inner membrane.
AC   SL-0373
DE   The prokaryotic host cell inner membrane is the selectively permeable
DE   membrane which separates the host cytoplasm from the host periplasm in
DE   prokaryotes with 2 membranes.
SY   Host inner membrane.
SL   Host cell inner membrane.
HI   Host cell membrane.
KW   KW-1030
GO   GO:0020002; host cell plasma membrane
//
ID   Host cell junction.
AC   SL-0374
DE   The host cell junction is a host cell-host cell or host cell-host
DE   extracellular matrix contact within a tissue of a host multicellular
DE   organism, especially abundant in host epithelia. In vertebrates, there
DE   are three major types of cell junctions: anchoring junctions (e.g.
DE   adherens junctions), communicating junctions (e.g. gap junctions) and
DE   occluding junctions (e.g. tight junctions).
SL   Host cell junction.
HP   Host.
KW   KW-1031
GO   GO:0044156; host cell junction
//
ID   Host cell membrane.
AC   SL-0375
DE   The host cell membrane is the selectively permeable membrane which
DE   separates the host cytoplasm from its surroundings. Known as the host
DE   cell inner membrane in prokaryotes with 2 membranes.
SY   Host cytoplasmic membrane; Host plasmalemma; Host plasma membrane.
SL   Host cell membrane.
HI   Host membrane.
HP   Host endomembrane system.
HP   Host cell envelope.
KW   KW-1032
GO   GO:0020002; host cell plasma membrane
//
ID   Host cell outer membrane.
AC   SL-0376
DE   The prokaryotic host cell outer membrane is the selectively permeable
DE   membrane which separates the prokaryotic periplasm from its
DE   surroundings in prokaryotes with 2 membranes. Traditionally only Gram-
DE   negative bacteria were thought of as having an outer membrane, but
DE   recent work has shown some Actinobacteria, including Mycobacterium
DE   tuberculosis, as well as at least 1 archaea (Ignicoccus hospitalis)
DE   have a cell outer membrane.
SY   Host outer membrane.
SL   Host cell outer membrane.
HI   Host membrane.
KW   KW-1033
GO   GO:0020002; host cell plasma membrane
//
ID   Host cell projection.
AC   SL-0377
DE   A host cell projection is a host cell protrusion such as pseudopodium,
DE   filopodium, lamellipodium, growth cone, flagellum, acrosome, axon,
DE   pili or bacterial comet tail. These membrane-cytoskeleton-coupled
DE   processes are involved in many biological functions, such as host cell
DE   motility, cancer-cell invasion, endocytosis, phagocytosis, exocytosis,
DE   pathogen infection, neurite extension and cytokinesis.
SY   Host cell protrusion.
SL   Host cell projection.
HP   Host cell.
KW   KW-1034
GO   GO:0044157; host cell projection
//
ID   Host cell surface.
AC   SL-0378
DE   The outermost side of the host cell.
SL   Host cell surface.
HP   Host cell.
GO   GO:0044228; host cell surface
//
ID   Host cell wall.
AC   SL-0424
DE   The complex and rigid layer surrounding the host cell. Host cell walls
DE   are found in bacteria, archaea, fungi, plants, and algae. The host
DE   cell wall is surrounded by an outer membrane in Gram-negative host
DE   bacteria, and envelopes the inner or plasma host membrane all host
DE   bacteria. It plays a role in host cell shape, cell stability and
DE   development, and protection against environmental dangers.
SL   Host cell wall.
HP   Host cell envelope.
GO   GO:0044158; host cell wall
//
ID   Host cellular thylakoid.
AC   SL-0429
DE   The host cellular thylakoids are formed usually by extensive
DE   invaginations of the host cyanobacterial cell membrane. In
DE   Synechocystis sp. strain PCC 6803, the thylakoid membranes are
DE   physically discontinuous from the plasma membrane, and thus represent
DE   bona fide intracellular organelles.
SL   Host cellular thylakoid.
HI   Host thylakoid.
HP   Host cell.
GO   GO:0044159; host thylakoid
AN   Use only in cyanobacteria, not eukaryotes
//
ID   Host cellular thylakoid membrane.
AC   SL-0430
DE   The membrane of the host cyanobacterial cellular thylakoid.
SL   Host cellular thylakoid membrane.
HI   Host membrane.
HP   Host endomembrane system.
HP   Host cellular thylakoid.
GO   GO:0044160; host thylakoid membrane
AN   Use only in cyanobacteria, not eukaryotes
//
ID   Host chloroplast envelope.
AC   SL-0483
DE   The envelope of a host chloroplast comprises the inner and outer
DE   chloroplast membrane including the intermembrane space.
SY   Host chloroplastic envelope.
SL   Host chloroplast envelope.
//
ID   Host cis-Golgi network.
AC   SL-0396
DE   The host cis-Golgi network is an extensive tubulovesicular network
DE   bound to the cis face of the Golgi stack and whose function is to
DE   receive process the biosynthetic output from the ER.
SY   Host CGN; Host cis-Golgi; Host cis-Golgi complex; Host Golgi cis-face.
SL   Host Golgi apparatus, host cis-Golgi network.
HP   Host Golgi apparatus.
//
ID   Host cis-Golgi network membrane.
AC   SL-0397
DE   The lipid bilayer surrounding any of the compartments that make up the
DE   host cis-Golgi network.
SY   Host CGN membrane; Host cis-Golgi complex membrane;
SY   Host cis-Golgi membrane; Host Golgi cis-face membrane.
SL   Host Golgi apparatus, host cis-Golgi network membrane.
HI   Host Golgi apparatus membrane.
HP   Host cis-Golgi network.
//
ID   Host cytoplasm.
AC   SL-0381
DE   The host cytoplasm is the content of a host cell within the plasma
DE   membrane and, in eukaryotics cells, surrounds the host nucleus.
SL   Host cytoplasm.
HP   Host cell.
KW   KW-1035
GO   GO:0030430; host cell cytoplasm
//
ID   Host cytoplasmic vesicle.
AC   SL-0386
DE   The host cytoplasmic vesicles mediate vesicular transport among the
DE   organelles of host secretory and endocytic systems.
SL   Host cytoplasmic vesicle.
HP   Host cell.
KW   KW-1036
GO   GO:0044161; host cell cytoplasmic vesicle
//
ID   Host cytoplasmic vesicle membrane.
AC   SL-0387
DE   The membrane surrounding a host cytoplasmic vesicle. These vesicles
DE   mediate vesicular transport among the organelles of secretory and
DE   endocytic systems.
SL   Host cytoplasmic vesicle membrane.
HI   Host membrane.
HP   Host cytoplasmic vesicle.
HP   Host endomembrane system.
GO   GO:0044162; host cell cytoplasmic vesicle membrane
//
ID   Host cytoskeleton.
AC   SL-0383
DE   The host cytoskeleton is a dynamic three-dimensional structure that
DE   fills the host cytoplasm of eukaryotic cells. It is responsible for
DE   cell movement, cytokinesis, and the organization of the organelles or
DE   organelle-like structures within the host cell.
SL   Host cytoplasm, host cytoskeleton.
HP   Host cytoplasm.
KW   KW-1037
GO   GO:0044163; host cytoskeleton
//
ID   Host cytosol.
AC   SL-0384
DE   The host cytosol is the unstructured aqueous phase of the host
DE   cytoplasm excluding organelles, membranes, and insoluble cytoskeletal
DE   components.
SL   Host cytoplasm, host cytosol.
HP   Host cytoplasm.
GO   GO:0044164; host cell cytosol
//
ID   Host early endosome.
AC   SL-0461
DE   The host early endosomes form a tubulovesicular network spread
DE   throughout the cortical cytoplasm of the host cell. Host early
DE   endosomes are the primary sorting station in the endocytic pathway
DE   from which endocytosed molecules can be recycled back to the host cell
DE   membrane or targeted to degradation in the host lysosomes.
SL   Host early endosome.
HP   Host endosome.
//
ID   Host early endosome membrane.
AC   SL-0462
DE   The membrane surrounding the host early endosomes, which form a
DE   tubulovesicular network spread throughout the cortical cytoplasm of
DE   the host cell.
SY   Host early endosomal membrane.
SL   Host early endosome membrane.
HI   Host endosome membrane.
HP   Host early endosome.
//
ID   Host endomembrane system.
AC   SL-0398
DE   A collection of membranous structures involved in transport within the
DE   host cell. The main components of the host endomembrane system are
DE   endoplasmic reticulum, Golgi apparatus, vesicles, and cell membrane
DE   and nuclear envelope. The endomembrane system does not include the
DE   membranes of mitochondria or plastids.
SY   Host endomembrane.
SL   Host endomembrane system.
HI   Host membrane.
GO   GO:0033645; host cell endomembrane system
//
ID   Host endoplasmic reticulum.
AC   SL-0388
DE   The host endoplasmic reticulum (ER) is an extensive network of
DE   membrane tubules, vesicles and flattened cisternae (sac-like
DE   structures) found throughout the eukaryotic host cell, especially
DE   those responsible for the production of hormones and other secretory
DE   products.
SL   Host endoplasmic reticulum.
HP   Host cell.
KW   KW-1038
GO   GO:0044165; host cell endoplasmic reticulum
//
ID   Host endoplasmic reticulum lumen.
AC   SL-0389
DE   The lumen of the host endoplasmic reticulum (ER) is the area enclosed
DE   by the host endoplasmic reticulum membrane, an extensive network of
DE   membrane tubules, vesicles and flattened cisternae (sac-like
DE   structures) found throughout the eukaryotic cell, especially those
DE   responsible for the production of hormones and other secretory
DE   products.
SL   Host endoplasmic reticulum lumen.
HP   Host endoplasmic reticulum.
GO   GO:0044166; host cell endoplasmic reticulum lumen
//
ID   Host endoplasmic reticulum membrane.
AC   SL-0390
DE   The membrane surrounding the host endoplasmic reticulum (ER). The host
DE   endoplasmic reticulum is an extensive network of membrane tubules,
DE   vesicles and flattened cisternae (sac-like structures) found
DE   throughout the eukaryotic host cell, especially those responsible for
DE   the production of hormones and other secretory products.
SL   Host endoplasmic reticulum membrane.
HI   Host membrane.
HP   Host endoplasmic reticulum.
HP   Host endomembrane system.
GO   GO:0044167; host cell endoplasmic reticulum membrane
//
ID   Host endoplasmic reticulum-Golgi intermediate compartment.
AC   SL-0391
DE   The host ER-Golgi intermediate compartment is a collection of
DE   tubulovesicular membrane clusters in the vicinity of host ER exit
DE   sites. The host ERGIC mediates transport between the endoplasmic
DE   reticulum and the Golgi and is the first anterograde/retrograde
DE   sorting station in the host secretory pathway.
SY   Host ERGIC; Host ER-Golgi intermediate compartment; Host IC;
SY   Host intermediate compartment; Host vesiculo-tubular cluster;
SY   Host VTC.
SL   Host endoplasmic reticulum-Golgi intermediate compartment.
HP   Host cell.
GO   GO:0044172; host cell endoplasmic reticulum-Golgi intermediate compartment
//
ID   Host endoplasmic reticulum-Golgi intermediate compartment membrane.
AC   SL-0392
DE   The membrane surrounding the host ER-Golgi intermediate compartment,
DE   which is a collection of tubulovesicular membrane clusters in the
DE   vicinity of host ER exit sites.
SY   Host ERGIC membrane; Host ER-Golgi intermediate compartment membrane;
SY   Host IC membrane; Host intermediate compartment membrane;
SY   Host vesiculo-tubular cluster membrane; Host VTC membrane.
SL   Host endoplasmic reticulum-Golgi intermediate compartment membrane.
HI   Host membrane.
HP   Host endoplasmic reticulum-Golgi intermediate compartment.
HP   Host endomembrane system.
GO   GO:0044173; host cell endoplasmic reticulum-Golgi intermediate compartment membrane
//
ID   Host endosome.
AC   SL-0393
DE   Host endosomes are highly dynamic membrane systems involved in
DE   transport within the host cell, they receive endocytosed host cell
DE   membrane molecules and sort them for either degradation or recycling
DE   back to the host cell surface. They also receive newly synthesised
DE   proteins destined for host vacuolar/lysosomal compartments.
SL   Host endosome.
HP   Host cell.
KW   KW-1039
GO   GO:0044174; host cell endosome
//
ID   Host endosome membrane.
AC   SL-0394
DE   The membrane surrounding the host endosome. Host endosomes are highly
DE   dynamic membrane systems involved in transport within the cell, they
DE   receive endocytosed host cell membrane molecules and sort them for
DE   either degradation or recycling back to the host cell surface.
SY   Host endosomal membrane.
SL   Host endosome membrane.
HI   Host membrane.
HP   Host endosome.
HP   Host endomembrane system.
GO   GO:0044175; host cell endosome membrane
//
ID   Host extracellular space.
AC   SL-0425
DE   The host extracellular space is the space outside of the host cell
DE   membrane but part of a multicellular host organism.
SY   Host intercellular space.
SL   Host extracellular space.
HP   Host.
GO   GO:0043655; host extracellular space
//
ID   Host filopodium.
AC   SL-0379
DE   The host filopodium is a thin, tubular, finger-like host cell
DE   protrusion filled with straight bundled, crosslinked actin filaments
DE   having their barbed ends directed towards the host cell membrane.
SY   Host filopodia; Host microspike.
SL   Host cell projection, host filopodium.
HI   Host cell projection.
GO   GO:0044176; host cell filopodium
//
ID   Host glyoxysome.
AC   SL-0474
DE   The host glyoxysome is a plant peroxisome, especially found in
DE   germinating seeds, involved in the breakdown and conversion of fatty
DE   acids to acetyl-CoA for the glyoxylate bypass. Since it is also rich
DE   in catalase, the glyoxysome may be related to the microbodies or
DE   peroxisomes or derived from them.
SL   Host glyoxysome.
HI   Host peroxisome.
//
ID   Host Golgi apparatus.
AC   SL-0395
DE   The host Golgi apparatus is a series of flattened, cisternal membranes
DE   and similar vesicles usually arranged in close apposition to each
DE   other to form stacks. In mammalian cells, the host Golgi apparatus is
DE   juxtanuclear, often pericentriolar. The stacks are connected laterally
DE   by tubules to create a perinuclear ribbon structure, the 'Golgi
DE   ribbon'. In plants and lower animal cells, the host Golgi exists as
DE   many copies of discrete stacks dispersed throughout the host
DE   cytoplasm. It is a polarized structure with, in most higher eukaryotic
DE   cells, a cis-face associated with a tubular reticular network of
DE   membranes facing the endoplasmic reticulum, the cis-Golgi network
DE   (CGN), a medial area of disk-shaped flattened cisternae, and a trans-
DE   face associated with another tubular reticular membrane network, the
DE   trans-Golgi network (TGN) directed toward the host plasma membrane and
DE   compartments of the host endocytic pathway.
SY   Host apparatus golgiensis; Host complexus golgiensis; Host Golgi;
SY   Host Golgi complex.
SL   Host Golgi apparatus.
HP   Host cell.
KW   KW-1040
GO   GO:0044177; host cell Golgi apparatus
//
ID   Host Golgi apparatus membrane.
AC   SL-0426
DE   The host membrane surrounding the host Golgi apparatus.
SY   Host apparatus golgiensis membrane;
SY   Host complexus golgiensis membrane; Host Golgi complex membrane;
SY   Host Golgi membrane.
SL   Host Golgi apparatus membrane.
HI   Host membrane.
HP   Host Golgi apparatus.
HP   Host endomembrane system.
GO   GO:0044178; host cell Golgi membrane
//
ID   Host late endosome.
AC   SL-0399
DE   Host late endosomes are pleiomorphic with cisternal, tubular and
DE   multivesicular regions. They are found in juxtanuclear regions and
DE   concentrated at the host microtubule organizing center. They are an
DE   important sorting station in the endocytic pathway. Recycling to the
DE   plasma membrane and to the Golgi occurs in late endosomes.
SL   Host late endosome.
HP   Host endosome.
GO   GO:0044184; host cell late endosome
//
ID   Host late endosome membrane.
AC   SL-0400
DE   The membrane surrounding the host late endosomes.
SY   Host late endosomal membrane.
SL   Host late endosome membrane.
HI   Host endosome membrane.
HP   Host late endosome.
GO   GO:0044185; host cell late endosome membrane
//
ID   Host lipid droplet.
AC   SL-0401
DE   The host lipid droplet is a dynamic cytoplasmic host organelle which
DE   consists of an heterogeneous macromolecular assembly of lipids and
DE   proteins covered by a unique phospholipid monolayer. They may play a
DE   role in host lipid metabolism and storage, and they may be involved in
DE   the regulation of intracellular trafficking and signal transduction.
SY   Host adiposome; Host lipid bodies; Host lipid body;
SY   Host lipid particle; Host monolayer-surrounded lipid storage body;
SY   Host oil bodies; Host oil body; Host oleosome; Host spherosome.
SL   Host lipid droplet.
HP   Host cell.
KW   KW-1041
GO   GO:0044186; host cell lipid droplet
//
ID   Host lysosome.
AC   SL-0403
DE   The host lysosome is a membrane-limited organelle present in all
DE   eukaryotic cells, which contains a large number of hydrolytic enzymes
DE   that are used for degrading almost any kind of cellular constituent,
DE   including entire organelles. The mechanisms responsible for delivering
DE   cytoplasmic cargo to the host lysosome/vacuole are known collectively
DE   as autophagy and play an important role in the maintenance of
DE   homeostasis.
SL   Host lysosome.
HP   Host cell.
KW   KW-1042
GO   GO:0044187; host cell lysosome
//
ID   Host lysosome membrane.
AC   SL-0404
DE   The membrane surrounding a host lysosome.
SY   Host lysosomal membrane.
SL   Host lysosome membrane.
HI   Host membrane.
HP   Host endomembrane system.
HP   Host lysosome.
GO   GO:0044188; host cell lysosomal membrane
//
ID   Host membrane.
AC   SL-0380
DE   A host membrane is a lipid bilayer which surrounds host enclosed
DE   spaces and compartments. This selectively permeable structure is
DE   essential for effective separation of a host cell or organelle from
DE   its surroundings.
SL   Host membrane.
HI   Membrane.
KW   KW-1043
GO   GO:0033644; host cell membrane
//
ID   Host microsome.
AC   SL-0405
DE   The host microsomes are a heterogenous set of vesicles 20-200nm in
DE   diameter and formed from the host endoplasmic reticulum when host
DE   cells are disrupted.
SL   Host microsome.
HP   Host cell.
KW   KW-1044
GO   GO:0033648; host intracellular membrane-bounded organelle
//
ID   Host microsome membrane.
AC   SL-0406
DE   The membrane surrounding the host microsome.
SY   Host microsomal membrane.
SL   Host microsome membrane.
HI   Host membrane.
HP   Host endomembrane system.
HP   Host microsome.
GO   GO:0033648; host intracellular membrane-bounded organelle
//
ID   Host mitochondrion.
AC   SL-0407
DE   The host mitochondrion is a semiautonomous, self-reproducing organelle
DE   that occurs in the cytoplasm of all cells of most, but not all, host
DE   eukaryotes. Each host mitochondrion is surrounded by a double limiting
DE   membrane. The inner membrane is highly invaginated, and its
DE   projections are called cristae. They are the sites of the reactions of
DE   oxidative phosphorylation, which result in the formation of ATP.
SL   Host mitochondrion.
HP   Host cell.
KW   KW-1045
GO   GO:0033650; host cell mitochondrion
//
ID   Host mitochondrion envelope.
AC   SL-0408
DE   The host mitochondrial envelope comprises the inner and outer host
DE   mitochondrial membrane including the mitochondrial intermembrane
DE   space.
SY   Host mitochondrial envelope.
SL   Host mitochondrion envelope.
HP   Host mitochondrion.
GO   GO:0044190; host cell mitochondrial envelope
//
ID   Host mitochondrion inner membrane.
AC   SL-0409
DE   The host mitochondrion inner membrane is the membrane which separates
DE   the host mitochondrial matrix from the host mitochondrial
DE   intermembrane space.
SY   Host inner mitochondrial membrane; Host mitochondrial inner membrane.
SL   Host mitochondrion inner membrane.
HI   Host mitochondrion membrane.
KW   KW-1046
GO   GO:0044192; host cell mitochondrial inner membrane
//
ID   Host mitochondrion membrane.
AC   SL-0410
DE   The membrane surrounding a host mitochondrion. This term is used when
DE   it is not known if the protein is found in or associated with the
DE   inner or outer host mitochondrial membrane.
SY   Host mitochondrial membrane.
SL   Host mitochondrion membrane.
HI   Host membrane.
HP   Host mitochondrion envelope.
GO   GO:0044191; host cell mitochondrial membrane
//
ID   Host mitochondrion outer membrane.
AC   SL-0411
DE   The host mitochondrion outer membrane is the host mitochondrial
DE   membrane facing the host cytoplasm.
SY   Host mitochondrial outer membrane; Host outer mitochondrial membrane.
SL   Host mitochondrion outer membrane.
HI   Host mitochondrion membrane.
KW   KW-1047
GO   GO:0044193; host cell mitochondrial outer membrane
//
ID   Host multivesicular body.
AC   SL-0453
DE   The host multivesicular bodies are a type of late endosome containing
DE   internal vesicles formed following the inward budding of the host
DE   outer endosomal membrane. The contents of the MVBs are then released
DE   into the lysosome lumen. The proteins found in the limiting membrane
DE   of MVBs are recycled to other compartments.
SY   Host corpuscula multivesicularis; Host ECV;
SY   Host endosomal carrier vesicle; Host multivesicular bodies; Host MVB.
SL   Host endosome, host multivesicular body.
HP   Host endosome.
GO   GO:0072494; host multivesicular body
//
ID   Host nucleolus.
AC   SL-0412
DE   The host nucleolus is a dark, dense, roughly spherical area of fibers
DE   and granules in the host nucleus. Only plant and animal nuclei contain
DE   one or more nucleoli, although some do not. No membrane separates the
DE   host nucleolus from the host nucleoplasm. It mediates ribosomal RNA
DE   biogenesis.
SY   Host nucleoli.
SL   Host nucleus, host nucleolus.
HP   Host nucleus.
GO   GO:0044196; host cell nucleolus
//
ID   Host nucleoplasm.
AC   SL-0413
DE   The host nucleoplasm is a highly viscous liquid contained within the
DE   host nucleus that surrounds the chromosomes and other subnuclear
DE   organelles. A network of fibers known as the host nuclear matrix can
DE   also be found in there.
SY   Host karyolymph; Host karyoplasm.
SL   Host nucleus, host nucleoplasm.
HP   Host nucleus.
GO   GO:0044095; host cell nucleoplasm
//
ID   Host nucleus.
AC   SL-0414
DE   The host nucleus is the most obvious organelle in any host eukaryotic
DE   cell. It is a membrane-bound organelle and is surrounded by double
DE   membranes. It communicates with the surrounding cytosol via numerous
DE   nuclear pores.
SL   Host nucleus.
HP   Host cell.
KW   KW-1048
GO   GO:0042025; host cell nucleus
//
ID   Host nucleus envelope.
AC   SL-0415
DE   The host nuclear envelope is a membrane system which surrounds the
DE   host nucleoplasm of eukaryotic cells. It is composed of the nuclear
DE   lamina, nuclear pore complexes and two nuclear membranes. The space
DE   between the two membranes is called the host nuclear intermembrane
DE   space.
SY   Host karyotheca; Host nuclear envelope; Host nucleolemma;
SY   Host perinuclear envelope.
SL   Host nucleus envelope.
HP   Host nucleus.
GO   GO:0044199; host cell nuclear envelope
//
ID   Host nucleus inner membrane.
AC   SL-0419
DE   The inner membrane surrounding the host nucleus is the membrane which
DE   separates the host nuclear matrix from the host intermembrane space.
SY   Host inner nuclear membrane; Host nuclear inner membrane.
SL   Host nucleus inner membrane.
HI   Host nucleus membrane.
GO   GO:0044201; host cell nuclear inner membrane
//
ID   Host nucleus lamina.
AC   SL-0416
DE   The host nuclear lamina is a meshwork of intermediate filament
DE   proteins called lamins and lamin-binding proteins that are embedded in
DE   the host inner nuclear membrane.
SY   Host nuclear lamina.
SL   Host nucleus lamina.
HP   Host nucleus envelope.
GO   GO:0044203; host cell nuclear lamina
//
ID   Host nucleus matrix.
AC   SL-0417
DE   The host nuclear matrix is a three-dimensional filamentous protein
DE   network, found in the host nucleoplasm, which provides a structural
DE   framework for organising host chromatin, while facilitating
DE   transcription and replication.
SY   Host nuclear matrix; Host nuclear scaffold; Host nuclear skeleton.
SL   Host nucleus matrix.
HP   Host nucleus.
GO   GO:0044204; host cell nuclear matrix
//
ID   Host nucleus membrane.
AC   SL-0418
DE   The membrane surrounding the host nucleus. This term is used when it
DE   is not known if the protein is found in or associated with the inner
DE   or outer host nuclear membrane.
SY   Host nuclear membrane.
SL   Host nucleus membrane.
HI   Host membrane.
HP   Host endomembrane system.
HP   Host nucleus envelope.
GO   GO:0044200; host cell nuclear membrane
//
ID   Host nucleus outer membrane.
AC   SL-0446
DE   The outer membrane of the host nucleus is the membrane facing the host
DE   cytoplasm. In host mammals, the host outer nuclear membrane is
DE   continuous in many places with the host rough endoplasmic reticulum
DE   and is dotted with ribosomes.
SY   Host nuclear outer membrane; Host outer nuclear membrane.
SL   Host nucleus outer membrane.
HI   Host nucleus membrane.
GO   GO:0044202; host cell nuclear outer membrane
//
ID   Host pathogen-containing vacuole.
AC   SL-0507
DE   A host-derived vacuole formed upon pathogen internalization by a host
DE   cell, within which the pathogen resides. The pathogen extensively
DE   modifies the vacuole membrane and contents, as well as its fate, in
DE   the process protecting the pathogen from destruction.
SY   Pathogen inclusion.
SL   Host vacuole, host pathogen-containing vacuole.
HP   Host vacuole.
GO   GO:0140220; pathogen-containing vacuole
//
ID   Host pathogen-containing vacuole lumen.
AC   SL-0508
DE   The volume enclosed in a host-derived vacuole formed upon pathogen
DE   internalization by a host cell.
SY   Pathogen inclusion lumen.
SL   Host vacuole, host pathogen-containing vacuole, host pathogen-containing vacuole lumen.
HI   Host pathogen-containing vacuole.
GO   GO:0140222; pathogen-containing vacuole lumen
//
ID   Host pathogen-containing vacuole membrane.
AC   SL-0509
DE   The host-derived membrane which encloses a vacuole formed upon
DE   pathogen internalization by a host cell.
SY   Pathogen inclusion membrane.
SL   Host vacuole, host pathogen-containing vacuole, host pathogen-containing vacuole membrane.
HI   Host membrane.
HP   Host pathogen-containing vacuole.
GO   GO:0140221; pathogen-containing vacuole membrane
//
ID   Host perinuclear region.
AC   SL-0382
DE   The host perinuclear region is the host cytoplasmic region just around
DE   the host nucleus.
SY   Host nuclear periphery; Host perinuclear region of cytoplasm.
SL   Host cytoplasm, host perinuclear region.
HP   Host cytoplasm.
GO   GO:0044220; host cell perinuclear region of cytoplasm
//
ID   Host periplasm.
AC   SL-0420
DE   The host periplasm is the space between the inner and outer membrane
DE   in host Gram-negative bacteria. In Gram-positive bacteria a smaller
DE   periplasmic space is found between the inner membrane and the
DE   peptidoglycan layer. Also used for the host intermembrane spaces of
DE   host fungi and host organelles.
SY   Host periplasmic space.
SL   Host periplasm.
HP   Host cell envelope.
KW   KW-1049
GO   GO:0044229; host cell periplasmic space
//
ID   Host peroxisome.
AC   SL-0475
DE   The host peroxisome is a small eukaryotic organelle limited by a
DE   single membrane, specialized for carrying out oxidative reactions.
DE   Contains mainly peroxidases, several other oxidases and catalase. The
DE   catalase regulates the contents of the produced toxic hydrogen
DE   peroxide thus protecting the cell. Beta-oxidation of fatty acids is
DE   another major function of peroxisomes. In plants and fungi this
DE   degradation occurs only in this cellular compartment.
SL   Host peroxisome.
//
ID   Host phagosome.
AC   SL-0432
DE   The host phagosome is a phagocytic host cell-specific compartment.
DE   These large endocytic membrane-bound vesicles form upon ingestion by
DE   the host cell of extracellular materials.
SY   Host phagocytic vesicle.
SL   Host cytoplasmic vesicle, host phagosome.
HI   Host cytoplasmic vesicle.
//
ID   Host phagosome membrane.
AC   SL-0433
DE   The membrane surrounding a host phagosome.
SY   Host phagocytic vesicle membrane; Host phagosomal membrane.
SL   Host cytoplasmic vesicle, host phagosome membrane.
HI   Host cytoplasmic vesicle membrane.
HP   Host phagosome.
//
ID   Host plasmodesma.
AC   SL-0385
DE   The host plasmodesma (plural host plasmodesmata) is a plasma membrane-
DE   lined channel that crosses the cell wall between two adjacent host
DE   plant cells and which allows a cytoplasmic exchange between the cells.
DE   It provides passage of ions and small molecules, but also of
DE   macromolecules such as RNA or proteins. Host plasmodesmata are
DE   sheathed by a host plasma membrane that is simply an extension of the
DE   cell membrane of the adjoining cells.
SY   Host PD; Host plasmodesmata.
SL   Host cell junction, host plasmodesma.
HI   Host cell junction.
GO   GO:0044219; host cell plasmodesma
//
ID   Host presynaptic cell membrane.
AC   SL-0434
DE   In a host chemical synapse, the host presynaptic membrane is the cell
DE   membrane of an axon terminal that faces the receiving cell. The
DE   postsynaptic membrane is separated from the presynaptic membrane by
DE   the synaptic cleft.
SY   Host presynaptic membrane.
SL   Host synapse, host presynaptic cell membrane.
HP   Host cell membrane.
HP   Host synapse.
GO   GO:0044231; host cell presynaptic membrane
//
ID   Host rough endoplasmic reticulum.
AC   SL-0422
DE   The host rough endoplasmic reticulum (host RER) is the portion of the
DE   host ER which is covered with ribosomes.
SY   Host RER; Host rough ER.
SL   Host rough endoplasmic reticulum.
HP   Host endoplasmic reticulum.
GO   GO:0044168; host cell rough endoplasmic reticulum
//
ID   Host rough endoplasmic reticulum membrane.
AC   SL-0423
DE   The membrane surrounding the host rough endoplasmic reticulum.
SL   Host rough endoplasmic reticulum membrane.
HI   Host endoplasmic reticulum membrane.
HP   Host rough endoplasmic reticulum.
GO   GO:0044169; host cell rough endoplasmic reticulum membrane
//
ID   Host secretory vesicle.
AC   SL-0504
DE   The host secretory vesicle is a host vesicle that mediates the
DE   vesicular transport of cargo - e.g. hormones or neurotransmitters
DE   - from an organelle to specific sites at the host cell membrane, where
DE   it docks and fuses to release its content.
SL   Host cytoplasmic vesicle, host secretory vesicle.
HI   Host cytoplasmic vesicle.
//
ID   Host smooth endoplasmic reticulum.
AC   SL-0444
DE   The host smooth endoplasmic reticulum (host SER) is the portion of the
DE   host ER which is free of ribosomes.
SY   Host SER; Host smooth ER.
SL   Host smooth endoplasmic reticulum.
HP   Host endoplasmic reticulum.
GO   GO:0044170; host cell smooth endoplasmic reticulum
//
ID   Host smooth endoplasmic reticulum membrane.
AC   SL-0445
DE   The membrane surrounding the host smooth endoplasmic reticulum.
SL   Host smooth endoplasmic reticulum membrane.
HI   Host endoplasmic reticulum membrane.
HP   Host rough endoplasmic reticulum.
GO   GO:0044171; host cell smooth endoplasmic reticulum membrane
//
ID   Host synapse.
AC   SL-0435
DE   Host synapses are the communicating cell-cell junctions that allow
DE   signals to pass from a host nerve cell to a target cell. In a chemical
DE   synapse, the signal is carried by a neurotransmitter which diffuses
DE   across a narrow synaptic cleft and activates a receptor on the
DE   postsynaptic membrane of the target cell. The target may be a
DE   dendrite, cell body, neuronal axon, a specialized region of a muscle
DE   or a secretory cell. In an electrical synapse, a direct connection is
DE   made between the cytoplasms of two cells via gap junctions.
SL   Host synapse.
KW   KW-1051
GO   GO:0044221; host cell synapse
//
ID   Host synaptic vesicle.
AC   SL-0502
DE   In a host synapse, host synaptic vesicles mediate the exocytosis of
DE   neurotransmitters and subsequent re-uptake by endocytosis of vesicular
DE   components. Re-uptake is a crucial element in the maintenance of host
DE   synaptic transmission in the nervous system.
SL   Host secretory vesicle, host synaptic vesicle.
HI   Host secretory vesicle.
HP   Host synapse.
//
ID   Host synaptic vesicle membrane.
AC   SL-0503
DE   The host membrane surrounding a host synaptic vesicle
SY   Host synaptic vesicular membrane.
SL   Host cytoplasmic vesicle, host secretory vesicle, host synaptic vesicle membrane.
HP   Host synaptic vesicle.
//
ID   Host thylakoid.
AC   SL-0449
DE   The host thylakoid is a membranous cellular structure containing the
DE   photosynthetic pigments, reaction centers and electron-transport
DE   chain. In host chloroplast, thylakoids stack up to form the grana or
DE   stay as single cisternae and interconnect the grana. Thylakoid, where
DE   photosynthesis occurs, are found in chloroplasts, cyanelles and in
DE   photosynthetic bacteria where they are the extensive invaginations of
DE   the plasma membrane.
SL   Host thylakoid.
HP   Host cell.
KW   KW-1050
GO   GO:0044159; host thylakoid
//
ID   Host trans-Golgi network.
AC   SL-0463
DE   The host trans-Golgi network is a highly dynamic series of
DE   interconnected tubules and vesicles at the trans face of the host
DE   Golgi stack. The host trans-Golgi network functions in the processing
DE   and sorting of glycoproteins and glycolipids at the interface of the
DE   biosynthetic and endosomal pathways. The generation and maintenance of
DE   host apical and basolateral membranes rely on sorting events that
DE   occur in the host TGN.
SY   Host Golgi trans-face; Host TGN; Host trans-Golgi;
SY   Host trans-Golgi complex.
SL   Host Golgi apparatus, host trans-Golgi network.
HP   Host Golgi apparatus.
//
ID   Host trans-Golgi network membrane.
AC   SL-0464
DE   The membrane surrounding the host trans-Golgi network.
SY   Host Golgi trans-face membrane; Host TGN membrane;
SY   Host trans-Golgi complex membrane; Host trans-Golgi membrane.
SL   Host Golgi apparatus, host trans-Golgi network membrane.
HI   Host Golgi apparatus membrane.
HP   Host trans-Golgi network.
//
ID   Host vacuole.
AC   SL-0506
DE   The host vacuole is a fluid-filled, membrane-bound compartment in the
DE   cytoplasm. The precise form and function of vacuoles may vary between
DE   phyla. They are employed for a variety of purposes, including storage,
DE   as a degradative compartment, cell size control, secretion and
DE   following phagocytosis.
SL   Host vacuole.
HP   Host cell.
//
ID   Hyaline layer.
AC   SL-0143
DE   The hyaline layer is a multilayered extracellular matrix that coats
DE   the external surfaces of sea urchin and starfish embryos.
SL   Secreted, extracellular space, extracellular matrix, hyaline layer.
HI   Extracellular matrix.
GO   GO:0033166; hyaline layer
//
ID   Hydrogenosome.
AC   SL-0145
DE   The hydrogenosome is a redox organelle of anaerobic unicellular
DE   eukaryotes which contains hydrogenase and produces hydrogen and ATP by
DE   glycolysis. They are found in various unrelated eukaryotes, such as
DE   anaerobic flagellates, chytridiomycete fungi and ciliates. Most
DE   hydrogenosomes lack a genome, but some like that of the anaerobic
DE   ciliate Nyctotherus ovalis, have retained a rudimentary genome.
SL   Hydrogenosome.
KW   KW-0377
GO   GO:0042566; hydrogenosome
//
ID   Hydrogenosome lumen.
AC   SL-0335
DE   The hydrogenosomal compartment bounded by the membrane of the
DE   hydrogenosome, a redox organelle found in anaerobic unicellular
DE   eukaryotes.
SY   Hydrogenosomal lumen.
SL   Hydrogenosome lumen.
HP   Hydrogenosome.
GO   GO:0034492; hydrogenosome lumen
//
ID   Hydrogenosome membrane.
AC   SL-0144
DE   The membrane surrounding the hydrogenosome, a redox organelle found in
DE   anaerobic unicellular eukaryotes.
SY   Hydrogenosomal membrane.
SL   Hydrogenosome membrane.
HI   Membrane.
HP   Hydrogenosome.
GO   GO:0046859; hydrogenosomal membrane
//
ID   I band.
AC   SL-0478
DE   The appearance of the striated muscle is created by a pattern of
DE   alternating dark A bands and light I bands. I bands are composed of
DE   thin actin filaments and proteins that bind actin and they are
DE   bisected by the Z line. The thin filaments extend in each direction
DE   from the Z-disk, where they do not overlap the thick filaments, they
DE   create the light I band.
SY   I-band; I disc; I disk.
SL   Cytoplasm, myofibril, sarcomere, I band.
HP   Sarcomere.
GO   GO:0031674; I band
WW   http://www.sarcomere.org/
//
ID   Inflammasome.
AC   SL-0488
DE   Inflammasomes are supramolecular micron-sized complexes that assemble
DE   in the cytosol adjacent to the nucleus in response to pathogens and
DE   other damage-associated signals. The inflammasome assembly leads to
DE   the activation of proinflammatory procaspases, hence is usually
DE   involved in innate immunity and inflammation. The core of
DE   inflammasomes consists of at least 2 components: a signal sensor and
DE   an effector inflammatory caspase (mostly CASP1). However, most
DE   inflammasomes contain a third element, an adaptor (often ASC/PYCARD).
DE   The interaction between the sensor component and the adaptor initiates
DE   speck formation (nucleation) which greatly enhances further addition
DE   of soluble adaptor molecules to the speck in a prion-like
DE   polymerization process. The kinetic properties of the adaptor
DE   aggregation have been shown to generate a rapid 'all-or-none'
DE   response, this is why only one speck by cell is observed.
SY   ASC focus; ASC speck.
SL   Inflammasome.
HP   Cytosol.
KW   KW-1271
GO   GO:0061702; inflammasome complex
//
ID   Inner membrane complex.
AC   SL-0362
DE   The inner membrane complex, found in apicocomplexan parasites, is
DE   composed of flattened membrane cisternae closely associated to the
DE   cell membrane. Together, the cell membrane and the IMC form a triple
DE   lipid bilayer called the pellicle (or cell wall).
SY   IMC.
SL   Inner membrane complex.
HP   Membrane.
GO   GO:0070258; inner membrane pellicle complex
//
IO   Intermembrane side.
AC   SL-9912
DE   Protein found mostly on the intermembrane side of the membrane.
SL   Intermembrane side.
//
ID   Interphotoreceptor matrix.
AC   SL-0146
DE   In vertebrates, the photoreceptors are separated from the retinal
DE   pigment epithelium by the subretinal space, which contains a
DE   specialized extracellular material referred to as interphotoreceptor
DE   matrix. The IPM mediates key interactions between the photoreceptors
DE   and RPE including adhesion, phagocytosis, outer segment stability,
DE   nutrient exchange, development, and vitamin A trafficking in the
DE   visual cycle.
SY   IPM.
SL   Secreted, extracellular space, extracellular matrix, interphotoreceptor matrix.
HI   Extracellular matrix.
GO   GO:0033165; interphotoreceptor matrix
//
IO   Intravirionic side.
AC   SL-9919
DE   Protein found mostly on the intravirionic side of the virion membrane.
SL   Intravirionic side.
//
ID   Invadopodium.
AC   SL-0148
DE   The invadopodium is a localized and persitent cell protrusion similar
DE   to the highly dynamic podosome, but larger. These structures protrudes
DE   into the extracellular matrix. Invadopodial protrusions are enriched
DE   in integrins, tyrosine kinase signaling machinery, soluble and
DE   membrane proteases including matrix metalloproteases, actin and actin-
DE   associated proteins. Essential for physiological and pathological cell
DE   invasion and metastasis these structures are involved in focalized
DE   degradation of the extracellular matrix. Invadopodia form underneath
DE   the cell body, often close to the nucleus and proximal to the Golgi
DE   complex, and are rarely found at the cell periphery. Their half-life
DE   is quite extended. As invadopodia and podosomes are similar in
DE   appearance, location and composition, it is likely that a thin line
DE   separates these two entities in time and function.
SY   Invadopodia.
SL   Cell projection, invadopodium.
HI   Cell junction.
HI   Cell projection.
RX   PubMed=16546558; DOI=10.1016/j.ejcb.2005.09.005;
//
ID   Invadopodium membrane.
AC   SL-0290
DE   The portion of the cell membrane surrounding an invadopodium.
SL   Cell projection, invadopodium membrane.
HP   Cell membrane.
HP   Invadopodium.
//
ID   Kinetochore.
AC   SL-0149
DE   The kinetochore is a protein complex assembled on the centromeric
DE   region of DNA. It provides the major attachement point for the spindle
DE   microtubules during mitotic or meiotic division to pull the
DE   chromosomes apart. In monocentric chromosomes, the kinetochores of
DE   point centromeres bind a single microtubule and the larger
DE   kinetochores of regional centromeres interact with a number of
DE   microtubules. In holocentric chromosomes, the kinetochores bind the
DE   diffuse centromere along the length of the chromosomes.
SL   Chromosome, centromere, kinetochore.
HP   Centromere.
KW   KW-0995
//
ID   Kinetoplast.
AC   SL-0150
DE   The mitochondrial DNA of trypanosomatid protozoa is termed kinetoplast
DE   DNA (kDNA). kDNA is a massive network, composed of thousands of
DE   topologically interlocked DNA circles. Each cell contains one network
DE   condensed into a disk-shaped structure within the matrix of its single
DE   mitochondrion. The kDNA circles are of two types, maxicircles present
DE   in a few dozen copies and minicircles present in several thousand
DE   copies.
SL   Mitochondrion matrix, kinetoplast.
HP   Mitochondrion matrix.
KW   KW-0419
GO   GO:0020023; kinetoplast
//
ID   Kinocilium.
AC   SL-0460
DE   The kinocilium is an immotile primary cilium that is found at the
DE   apical surface of auditory receptor cells. Hair bundles, the
DE   mechanosensory device of the sensory hair cells, are composed of
DE   height-ranked rows of stereocilia and a single kinocilium that are
DE   interconnected by extracellular proteinaceous links.
SY   Kinocilia.
SL   Cell projection, kinocilium.
HI   Cilium.
GO   GO:0060091; kinocilium
//
ID   Lamellipodium.
AC   SL-0291
DE   The lamellipodium is a broad, flat, veil-shaped cell protrusion formed
DE   at the leading edge of migrating cells. Lamellipodium contain a
DE   branched dendritic network of actin filaments having their barbed ends
DE   directed towards the cell membrane. It is associated with ameboid
DE   motility (or crawling motility).
SY   Lamellipodia; Veil.
SL   Cell projection, lamellipodium.
HI   Cell projection.
GO   GO:0030027; lamellipodium
//
ID   Lamellipodium membrane.
AC   SL-0292
DE   The portion of the cell membrane surrounding a lamellipodium.
SL   Cell projection, lamellipodium membrane.
HP   Cell membrane.
HP   Lamellipodium.
GO   GO:0031258; lamellipodium membrane
//
ID   Late endosome.
AC   SL-0152
DE   Late endosomes are pleiomorphic with cisternal, tubular and
DE   multivesicular regions. They are found in juxtanuclear regions and
DE   concentrated at the microtubule organizing center. They are an
DE   important sorting station in the endocytic pathway. Recycling to the
DE   plasma membrane and to the Golgi occurs in late endosomes. More acidic
DE   than early endosomes they are also loaded more slowly in a range of 4
DE   to 30 minutes depending on the cell type. They can be distinguished
DE   from lysosome for their enrichment in M6PR.
SL   Late endosome.
HP   Endosome.
GO   GO:0005770; late endosome
AN   Compartment specific marker: Rab7; Rab9; LBPA.
//
ID   Late endosome lumen.
AC   SL-0336
DE   The late endosomal comaprtment bounded by the membrane of the late
DE   endosome.
SY   Late endosomal lumen.
SL   Late endosome lumen.
HI   Endosome lumen.
HP   Late endosome.
GO   GO:0031906; late endosome lumen
//
ID   Late endosome membrane.
AC   SL-0151
DE   The membrane surrounding the late endosomes.
SY   Late endosomal membrane.
SL   Late endosome membrane.
HI   Endosome membrane.
HP   Late endosome.
GO   GO:0031902; late endosome membrane
//
ID   Lateral cell membrane.
AC   SL-0153
DE   The portion of the plasma membrane at the lateral side of the cell.
SY   Lateral plasma membrane.
SL   Lateral cell membrane.
HP   Cell membrane.
GO   GO:0016328; lateral plasma membrane
//
ID   Lipid droplet.
AC   SL-0154
DE   The lipid droplet is a dynamic cytoplasmic organelle which consists of
DE   an heterogeneous macromolecular assembly of lipids and proteins
DE   covered by a unique phospholipid monolayer. Lipid droplets may play a
DE   role in lipid metabolism and storage, and they may be involved in the
DE   regulation of intracellular trafficking and signal transduction.
SY   Adiposome; Lipid bodies; Lipid body; Lipid particle;
SY   Monolayer-surrounded lipid storage body; Oil bodies; Oil body;
SY   Oleosome; Spherosome.
SL   Lipid droplet.
KW   KW-0551
GO   GO:0005811; lipid droplet
//
IT   Lipid-anchor.
AC   SL-9901
DE   Protein bound to the lipid bilayer of a membrane through a
DE   posttranslationally modification by the attachment of at least one
DE   lipid or fatty acid, e.g. farnesyl, palmitate and myristate.
SL   Lipid-anchor.
KW   KW-0449
//
IO   Lumenal side.
AC   SL-9914
DE   Protein found mostly on the lumenal side of the membrane.
SL   Lumenal side.
//
ID   Lysosome.
AC   SL-0158
DE   The lysosome is a membrane-limited organelle present in all eukaryotic
DE   cells, which contains a large number of hydrolytic enzymes that are
DE   used for degrading almost any kind of cellular constituent, including
DE   entire organelles. The mechanisms responsible for delivering
DE   cytoplasmic cargo to the lysosome/vacuole are known collectively as
DE   autophagy and play an important role in the maintenance of
DE   homeostasis.
SL   Lysosome.
KW   KW-0458
GO   GO:0005764; lysosome
AN   Compartment specific marker: LAMP-1; LAMP-2?.
//
ID   Lysosome lumen.
AC   SL-0156
DE   The lumen of a lysosome is the volume enclosed within the lysosomal
DE   membrane.
SY   Lysosomal lumen.
SL   Lysosome lumen.
HP   Lysosome.
GO   GO:0043202; lysosomal lumen
//
ID   Lysosome membrane.
AC   SL-0157
DE   The membrane surrounding a lysosome.
SY   Lysosomal membrane.
SL   Lysosome membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Lysosome.
GO   GO:0005765; lysosomal membrane
//
ID   Lytic vacuole.
AC   SL-0159
DE   The lytic vacuole is a plant specialized vacuole equivalent to animal
DE   lysosomes or yeast vacuoles, functioning as compartments for
DE   degradation and waste storage.
SL   Lytic vacuole.
HI   Vacuole.
GO   GO:0000323; lytic vacuole
//
ID   M line.
AC   SL-0315
DE   In electron micrographs of the sarcomere, the M line appears as a
DE   series of parallel electron-dense lines in the central zone of the A
DE   band impliing that the M line is needed for the regular packing of the
DE   thick filaments. The M line maintains the myosin filaments in a
DE   hexagonal lattice.
SY   M band; M-band; M-line.
SL   Cytoplasm, myofibril, sarcomere, M line.
HP   H zone.
GO   GO:0031430; M band
WW   http://www.sarcomere.org/
//
ID   Magnetosome.
AC   SL-0510
DE   A specialized, membrane-bound bacterial organelle that envelops
DE   nanometer-sized crystals of magnetic iron minerals. They form linear
DE   chains at midcell along the cellular motility axis.
SL   Magnetosome.
KW   KW-1281
GO   GO:0110143; magnetosome
//
ID   Magnetosome lumen.
AC   SL-0511
DE   The magnetosome lumen.
SL   Magnetosome, Magnetosome lumen.
HP   Magnetosome.
GO   GO:0110145; magnetosome lumen
//
ID   Magnetosome membrane.
AC   SL-0512
DE   The magnetosome membrane.
SL   Magnetosome membrane.
HI   Membrane.
HP   Magnetosome.
GO   GO:0110146; magnetosome membrane
//
IO   Matrix side.
AC   SL-9913
DE   Protein found mostly on the matrix side of the membrane.
SL   Matrix side.
//
ID   Melanosome.
AC   SL-0161
DE   The melanosome is a melanin-containing organelle found in melanocytes
DE   and melanophores. Fish and amphibians possess specialized cells,
DE   called melanophores, which contain hundreds of melanin-filled pigment
DE   granules, termed melanosomes. The sole function of these cells is
DE   pigment aggregation in the center of the cell or dispersion throughout
DE   the cytoplasm. This alternative transport of pigment allows the animal
DE   to effect color changes important for camouflage and social
DE   interactions. Melanophores transport their pigment in response to
DE   extracellular cues: neurotransmitters in the case of fish and hormonal
DE   stimuli in the case of frogs. In both cases, melanosome dispersion is
DE   induced by elevation of intracellular cAMP levels, while aggregation
DE   is triggered by depression of cAMP. The regulatory mechanisms
DE   downstream of these second-messengers are poorly understood. Mammalian
DE   melanocytes also produce melanosomes but, unlike melanophores, pigment
DE   in these cells is transported to the cell periphery for subsequent
DE   exocytosis to surrounding epithelial cells.
SL   Melanosome.
GO   GO:0042470; melanosome
WW   http://www.proweb.org/kinesin/Melanophore.html
//
ID   Melanosome lumen.
AC   SL-0338
DE   The melanosomal compartment bounded by the membrane surrounding a
DE   melanosome.
SY   Melanosomal lumen.
SL   Melanosome lumen.
HP   Melanosome.
GO   GO:0034493; melanosome lumen
//
ID   Melanosome membrane.
AC   SL-0160
DE   The membrane surrounding a melanosome.
SY   Melanosomal membrane.
SL   Melanosome membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Melanosome.
GO   GO:0033162; melanosome membrane
//
ID   Membrane.
AC   SL-0162
DE   A membrane is a lipid bilayer which surrounds enclosed spaces and
DE   compartments. This selectively permeable structure is essential for
DE   effective separation of a cell or organelle from its surroundings.
DE   Membranes are composed of various types of molecules such as
DE   phospholipids, integral membrane proteins, peripheral proteins,
DE   glycoproteins, glycolipids, etc. The relative amounts of these
DE   components as well as the types of lipids are non-randomly distributed
DE   from membrane to membrane as well as between the two leaflets of a
DE   membrane.
SL   Membrane.
KW   KW-0472
GO   GO:0016020; membrane
//
ID   Membrane raft.
AC   SL-0370
DE   Membrane rafts are small (10-200 nm), heterogeneous, highly dynamic,
DE   sterol- and sphingolipid-enriched domains that compartmentalize
DE   cellular processes. Small rafts can sometimes be stabilized to form
DE   larger platforms through protein-protein and protein-lipid
DE   interactions. Multiple types of rafts are likely to exist, based both
DE   on their lipid and protein composition.
SY   Lipid microdomain; Lipid raft; Membrane microdomain.
SL   Membrane raft.
HP   Endomembrane system.
GO   GO:0045121; membrane raft
RX   PubMed=16645198; DOI=10.1194/jlr.E600002-JLR200;
//
ID   Microneme.
AC   SL-0163
DE   The microneme is an Apicomplexan parasite organelle. Apicomplexa are
DE   named for the unique set of morphologically distinct secretory
DE   organelles (refered to as the apical complex)- micronemes, rhoptries
DE   and dense granules - whose sequential secretion is required for the
DE   invasion of host cells. Micronemes are the smallest, they are involved
DE   in the early stages of invasion.
SL   Cytoplasmic vesicle, secretory vesicle, microneme.
HI   Secretory vesicle.
GO   GO:0020009; microneme
//
ID   Microneme lumen.
AC   SL-0339
DE   The micronemal compartment bounded by the membrane of a microneme.
SY   Micronemal lumen.
SL   Cytoplasmic vesicle, secretory vesicle, microneme lumen.
HI   Secretory vesicle lumen.
HP   Microneme.
GO   GO:0034494; microneme lumen
//
ID   Microneme membrane.
AC   SL-0164
DE   The membrane surrounding a microneme.
SY   Micronemal membrane.
SL   Cytoplasmic vesicle, secretory vesicle, microneme membrane.
HI   Secretory vesicle membrane.
HP   Microneme.
GO   GO:0033163; microneme membrane
//
ID   Microsome.
AC   SL-0166
DE   The microsomes are a heterogenous set of vesicles 20-200nm in diameter
DE   and formed from the endoplasmic reticulum when cells are disrupted.
DE   The vesicles are isolated by differential centrifugation and are
DE   composed of three structural features: rough vesicles, smooth vesicles
DE   and ribosomes. Numerous enzyme activities are associated with the
DE   microsomal fraction.
SL   Microsome.
HP   Endoplasmic reticulum.
KW   KW-0492
//
ID   Microsome membrane.
AC   SL-0165
DE   The membrane surrounding the microsome.
SY   Microsomal membrane.
SL   Microsome membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Microsome.
//
ID   Microtubule organizing center.
AC   SL-0484
DE   The microtubule organizing center (MTOC) is an intracellular structure
DE   that can catalyze gamma-tubulin-dependent microtubule nucleation and
DE   that can anchor microtubules.
SY   MTOC.
SL   Cytoplasm, cytoskeleton, microtubule organizing center.
HP   Cytoskeleton.
//
ID   Microvillus.
AC   SL-0293
DE   Microvilli are thin cylindrical dynamic cell projections containing a
DE   core bundle of actin filaments. They serve a diverse set of functions,
DE   such as increasing absorptive surface area in the epithelial brush
DE   border, tethering leukocytes to the surface of endothelial cells or
DE   participate in sperm-oocyte fusion.
SY   Microvilli.
SL   Cell projection, microvillus.
HI   Cell projection.
GO   GO:0005902; microvillus
//
ID   Microvillus membrane.
AC   SL-0294
DE   The portion of the cell membrane surrounding a microvillus.
SY   Microvillar membrane.
SL   Cell projection, microvillus membrane.
HP   Cell membrane.
HP   Microvillus.
GO   GO:0031528; microvillus membrane
//
ID   Midbody.
AC   SL-0469
DE   The midbody is the central region of the thin intercellular
DE   cytoplasmic bridge formed between daughter cells during cytokinesis.
DE   It consists of tightly bundled antiparallel microtubules, which
DE   embrace a phase-dense circular structure, called midbody ring. At the
DE   final stage of cytokinesis, the intercellular bridge is cleaved, in a
DE   process termed abscission, and two daughter cells are formed.
DE   Following abscission, the residual midbody structure, known as the
DE   midbody remnant or midbody derivative, can have different fates
DE   depending on the cell type. It can be either released to the
DE   extracellular medium, degraded by autophagy or persists in the
DE   cytoplasm, showing asymmetric accumulation in the daughter cells.
SY   Midbody derivative; Midbody remnant.
SL   Midbody.
GO   GO:0030496; midbody
AN   Some authors consider that Flemming body and Midbody are synonyms.
AN   This is not the case in UniProtKB, where we use Flemming body as a
AN   synonym for Midbody ring, a specific part of the midbody. If you have
AN   doubt, use the broader term, Midbody.
//
ID   Midbody ring.
AC   SL-0490
DE   The midbody ring is the central region of the midbody characterized by
DE   a gap in alpha-tubulin staining, although interdigitating microtubules
DE   persist through the gap. It is thought that high local protein density
DE   masks tubulin epitopes known to be present. The midbody ring serves as
DE   a scaffold for a wide variety of structural and regulatory proteins
DE   required for completion of cytokinesis.
SY   Flemming body; Stembody.
SL   Midbody, Midbody ring.
HI   Midbody.
GO   GO:0090543; Flemming body
AN   Some authors consider that Flemming body and Midbody are synonyms.
AN   This is not the case in UniProtKB, where we use Flemming body as a
AN   synonym for Midbody ring, a specific part of the midbody. If you have
AN   doubt, use the broader term, Midbody.
//
ID   Mitochondrion.
AC   SL-0173
DE   The mitochondrion is a semiautonomous, self-reproducing organelle that
DE   occurs in the cytoplasm of all cells of most, but not all, eukaryotes.
DE   Each mitochondrion is surrounded by a double limiting membrane. The
DE   inner membrane is highly invaginated, and its projections are called
DE   cristae. Mitochondria are the sites of the reactions of oxidative
DE   phosphorylation, which result in the formation of ATP. The size and
DE   coding capacity of the mitochondrial DNA varies considerably in
DE   different organisms, and encodes rRNAs, tRNAs and essential
DE   mitochondrial proteins.
SL   Mitochondrion.
KW   KW-0496
GO   GO:0005739; mitochondrion
//
ID   Mitochondrion envelope.
AC   SL-0167
DE   The mitochondrial envelope comprises the inner and outer mitochondrial
DE   membrane including the intermembrane space.
SY   Mitochondrial envelope.
SL   Mitochondrion envelope.
HP   Mitochondrion.
GO   GO:0005740; mitochondrial envelope
//
ID   Mitochondrion inner membrane.
AC   SL-0168
DE   The inner membrane of a mitochondrion is the membrane which separates
DE   the mitochondrial matrix from the intermembrane space.
SY   Inner mitochondrial membrane; Mitochondrial inner membrane.
SL   Mitochondrion inner membrane.
HI   Mitochondrion membrane.
KW   KW-0999
GO   GO:0005743; mitochondrial inner membrane
//
ID   Mitochondrion intermembrane space.
AC   SL-0169
DE   The mitochondrial intermembrane space is the space between inner and
DE   outer mitochondrial membrane.
SY   Mitochondrial intermembrane space; Mitochondrial periplasm;
SY   Mitochondrial periplasmic space.
SL   Mitochondrion intermembrane space.
HP   Mitochondrion envelope.
GO   GO:0005758; mitochondrial intermembrane space
//
ID   Mitochondrion matrix.
AC   SL-0170
DE   The matrix of a mitochondrion is the mitochondrion internal spaces
DE   enclosed by the inner membrane. Several of the steps in cellular
DE   respiration occur in the matrix due to its high concentration of
DE   enzymes.
SY   Mitochondrial matrix.
SL   Mitochondrion matrix.
HP   Mitochondrion.
GO   GO:0005759; mitochondrial matrix
//
ID   Mitochondrion membrane.
AC   SL-0171
DE   The membrane surrounding a mitochondrion. This term is used when it is
DE   not known if the protein is found in or associated with the inner or
DE   outer mitochondrial membrane.
SY   Mitochondrial membrane.
SL   Mitochondrion membrane.
HI   Membrane.
HP   Mitochondrion envelope.
GO   GO:0031966; mitochondrial membrane
//
ID   Mitochondrion nucleoid.
AC   SL-0269
DE   The mitochondrial nucleoid is the mitochondrial pseudocompartment
DE   formed by the chromatin-dense area. This region, which is functionally
DE   equivalent to the eukaryotic nucleus, is not surrounded by a membrane.
SY   Mitochondrial nucleoid; Mitochromosome.
SL   Mitochondrion matrix, mitochondrion nucleoid.
HP   Mitochondrion matrix.
KW   KW-1135
GO   GO:0042645; mitochondrial nucleoid
//
ID   Mitochondrion outer membrane.
AC   SL-0172
DE   The outer membrane of a mitochondrion is the mitochondrial membrane
DE   facing the cytoplasm.
SY   Mitochondrial outer membrane; Outer mitochondrial membrane.
SL   Mitochondrion outer membrane.
HI   Mitochondrion membrane.
KW   KW-1000
GO   GO:0005741; mitochondrial outer membrane
//
ID   Mitosome.
AC   SL-0437
DE   The mitosome is an organelle found in "amitochondrial" unicellular
DE   organisms which do not have the capability of gaining energy from
DE   oxidative phosphorylation. Mitosomes are almost certainly derived from
DE   mitochondria, they have a double membrane and most proteins are
DE   delivered to them by a targeting sequence. Unlike mitochondria,
DE   mitosomes do not contain any DNA. The mitosome functions in iron-
DE   sulphur cluster assembly.
SL   Mitosome.
KW   KW-1025
GO   GO:0032047; mitosome
//
ID   Mitosome envelope.
AC   SL-0438
DE   The mitosomal envelope comprises the inner and outer mitosomal
DE   membrane including the intermembrane space.
SY   Mitosomal envelope.
SL   Mitosome envelope.
HP   Mitosome.
//
ID   Mitosome inner membrane.
AC   SL-0439
DE   The inner membrane of a mitosome is the membrane which separates the
DE   mitosomal matrix from the intermembrane space.
SY   Inner mitosomal membrane; Mitosomal inner membrane.
SL   Mitosome inner membrane.
HI   Mitosome membrane.
//
ID   Mitosome intermembrane space.
AC   SL-0440
DE   The mitosomal intermembrane space is the space between inner and outer
DE   mitosomal membranes.
SY   Mitosomal intermembrane space; Mitosomal periplasm;
SY   Mitosomal periplasmic space.
SL   Mitosome intermembrane space.
HP   Mitosome envelope.
//
ID   Mitosome matrix.
AC   SL-0441
DE   The matrix of a mitosome is the mitosomal internal spaces enclosed by
DE   the inner membrane.
SY   Mitosomal matrix.
SL   Mitosome matrix.
HP   Mitosome.
//
ID   Mitosome membrane.
AC   SL-0442
DE   The membrane surrounding a mitosome. This term is used when it is not
DE   known if the protein is found in or associated with the inner or outer
DE   mitosomal membrane.
SY   Mitosomal membrane.
SL   Mitosome membrane.
HI   Membrane.
HP   Mitosome envelope.
//
ID   Mitosome outer membrane.
AC   SL-0443
DE   The outer membrane of a mitosome is the mitosomal membrane facing the
DE   cytoplasm.
SY   Mitosomal outer membrane; Outer mitosomal membrane.
SL   Mitosome outer membrane.
HI   Mitosome membrane.
//
IT   Multi-pass membrane protein.
AC   SL-9909
DE   Protein spanning the membrane more than once.
SY   Multipass; Multi pass; Multi-pass; Multispan; Multi span;
SY   Polytopic membrane protein.
SL   Multi-pass membrane protein.
HI   Membrane.
//
ID   Multivesicular body.
AC   SL-0174
DE   The multivesicular bodies are a type of late endosome containing
DE   internal vesicles formed following the inward budding of the outer
DE   endosomal membrane. The contents of the MVBs are then released into
DE   the lysosome lumen. The proteins found in the limiting membrane of
DE   MVBs are recycled to other compartments.
SY   Corpuscula multivesicularis; ECV; Endosomal carrier vesicle;
SY   Multivesicular bodies; MVB.
SL   Endosome, multivesicular body.
HI   Late endosome.
GO   GO:0005771; multivesicular body
WW   http://www.uni-mainz.de/FB/Medizin/Anatomie/workshop/EM/EMMVBE.html
//
ID   Multivesicular body lumen.
AC   SL-0340
DE   The multivesicular body compartment bounded by the membrane of the
DE   multivesicular bodies.
SY   Corpuscula multivesicularis lumen; ECV lumen;
SY   Endosomal carrier vesicle lumen; Multivesicular bodies lumen;
SY   MVB lumen.
SL   Endosome, multivesicular body lumen.
HI   Endosome lumen.
HP   Multivesicular body.
//
ID   Multivesicular body membrane.
AC   SL-0175
DE   The membrane surrounding the multivesicular bodies.
SY   Corpuscula multivesicularis membrane; ECV membrane;
SY   Endosomal carrier vesicle membrane; Multivesicular bodies membrane;
SY   MVB membrane.
SL   Endosome, multivesicular body membrane.
HI   Endosome membrane.
HP   Multivesicular body.
GO   GO:0032585; multivesicular body membrane
//
ID   Myelin membrane.
AC   SL-0176
DE   The myelin membrane is the white matter coating our nerves, enabling
DE   them to conduct impulses between the brain and other parts of the
DE   body. It consists of a layer of proteins packed between two layers of
DE   lipids. This specialized cell membrane is produced by oligodendrocytes
DE   in the central nervous system, and Schwann cells in the peripheral
DE   nervous system. Myelin sheaths wrap themselves around axons, the
DE   threadlike extensions of neurons that make up nerve fibers. Each
DE   oligodendrocyte can myelinate several axons. The major function of
DE   myelin is to increase the velocity of propagation of nerve impulses.
SY   Myelin; Myelin sheath.
SL   Myelin membrane.
HI   Cell membrane.
GO   GO:0043209; myelin sheath
WW   https://www.myelin.org/
//
ID   Myofibril.
AC   SL-0312
DE   A myofibril is a long cylindrical organelle found in muscle cells
DE   formed by two transverse filament systems: the thick and thin
DE   filaments. The thin filament is composed primarily of actin; it is
DE   tethered at one end to the Z-disk, and it interdigitates with the
DE   thick filaments. The main constituent of the thick filament is myosin;
DE   the direction of the myosin heads changes polarity at the M-line,
DE   allowing interaction with the thin filaments anchored from the next
DE   adjacent Z-disk. A third and a fourth filament complex exist,
DE   comprising the giant proteins titin and nebulin.
SL   Cytoplasm, myofibril.
HI   Sarcoplasm.
GO   GO:0030016; myofibril
//
ID   Nematocyst.
AC   SL-0177
DE   The nematocyst is an organelle found in nematoblast (cnidoblast)
DE   cells. When matured, these stinging organelles store toxins and can
DE   deliver them when the cnidocil (a short extension of the nematocyst)
DE   is stimulated by a prey or another stimulus. These proteins are
DE   principally found in anemones and jellyfishes.
SY   Cnidocyst.
SL   Nematocyst.
KW   KW-0166
GO   GO:0042151; nematocyst
//
ID   Neuron projection.
AC   SL-0518
DE   Prolongation or process extending from a nerve cell, such as an axon
DE   or a dendrite. Used when speaking of immature or developing neurons,
DE   especially of cells in culture, because it can be difficult to tell
DE   axons from dendrites before differentiation is complete.
SY   Neurite; Neuronal process.
SL   Cell projection, neuron projection.
HI   Cell projection.
GO   GO:0043005; neuron projection
//
ID   Neuronal dense core vesicle.
AC   SL-0526
DE   Dense core vesicle that is part of a neuron. Stores and releases
DE   neuropeptides (peptide neurotransmitters) and neurotrophins by
DE   exocytosis. Filled with cargo at the Golgi network, they are
DE   transported through axons and dendrites to the synapses where the
DE   release takes place. They can be found in all parts of neurons,
DE   including the soma, dendrites, axonal swellings (varicosities) and
DE   synaptic terminals.
SY   Large dense-core vesicles; Neuronal dense core granule;
SY   Neuronal large dense-core vesicles.
SL   Cytoplasmic vesicle, secretory vesicle, neuronal dense core vesicle.
HI   Secretory vesicle.
GO   GO:0098992; neuronal dense core vesicle
//
ID   Neuronal dense core vesicle membrane.
AC   SL-0532
DE   The membrane surrounding a neuronal dense core vesicle.
SL   Cytoplasmic vesicle, secretory vesicle, neuronal dense core vesicle membrane.
HI   Secretory vesicle membrane.
HP   Neuronal dense core vesicle.
GO   GO:0099012; neuronal dense core vesicle membrane
//
ID   Nuclear body.
AC   SL-0494
DE   Nuclear body is a collective term for several nuclear, extra-
DE   nucleolar, non-membrane-bound sub-compartments, including, but not
DE   limited to Cajal bodies, Gemini of Cajal bodies (gems), nuclear
DE   speckles and PML bodies. Nuclear bodies are visible as distinct spots
DE   in the nucleoplasm. They can vary in number and size depending on the
DE   cell line and the type of nuclear body.
SL   Nucleus, nuclear body.
HP   Nucleus.
GO   GO:0016604; nuclear body
//
ID   Nuclear pore complex.
AC   SL-0185
DE   The nuclear pore complex (NPC) constitutes the exclusive means of
DE   nucleocytoplasmic transport in eukaryotes during interphase. NPCs
DE   allow the passive diffusion of ions and small molecules (up to about
DE   20 kDa or 5 nm) and the active, nuclear transport receptor
DE   (karyopherin: importin and exportin)-mediated bidirectional transport
DE   of macromolecules such as proteins, RNAs, ribonucleoprotein (RNPs),
DE   and ribosomal subunits (up to about 10 MDa) across the double-membrane
DE   nuclear envelope. NPC components, collectively referred to as
DE   nucleoporins (NUPs), can play the role of both NPC structural
DE   components and of docking or interaction partners for transiently
DE   associated nuclear transport factors. The NPC is composed of at least
DE   30 distinct subunits, shows 8-fold rotational symmetry with
DE   specialized structures on the cyto- and nucleoplasmic side and in the
DE   nuclear envelope embedded core. The MW varies from about 44-60 MDa in
DE   S. cerevisiae to 60-120 MDa in vertebrates, yet the overall
DE   architecture is conserved.
SY   NPC; Nuclear pore.
SL   Nucleus, nuclear pore complex.
HP   Nucleus envelope.
KW   KW-0906
GO   GO:0005643; nuclear pore
//
ID   Nucleoid.
AC   SL-0187
DE   The nucleoid is the prokaryotic pseudocompartment formed by the
DE   chromatin-dense area. This region, which is functionally equivalent to
DE   the eukaryotic nucleus, is not surrounded by a membrane.
SL   Cytoplasm, nucleoid.
HP   Cytoplasm.
GO   GO:0009295; nucleoid
//
ID   Nucleolus.
AC   SL-0188
DE   The nucleolus is a non-membrane bound nuclear compartment found in
DE   eukaryotic cells which is the site of ribosome biogenesis. The
DE   interphase nucleolus is organized around the tandemly repeated genes
DE   for preribosomal RNA (rRNA). It is composed of at least 2 sub-
DE   compartments: the dense fibrillar component (DFC, also called pars
DE   fibrosa) and the granular component (GC or pars granulosa). The DFC
DE   contains newly synthesized preribosomal RNA and a collection of
DE   proteins; the GC is made up of nearly completed preribosomal particles
DE   destined for the cytoplasm. In most metazoans, but generally not in
DE   lower eukaryotes, a third component, the fibrillar center (FC), can be
DE   seen. Plant and animal nuclei can contain more than one nucleolus.
SY   Nucleoli.
SL   Nucleus, nucleolus.
HP   Nucleus.
GO   GO:0005730; nucleolus
//
ID   Nucleolus fibrillar center.
AC   SL-0497
DE   The nucleolus fibrillar center (FC) is a sub-compartment of most
DE   metazoan nucleoli. The transcription of ribosomal RNA (rRNA) genes
DE   generates 2 structures that are found in all nucleoli: the dense
DE   fibrillar component (DFC) and the granular component (GC). The DFC
DE   contains newly synthesized preribosomal RNA and a collection of
DE   proteins; the GC is made up of nearly completed preribosomal particles
DE   destined for the cytoplasm. In most metazoans, but generally not in
DE   lower eukaryotes, a third component, the FC, can be seen. The FC is
DE   surrounded by the DFC. The zone of transcription from multiple copy
DE   rRNA genes is in the border region between these 2 structures.
SY   Nucleoli fibrillar center.
SL   Nucleus, nucleolus fibrillar center.
HP   Nucleolus.
GO   GO:0001650; fibrillar center
//
ID   Nucleomorph.
AC   SL-0189
DE   Nucleomorphs are vestigial endosymbiont found in cryptomonads and
DE   chlorachniophytes algae. These organisms respectively retain an
DE   enslaved red or green algal nucleus.
SL   Nucleomorph.
KW   KW-0542
GO   GO:0033009; nucleomorph
//
ID   Nucleoplasm.
AC   SL-0190
DE   The nucleoplasm is a highly viscous liquid contained within the
DE   nucleus that surrounds the chromosomes and other subnuclear
DE   organelles. A network of fibers known as the nuclear matrix can also
DE   be found in the nucleoplasm.
SY   Karyolymph; Karyoplasm.
SL   Nucleus, nucleoplasm.
HP   Nucleus.
GO   GO:0005654; nucleoplasm
//
IO   Nucleoplasmic side.
AC   SL-9915
DE   Protein found mostly on the nucleoplasmic side of the membrane.
SL   Nucleoplasmic side.
//
ID   Nucleus.
AC   SL-0191
DE   The nucleus is the most obvious organelle in any eukaryotic cell. It
DE   is a membrane-bound organelle surrounded by double membranes which
DE   contains most of the cell's genetic material. It communicates with the
DE   surrounding cytosol via numerous nuclear pores.
SY   Nuclear; Nuclei.
SL   Nucleus.
KW   KW-0539
GO   GO:0005634; nucleus
//
ID   Nucleus envelope.
AC   SL-0178
DE   The nuclear envelope is a membrane system which surrounds the
DE   nucleoplasm of eukaryotic cells. It is composed of the nuclear lamina,
DE   nuclear pore complexes and two nuclear membranes. The space between
DE   the two membranes is called the nuclear intermembrane space.
SY   Karyotheca; Nuclear envelope; Nucleolemma; Perinuclear envelope.
SL   Nucleus envelope.
HP   Nucleus.
GO   GO:0005635; nuclear envelope
//
ID   Nucleus inner membrane.
AC   SL-0179
DE   The inner membrane of the nucleus is the membrane which separates the
DE   nuclear matrix from the intermembrane space. In mammals, the inner
DE   nuclear membrane is associated with heterochromatin and the nuclear
DE   lamina.
SY   Inner nuclear membrane; Nuclear inner membrane.
SL   Nucleus inner membrane.
HI   Nucleus membrane.
GO   GO:0005637; nuclear inner membrane
//
ID   Nucleus intermembrane space.
AC   SL-0184
DE   The nuclear intermembrane space is the space between the inner and
DE   outer nuclear membranes.
SY   Nuclear envelope lumen; Nuclear intermembrane space;
SY   Nuclear periplasm; Nuclear periplasmic space; Nucleus envelope lumen;
SY   Perinuclear space.
SL   Nucleus intermembrane space.
HP   Nucleus envelope.
GO   GO:0005641; nuclear envelope lumen
//
ID   Nucleus lamina.
AC   SL-0180
DE   The nuclear lamina is a meshwork of intermediate filament proteins
DE   called lamins and lamin-binding proteins that are embedded in the
DE   inner nuclear membrane.
SY   Nuclear lamina.
SL   Nucleus lamina.
HP   Nucleus envelope.
GO   GO:0005652; nuclear lamina
//
ID   Nucleus matrix.
AC   SL-0181
DE   The nuclear matrix is a three-dimensional filamentous protein network,
DE   found in the nucleoplasm, which provides a structural framework for
DE   organising chromatin, while facilitating transcription and
DE   replication.
SY   Nuclear matrix; Nuclear scaffold; Nuclear skeleton.
SL   Nucleus matrix.
HP   Nucleus.
GO   GO:0016363; nuclear matrix
//
ID   Nucleus membrane.
AC   SL-0182
DE   The membrane surrounding the nucleus. This term is used when it is not
DE   known if the protein is found in or associated with the inner or outer
DE   nuclear membrane.
SY   Nuclear membrane.
SL   Nucleus membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Nucleus envelope.
GO   GO:0031965; nuclear membrane
//
ID   Nucleus outer membrane.
AC   SL-0183
DE   The outer membrane of the nucleus is the membrane facing the
DE   cytoplasm. In mammals, the outer nuclear membrane is continuous in
DE   many places with the rough endoplasmic reticulum and is dotted with
DE   ribosomes.
SY   Nuclear outer membrane; Outer nuclear membrane.
SL   Nucleus outer membrane.
HI   Nucleus membrane.
GO   GO:0005640; nuclear outer membrane
//
ID   Nucleus speckle.
AC   SL-0186
DE   The nuclear speckles are small subnuclear membraneless organelles or
DE   structures, also called the splicing factor (SF) compartments that
DE   correspond to nuclear domains located in interchromatin regions of the
DE   nucleoplasm of mammalian cells. Protein found in speckles serves as a
DE   reservoir of factors that participate in transcription and pre-mRNA
DE   processing. Speckles appear, at the immunofluorescence-microscope
DE   level, as irregular, punctuate structures, which vary in size and
DE   shape. Usually 25-50 speckles are observed per interphase mammalian
DE   nucleus. At the electronic-microscope level, they are composed of
DE   heterogeneous mixture of electro-dense particles with diameters
DE   ranging from 20-25 nm and are called interchromatin granules clusters
DE   (IGCs). Speckles are dynamic structures. Both their protein and RNA-
DE   protein components can cycle continuously between speckles and other
DE   nuclear locations depending on the transcriptional state of the cell.
DE   Structures similar to nuclear speckles have been identified in the
DE   amphibian oocyte nucleus (called B snurposomes) and in Drosophila
DE   melanogaster embryos, but not in yeast.
SY   B snurposome; IGC; Interchromatin granules clusters; Nuclear speck;
SY   Nuclear speckle; SF compartments; Splicing Factor compartments;
SY   Splicing speckle.
SL   Nucleus speckle.
HI   Nuclear body.
HP   Nucleus.
GO   GO:0016607; nuclear speck
//
ID   Organellar chromatophore.
AC   SL-0351
DE   The organellar chromatophore is the photosynthetic inclusion found in
DE   Paulinella species, which are photosynthetic thecate amoeba. It
DE   probably derives from a different endosymbiotic event than that which
DE   led to all other plastids. Houses the machinery necessary for
DE   photosynthesis and CO(2) fixation and may also be able to make a few
DE   amino acids, some fatty acids and a few cofactors. They are surrounded
DE   by 2 membranes, between which is found a residual peptidoglycan wall,
DE   and contain thylakoids.
SL   Plastid, organellar chromatophore.
HI   Plastid.
KW   KW-0994
GO   GO:0070111; organellar chromatophore
//
ID   Organellar chromatophore inner membrane.
AC   SL-0359
DE   The organellar chromatophore inner membrane is the membrane which
DE   separates the chromatophore stroma from the intermembrane space. Found
DE   exclusively in Paulinella species, which are photosynthetic thecate
DE   amoeba.
SL   Plastid, organellar chromatophore inner membrane.
HI   Plastid inner membrane.
HI   Organellar chromatophore membrane.
HP   Organellar chromatophore.
GO   GO:0070113; organellar chromatophore inner membrane
//
ID   Organellar chromatophore intermembrane space.
AC   SL-0360
DE   The intermembrane space between the inner and the outer organellar
DE   chromatophore membranes. Found exclusively in Paulinella species,
DE   which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore intermembrane space.
HI   Plastid intermembrane space.
HP   Organellar chromatophore.
GO   GO:0070115; organellar chromatophore intermembrane space
//
ID   Organellar chromatophore membrane.
AC   SL-0352
DE   One of the membranes of an organellar chromatophore. This term is used
DE   when it is not known with which membrane (outer membrane, inner
DE   membrane or thylakoid) a protein is associated. Found exclusively in
DE   Paulinella species, which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore membrane.
HI   Plastid membrane.
HP   Organellar chromatophore.
GO   GO:0070112; organellar chromatophore membrane
//
ID   Organellar chromatophore outer membrane.
AC   SL-0361
DE   The organellar chromatophore outer membrane is the organellar
DE   chromatophore membrane facing the cytoplasm. Found exclusively in
DE   Paulinella species, which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore outer membrane.
HI   Plastid outer membrane.
HI   Organellar chromatophore membrane.
HP   Organellar chromatophore.
GO   GO:0070114; organellar chromatophore outer membrane
//
ID   Organellar chromatophore stroma.
AC   SL-0353
DE   The internal space enclosed by the organellar chromatophore double
DE   membrane but excluding the thylakoid space. This space, filled with a
DE   colorless hydrophilic matrix, contains DNA, ribosomes and some
DE   temporary products of photosynthesis; other biosynthetic functions
DE   that could also occur there include amino acid, fatty acid and some
DE   cofactor biosynthesis. Found exclusively in Paulinella species, which
DE   are photosynthetic thecate amoeba.
SY   Organellar chromatophore plasma.
SL   Plastid, organellar chromatophore stroma.
HI   Plastid stroma.
HP   Organellar chromatophore.
//
ID   Organellar chromatophore thylakoid.
AC   SL-0354
DE   The thylakoid of an organellar chromatophore is an internal system of
DE   interconnected membranes that carry the complexes for the light
DE   reactions of photosynthesis. Found exclusively in Paulinella species,
DE   which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore thylakoid.
HI   Plastid thylakoid.
HP   Organellar chromatophore.
GO   GO:0070116; organellar chromatophore thylakoid
//
ID   Organellar chromatophore thylakoid lumen.
AC   SL-0355
DE   The organellar chromatophore thylakoid lumen is the compartment
DE   bounded by the thylakoid membrane. Found exclusively in Paulinella
DE   species, which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore thylakoid lumen.
HI   Plastid thylakoid lumen.
HP   Organellar chromatophore thylakoid.
GO   GO:0070117; organellar chromatophore thylakoid lumen
//
ID   Organellar chromatophore thylakoid membrane.
AC   SL-0356
DE   The organellar chromatophore thylakoid membrane is an internal system
DE   of interconnected membranes that house the complexes which carry out
DE   the light reactions of photosynthesis. Found exclusively in Paulinella
DE   species, which are photosynthetic thecate amoeba.
SL   Plastid, organellar chromatophore thylakoid membrane.
HI   Plastid thylakoid membrane.
HP   Organellar chromatophore thylakoid.
GO   GO:0070118; organellar chromatophore thylakoid membrane
//
ID   P-body.
AC   SL-0230
DE   P-bodies are dynamic non-membrane bound cytoplasmic structures. These
DE   discrete foci function in mRNA decay (decapping and breakdown), RNA-
DE   mediated gene silencing (microRNA and siRNA-based gene silencing),
DE   mRNA surveillance (or quality control) and translational control. In
DE   addition to being sites of mRNA degradation, P-bodies can temporarily
DE   sequester mRNAs away from the translation machinery. P-bodies are
DE   present in unstressed cells, but are further induced in response to
DE   various stresses.
SY   Cytoplasmic mRNA processing body; DCP bodies; Dcp body; Gawky bodies;
SY   Gawky body; GW182 bodies; GW182 body; GWB; GW bodies; GW body;
SY   mRNA-decay foci; mRNA processing bodies; mRNA processing body; PB;
SY   P bodies; P-bodies; P body; Processing bodies; Processing body.
SL   Cytoplasm, P-body.
HI   Cytoplasmic ribonucleoprotein granule.
GO   GO:0000932; P-body
RX   PubMed=17183357; DOI=10.1038/nrm2080;
//
ID   Paranodal septate junction.
AC   SL-0192
DE   The paranodal septate junction (PSJ) in vertebrate species is an
DE   occluding complex which occurs between neurons and the glial cells
DE   that myelinate them, the oligodendrocytes and the Schwann cells. Each
DE   glial cell wraps around and contacts the neuron multiple times in a
DE   spiral pattern to form the paranodal loops. The paranodal loops
DE   tightly adhere to the axon through a continuous spiral of axo-glial
DE   junctions that resemble invertebrate septate junctions (SJs). The
DE   paranodal loops are a spiraled cytoplasmic channel that is contiguous
DE   with the perikaryon of the myelin forming cell and thus can serve as a
DE   conduit for transmitting axonally induced signals that could regulate
DE   glial gene transcription. These junctions also form a physical barrier
DE   that prevents diffusion of nodal sodium channels and juxtaparanodal
DE   potassium channels. Axo-glial paranodal junctions, therefore, share
DE   adhesion, diffusion barrier and putative intercellular communication
DE   functions with invertebrate SJs.
SY   Paranodal junction; PSJ.
SL   Cell junction, paranodal septate junction.
HI   Cell junction.
GO   GO:0033010; paranodal junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
//
ID   Parasitophorous vacuole.
AC   SL-0194
DE   The parasitophorous vacuole is a vacuole found in the host cells where
DE   most apicomplexan parasites reside and develop. During host cell
DE   invasion, the apicomplexan parasites initiate the formation of a
DE   membrane (the parasitophorous vacuolar membrane), which surrounds the
DE   intracellular parasite.
SL   Parasitophorous vacuole.
GO   GO:0020003; symbiont-containing vacuole
//
ID   Parasitophorous vacuole lumen.
AC   SL-0341
DE   The parasitophorous vacuole compartment bounded by the membrane of the
DE   parasitophorous vacuole.
SY   Parasitophorous vacuolar lumen.
SL   Parasitophorous vacuole lumen.
HP   Parasitophorous vacuole.
//
ID   Parasitophorous vacuole membrane.
AC   SL-0193
DE   The membrane surrounding the parasitophorous vacuole.
SY   Parasitophorous vacuolar membrane.
SL   Parasitophorous vacuole membrane.
HI   Membrane.
HP   Parasitophorous vacuole.
GO   GO:0020005; symbiont-containing vacuole membrane
//
IT   Peptidoglycan-anchor.
AC   SL-9900
DE   Surface protein of a Gram-positive bacteria anchored to the cell wall
DE   envelope by a transpeptidation mechanism which requires a C-terminal
DE   sorting signal with a conserved LPXTG motif. An amide bond is created
DE   between the carboxyl-group of the conserved threonine and the amino-
DE   group of peptidoglycan cross-bridges.
SL   Peptidoglycan-anchor.
KW   KW-0572
//
ID   Peribacteroid membrane.
AC   SL-0195
DE   Symbiosis leads to the formation of a new compartment in the plant
DE   cell when bacteria enter the plant cell by endocytosis, the
DE   symbiosome. This compartment harbours the bacteroids surrounded by a
DE   peribacteroid membrane (PMB) originating from the plant plasma
DE   membrane. The space between this membrane and the bacteroid membrane
DE   is called the peribacteroid space.
SL   Symbiosome, peribacteroid membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Symbiosome.
GO   GO:0043661; peribacteroid membrane
//
ID   Peribacteroid space.
AC   SL-0196
DE   Symbiosis lead to the formation of a new compartment in the plant cell
DE   when bacteria enter the plant cell by endocytosis. This compartment
DE   harbours the bacteroids surrounded by a peribacteroid membrane (PMB)
DE   originating from the plant plasma membrane. The space between this
DE   membrane and the bacteroid membrane is called the peribacteroid space.
SL   Symbiosome, peribacteroid space.
HP   Symbiosome.
GO   GO:0043662; peribacteroid fluid
//
ID   Perikaryon.
AC   SL-0197
DE   The perikaryon is the cell body of a neuron.
SY   cell body; Perikarya; soma.
SL   Perikaryon.
GO   GO:0043204; perikaryon
//
ID   Perinuclear region.
AC   SL-0198
DE   The perinuclear region is the cytoplasmic region just around the
DE   nucleus.
SY   Nuclear periphery; Perinuclear region of cytoplasm.
SL   Cytoplasm, perinuclear region.
HP   Cytoplasm.
GO   GO:0048471; perinuclear region of cytoplasm
//
ID   Perinuclear theca.
AC   SL-0199
DE   The perinuclear theca is a cytoskeletal structure that covers the
DE   nucleus of mammalian spermatozoa except for a narrow zone around the
DE   insertion of the tail. It shows two distinct regions, a subacrosomal
DE   layer or perforatorium and, continuing caudally beyond the acrosomic
DE   system, the postacrosomal sheath.
SL   Cytoplasm, cytoskeleton, perinuclear theca.
HP   Cytoskeleton.
GO   GO:0033011; perinuclear theca
//
IT   Peripheral membrane protein.
AC   SL-9903
DE   Protein that is physically associated with a membrane, via
DE   interactions with lipid headgroups at the membrane surface or with
DE   another membrane protein. Peripheral membrane proteins are typically
DE   bound to the membrane surface, but may dip slightly into the lipid
DE   bilayer. Peripheral membrane protein.
SL   Peripheral membrane protein.
HI   Membrane.
//
ID   Periplasm.
AC   SL-0200
DE   The periplasm is the space between the inner and outer membrane in
DE   Gram-negative bacteria. In Gram-positive bacteria a smaller
DE   periplasmic space is found between the inner membrane and the
DE   peptidoglycan layer. Also used for the intermembrane spaces of fungi
DE   and organelles.
SY   Periplasmic space.
SL   Periplasm.
HP   Cell envelope.
KW   KW-0574
GO   GO:0042597; periplasmic space
//
ID   Periplasmic flagellum.
AC   SL-0201
DE   Spirochetes have a flagellum that resides inside the cell within the
DE   periplasmic space. The number of flagella varies from species to
DE   species. The rotation of these structures results in specific
DE   movements of the cell body, which in turn enable the locomotion of the
DE   cell. In particular they impart spirochetes the ability to propel
DE   themselves through viscous media that would inhibit the rotation of
DE   external flagellar filaments.
SY   Endoflagellum; Periplasmic fibril.
SL   Periplasmic flagellum.
HI   Bacterial flagellum.
GO   GO:0055040; periplasmic flagellum
RX   PubMed=15170401; DOI=10.1159/000077867;
//
IO   Periplasmic side.
AC   SL-9916
DE   Protein found mostly on the periplasmic side of the membrane.
SL   Periplasmic side.
//
ID   Perispore.
AC   SL-0367
DE   Protein found in the perispore. The perispore corresponds to the outer
DE   surface layer of mature bacterial spores and eukaryotic spores. The
DE   perispore, also called perine or exosporium, represents the primary
DE   contact surface between the spore and environment/host and is a site
DE   of spore antigens.
SY   Exosporium; Perine.
SL   Spore, perispore.
HP   Spore.
//
ID   Peroxisome.
AC   SL-0204
DE   The peroxisome is a small eukaryotic organelle limited by a single
DE   membrane, specialized for carrying out oxidative reactions. Contains
DE   mainly peroxidases, several other oxidases and catalase. The catalase
DE   regulates the contents of the produced toxic hydrogen peroxide thus
DE   protecting the cell. Beta-oxidation of fatty acids is another major
DE   function of peroxisomes. In plants and fungi this degradation occurs
DE   only in this cellular compartment.
SL   Peroxisome.
KW   KW-0576
GO   GO:0005777; peroxisome
//
ID   Peroxisome matrix.
AC   SL-0202
DE   The matrix of a peroxisome is the area enclosed by the peroxisomal
DE   membrane.
SY   Peroxisomal matrix.
SL   Peroxisome matrix.
HP   Peroxisome.
GO   GO:0005782; peroxisomal matrix
//
ID   Peroxisome membrane.
AC   SL-0203
DE   The membrane surrounding a peroxysome.
SY   Peroxisomal membrane.
SL   Peroxisome membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Peroxisome.
GO   GO:0005778; peroxisomal membrane
//
ID   Phagocytic cup.
AC   SL-0473
DE   Cup-shaped invaginations of the cell membrane that subsequently close
DE   at their distal margins to form phagosomes during phagocytosis. By
DE   progression of its rim along the particle surface, this phagocytic cup
DE   envelops and eventually encloses the particle by separation of the
DE   phagosome membrane from the cell membrane. Filamentous actin
DE   accumulates between the outer and inner leaflet of the cup membrane
DE   and is most strongly enriched at the rim of the cup, the site of its
DE   protrusion.
SL   Cell projection, phagocytic cup.
HI   Cell projection.
GO   GO:0001891; phagocytic cup
//
ID   Phagosome.
AC   SL-0206
DE   The phagosome is a phagocytic cell-specific compartment. These large
DE   endocytic membrane-bound vesicles form upon ingestion by the cell of
DE   extracellular materials.
SY   Phagocytic vesicle.
SL   Cytoplasmic vesicle, phagosome.
HI   Cytoplasmic vesicle.
GO   GO:0045335; phagocytic vesicle
//
ID   Phagosome lumen.
AC   SL-0342
DE   The phagosomal compartment bounded by the membrane a phagosome.
SY   Phagocytic vesicle lumen; Phagosomal lumen.
SL   Cytoplasmic vesicle, phagosome lumen.
HI   Cytoplasmic vesicle lumen.
HP   Phagosome.
//
ID   Phagosome membrane.
AC   SL-0205
DE   The membrane surrounding a phagosome.
SY   Phagocytic vesicle membrane; Phagosomal membrane.
SL   Cytoplasmic vesicle, phagosome membrane.
HI   Cytoplasmic vesicle membrane.
HP   Phagosome.
GO   GO:0030670; phagocytic vesicle membrane
//
ID   Photoreceptor inner segment.
AC   SL-0457
DE   The inner segment of a vertebrate photoreceptor containing
DE   mitochondria, ribosomes and membranes where opsin molecules are
DE   assembled and passed to be part of the outer segment discs.
SL   Photoreceptor inner segment.
GO   GO:0001917; photoreceptor inner segment
//
ID   Photoreceptor inner segment membrane.
AC   SL-0514
DE   The membrane surrounding the inner segment of a vertebrate
DE   photoreceptor. SL Photoreceptor inner segment membrane. HI Membrane.
DE   HP Endomembrane system. HP .
SL   Photoreceptor inner segment membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Photoreceptor inner segment.
//
ID   Photoreceptor outer segment.
AC   SL-0458
DE   The outer segment of a vertebrate photoreceptor that contains discs of
DE   photoreceptive membranes.
SL   Cell projection, cilium, photoreceptor outer segment.
HI   Cilium.
GO   GO:0001750; photoreceptor outer segment
//
ID   Photoreceptor outer segment membrane.
AC   SL-0513
DE   The membrane surrounding the outer segment of a vertebrate
DE   photoreceptor.
SL   Photoreceptor outer segment membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Photoreceptor outer segment.
//
ID   Phragmoplast.
AC   SL-0207
DE   The phragmoplast is a plant cell specific structure that forms during
DE   late cytokinesis. This complex assembly of microtubules, actin
DE   filaments and associated molecules acts as a framework for cell plate
DE   assembly and subsequent formation of the future cell wall separating
DE   the two daughter cells.
SL   Cytoplasm, cytoskeleton, phragmoplast.
HP   Cytoskeleton.
GO   GO:0009524; phragmoplast
//
ID   Plasmodesma.
AC   SL-0208
DE   The plasmodesma (plural plasmodesmata) is a plasma membrane-lined
DE   channel that crosses the cell wall between two adjacent plant cells
DE   and which allows a cytoplasmic exchange between the cells. It provides
DE   passage of ions and small molecules, but also of macromolecules such
DE   as RNA or proteins. Plasmodesmata are sheathed by a plasma membrane
DE   that is simply an extension of the cell membrane of the adjoining
DE   cells. Most plasmodesmata have a narrow cylindrical desmotubule at the
DE   center that is derived from the ER and appears to be continuous with
DE   the ER of both cells.
SY   PD; Plasmodesmata.
SL   Cell junction, plasmodesma.
HI   Cell junction.
GO   GO:0009506; plasmodesma
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
//
ID   Plastid.
AC   SL-0209
DE   The plastid is a semi-autonomous, self-reproducing organelle. Plastids
DE   are remnants of a photosynthetic organism that was engulfed by the
DE   host, although not all are now photosynthetic. Plastid genomes encode
DE   genes for rRNAs, tRNAs and between about 28 and 150 proteins. Plastids
DE   can be categorized in 4 main groups: chloroplasts, cyanelles,
DE   apicoplasts and non-photosynthetic. The latter are found is some land
DE   plants (Epifagus virginiana), chlorophyte algae (Prototheca
DE   wickerhamii) and euglenoids (Astasis longa), which do not encode the
DE   genes necessary for photosynthesis and so are not photosynthetic but
DE   still contain a plastid. Non-photosynthetic plastids probably do not
DE   contain thylakoids.
SL   Plastid.
KW   KW-0934
GO   GO:0009536; plastid
//
ID   Plastid envelope.
AC   SL-0210
DE   The envelope of a plastid comprises the inner and outer plastid
DE   membrane including the intermembrane space.
SY   Plastidic envelope.
SL   Plastid envelope.
HP   Plastid.
GO   GO:0009526; plastid envelope
//
ID   Plastid inner membrane.
AC   SL-0211
DE   The inner membrane of a plastid separates the plastid stroma from the
DE   intermembrane space.
SY   Inner plastidic membrane; Inner plastid membrane;
SY   Plastidic inner membrane.
SL   Plastid inner membrane.
HI   Plastid membrane.
KW   KW-1001
GO   GO:0009528; plastid inner membrane
//
ID   Plastid intermembrane space.
AC   SL-0212
DE   The plastid intermembrane space is the space between the plastid inner
DE   and outer membranes.
SY   Plastidic intermembrane space.
SL   Plastid intermembrane space.
HP   Plastid envelope.
GO   GO:0009529; plastid intermembrane space
//
ID   Plastid membrane.
AC   SL-0213
DE   The membrane surrounding or within a plastid. Also used when it is not
DE   clear in which plastid membrane (outer membrane, inner membrane or
DE   thylakoid) a protein is found.
SY   Plastidic membrane.
SL   Plastid membrane.
HI   Membrane.
HP   Plastid envelope.
GO   GO:0042170; plastid membrane
//
ID   Plastid nucleoid.
AC   SL-0140
DE   The plastid nucleoid is the plastidic pseudocompartment formed by the
DE   chromatin-dense area. This region, which is functionally equivalent to
DE   the eukaryotic nucleus, is not surrounded by a membrane.
SY   Plastidic nucleoid.
SL   Plastid stroma, plastid nucleoid.
HP   Plastid stroma.
GO   GO:0042646; plastid nucleoid
//
ID   Plastid outer membrane.
AC   SL-0214
DE   The outer membrane of a plastid is the membrane facing the cytoplasm.
SY   Outer plastidic membrane; Outer plastid membrane;
SY   Plastidic outer membrane.
SL   Plastid outer membrane.
HI   Plastid membrane.
KW   KW-1002
GO   GO:0009527; plastid outer membrane
//
ID   Plastid stroma.
AC   SL-0215
DE   The stroma of a plastid is the internal space enclosed by the plastid
DE   double membrane but excluding the thylakoid space. This space, filled
DE   with a colorless hydrophilic matrix.
SY   Plastidic stroma.
SL   Plastid stroma.
HP   Plastid.
GO   GO:0009532; plastid stroma
//
ID   Plastid thylakoid.
AC   SL-0278
DE   The thylakoid of a plastid is an internal system of interconnected
DE   membranes found within a plastid.
SY   Plastidic thylakoid.
SL   Plastid thylakoid.
HI   Thylakoid.
HP   Plastid.
GO   GO:0031976; plastid thylakoid
//
ID   Plastid thylakoid lumen.
AC   SL-0309
DE   The plastid thylakoid lumen is the plastid compartment bounded by the
DE   thylakoid membranes.
SY   Plastid thylakoidal lumen.
SL   Plastid thylakoid lumen.
HP   Plastid thylakoid.
GO   GO:0031978; plastid thylakoid lumen
//
ID   Plastid thylakoid membrane.
AC   SL-0216
DE   The thylakoid membranes of a plastid is an internal system of
DE   interconnected membranes found in a plastid.
SY   Plastid thylakoidal membrane.
SL   Plastid thylakoid membrane.
HI   Membrane.
HP   Plastid thylakoid.
GO   GO:0055035; plastid thylakoid membrane
//
ID   Plastoglobule.
AC   SL-0217
DE   A plastoglobule is a conspicuous lipid-containing structure in the
DE   chloroplast stroma thought to serve as lipid reservoirs for thylakoid
DE   membranes.
SL   Plastid, chloroplast, plastoglobule.
HP   Chloroplast.
GO   GO:0010287; plastoglobule
//
ID   PML body.
AC   SL-0465
DE   The PML bodies are dynamic nuclear protein aggregates interspersed
DE   between chromatin. These punctate nuclear structures are call PML
DE   bodies because the PML gene is essential for their formation. These
DE   discrete nuclear foci, 0.2-1.0 micrometer wide, are present in most
DE   mammalian cell nuclei and typically number 1 to 30 bodies per nucleus,
DE   depending on the cell type, cell-cycle phase and differentiation
DE   stage. Recent evidence implies that, although they appear to be
DE   uniform, PML-NBs are structurally and functionally heterogeneous and
DE   are dynamic structures.
SY   Kremer body; ND10; Nuclear domains-10; PML-NB; PML-nuclear body;
SY   PML oncogenic domain; Promyelocytic leukaemia nuclear body;
SY   Promyelocytic leukemia nuclear body.
SL   Nucleus, PML body.
HI   Nuclear body.
HP   Nucleus.
GO   GO:0016605; PML body
RX   PubMed=17928811; DOI=10.1038/nrm2277;
//
ID   Podosome.
AC   SL-0295
DE   The podosome is a ring-like cell protrusion which mediates cell-
DE   extracellular matrix interactions. Podosomes are composed of an actin-
DE   bundle core, flanked by a ring containing adhesion proteins connected
DE   to the core via dome-like radial actin fibers. Podosomes are rich in
DE   actin filaments, matrix-degrading enzymes, focal adhesion molecules
DE   and molecules involved in vesicle trafficking. These structures
DE   protrudes into the extracellular matrix and are essential for invasion
DE   and metastasis. Classical podosomes are highly dynamic structures
DE   formed by cell types of monocytic origin, such as macrophages,
DE   dendritic cells, and osteoclasts.
SL   Cell projection, podosome.
HI   Cell junction.
HI   Cell projection.
GO   GO:0002102; podosome
//
ID   Podosome membrane.
AC   SL-0296
DE   The portion of the cell membrane surrounding a podosome.
SY   Podosomal membrane.
SL   Cell projection, podosome membrane.
HP   Cell membrane.
HP   Podosome.
//
ID   Pollen coat.
AC   SL-0371
DE   The relatively impermeable, lipidic layer which surrounds the outer
DE   exine layer of a pollen grain.
SY   Pollenkitt.
SL   Secreted, extracellular space, extracellular matrix, pollen coat.
HI   Extracellular matrix.
GO   GO:0070505; pollen coat
//
ID   Porosome.
AC   SL-0218
DE   The porosome is an actin-regulated dynamic structure at the cell
DE   membrane, where membrane-bound secretory vesicles dock and fuse to
DE   release their contents.
SL   Cell membrane, porosome.
HP   Cell membrane.
GO   GO:0033012; porosome
//
ID   Postsynapse.
AC   SL-0515
DE   The receiving part of a synapse which contains the neurotransmitter-
DE   receptor scaffold and signaling machinery to respond to signals from
DE   the presynaptic cell.
SY   Post-synapse; Postsynaptic region; Postsynaptic terminal.
SL   Postsynapse.
HP   Synapse.
GO   GO:0098794; postsynapse
//
ID   Postsynaptic cell membrane.
AC   SL-0219
DE   In a chemical synapse, specialized area of the membrane that receives
DE   a signal (binds neurotransmitter) from the presynaptic cell and
DE   responds via depolarization or hyperpolarization. The postsynaptic
DE   membrane is separated from the presynaptic membrane by the synaptic
DE   cleft.
SY   Postsynaptic membrane.
SL   Postsynaptic cell membrane.
HI   Synaptic cell membrane.
HP   Postsynapse.
KW   KW-0628
GO   GO:0045211; postsynaptic membrane
//
ID   Postsynaptic density.
AC   SL-0297
DE   The postsynaptic density is a network of proteins within and adjacent
DE   to the postsynaptic membrane, consisting of anchoring and scaffolding
DE   molecules, signaling enzymes and cytoskeletal components that
DE   spatially and functionally organize the neurotransmitter receptors at
DE   the synapse. In asymmetric synapses, the postsynaptic density is a
DE   thick electron dense network but in symmetric synapses this structure
DE   is thinner and not electron dense.
SY   Postsynaptic specialization; PSD.
SL   Postsynaptic density.
HP   Postsynapse.
GO   GO:0014069; postsynaptic density
//
ID   Postsynaptic density membrane.
AC   SL-0520
DE   The membrane component of the postsynaptic specialization. Part of the
DE   postsynaptic membrane attached to the postsynaptic density in which
DE   the population of neurotransmitter receptors involved in synaptic
DE   transmission are concentrated and organized.
SL   Postsynaptic density membrane.
HP   Postsynaptic cell membrane.
HP   Postsynaptic density.
GO   GO:0098839; postsynaptic density membrane
//
ID   Postsynaptic early endosome.
AC   SL-0523
DE   An early endosome of the postsynapse. It acts as the major sorting
DE   station on the endocytic pathway, targeting neurotransmitter receptors
DE   for degredation or recycling.
SL   Postsynaptic early endosome.
HI   Early endosome.
HP   Postsynaptic endosome.
GO   GO:0098842; postsynaptic early endosome
//
ID   Postsynaptic early endosome membrane.
AC   SL-0534
DE   The membrane surrounding a postsynaptic early endosome
SL   Postsynaptic early endosome membrane.
HI   Membrane.
HP   Postsynaptic early endosome.
//
ID   Postsynaptic endocytic zone.
AC   SL-0528
DE   Stably positioned sites of clathrin adjacent to the postsynaptic
DE   density (PSD). The physical link with the PSD ensures localized
DE   endocytosis and recycling by recapturing and maintaining a proximate
DE   pool of cycling postsynaptic receptors.
SL   Postsynaptic endocytic zone.
HP   Postsynapse.
GO   GO:0098843; postsynaptic endocytic zone
//
ID   Postsynaptic endosome.
AC   SL-0522
DE   An endosomal compartment that is part of the postsynapse. The
DE   endosomal pathway in postsynapses and dendrites is essential for
DE   membrane receptor trafficking and proper synaptic function and
DE   plasticity. Only early and recycling endosomes are typically present
DE   in the postsynapse.
SY   postsynaptic endosome.
SL   Postsynaptic endosome.
HI   Endosome.
HP   Postsynapse.
GO   GO:0098845; postsynaptic endosome
//
ID   Postsynaptic recycling endosome.
AC   SL-0524
DE   A recycling endosome of the postsynapse. It is involved in recycling
DE   of neurotransmitter receptors to the postsynaptic membrane and serves
DE   as intracellular reserve pools of neurotransmitter receptors. In some
DE   cases at least, this recycling is activated by postsynaptic signalling
DE   and so can play a role in long term potentiation.
SL   Postsynaptic recycling endosome.
HI   Recycling endosome.
HI   Postsynaptic endosome.
HP   Postsynapse.
GO   GO:0098837; postsynaptic recycling endosome
//
ID   Postsynaptic recycling endosome membrane.
AC   SL-0533
DE   The membrane surrounding a postsynaptic recycling endosome
SL   Postsynaptic recycling endosome membrane.
HI   Membrane.
HP   Postsynaptic recycling endosome.
//
ID   Preautophagosomal structure.
AC   SL-0220
DE   The pre-autophagosomal structure is the potential site of organization
DE   for autophagosome formation located near the vacuole.
SY   PAS; Phagophore assembly site; Pre-autophagosomal structure.
SL   Preautophagosomal structure.
GO   GO:0000407; phagophore assembly site
//
ID   Preautophagosomal structure membrane.
AC   SL-0221
DE   The membrane surrounding the pre-autophagosomal structure.
SY   PAS membrane; Pre-autophagosomal structure membrane.
SL   Preautophagosomal structure membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Preautophagosomal structure.
GO   GO:0034045; phagophore assembly site membrane
//
ID   Presynapse.
AC   SL-0516
DE   In the synapse, the specialized axon's terminal end of the presynaptic
DE   cell that contains the specialized apparatus necessary to release
DE   neurotransmitters to the synaptic cleft.
SY   Axon terminal; Pre-synapse; Presynaptic bouton; Presynaptic region;
SY   Presynaptic terminal.
SL   Presynapse.
HP   Synapse.
HP   Axon.
GO   GO:0098793; presynapse
//
ID   Presynaptic active zone.
AC   SL-0519
DE   The active zone is the region that lies at the interface between the
DE   presynaptic terminal and the synaptic cleft and mediates
DE   neurotransmitter release. Consists of an electron dense protein
DE   network called the cytomatrix at the active zone (CAZ) that is tightly
DE   anchored to the presynaptic membrane, and precisely aligned with post-
DE   synaptic receptors. CAZ docks and fuses synaptic vesicles, recruits
DE   voltage-gated Ca(2+) channels to the presynaptic membrane to allow
DE   fast synchronous excitation/release coupling and mediates short- and
DE   long-term presynaptic plasticity.
SL   Presynaptic active zone.
HP   Presynapse.
GO   GO:0048786; presynaptic active zone
//
ID   Presynaptic active zone membrane.
AC   SL-0527
DE   The membrane portion of the presynaptic active zone that allows
DE   presynaptic vesicles to dock, fuse, and, ultimately, release
DE   neurotransmitter into the synaptic cleft.
SL   Presynaptic active zone membrane.
HP   Presynaptic cell membrane.
HP   Presynaptic active zone.
GO   GO:0048787; presynaptic active zone membrane
//
ID   Presynaptic cell membrane.
AC   SL-0222
DE   In a chemical synapse, the presynaptic membrane is the cell membrane
DE   of an axon terminal that faces the receiving cell. The postsynaptic
DE   membrane is separated from the presynaptic membrane by the synaptic
DE   cleft.
SY   Presynaptic membrane.
SL   Presynaptic cell membrane.
HI   Synaptic cell membrane.
HP   Presynapse.
GO   GO:0042734; presynaptic membrane
//
ID   Presynaptic endocytic zone.
AC   SL-0529
DE   Region of the presynaptic membrane and underlying cytoplasm that
DE   surrounds the active zone and where synaptic vesicles are endocytosed
DE   and recycled following release.
SY   Periactive zone; Peri-active zone.
SL   Presynaptic endocytic zone.
HP   Presynapse.
GO   GO:0098833; presynaptic endocytic zone
//
ID   Presynaptic endosome.
AC   SL-0525
DE   An endosome present in the presynapse that fuses with endocytic
DE   vesicles arising in the presynaptic endocytic zone. Presynaptic
DE   endosomes are involved on synaptic vesicle regeneration in GABAergic
DE   synapses at least, even if different modes of synaptic vesicles
DE   recycling exist depending on the type of synapse.
SL   Presynaptic endosome.
HI   Endosome.
HP   Presynapse.
GO   GO:0098830; presynaptic endosome
//
ID   Prevacuolar compartment.
AC   SL-0223
DE   The prevacuolar compartment is an endocytic multivesiculate
DE   compartment involved in Golgi-vacuole trafficking.
SY   PVC.
SL   Prevacuolar compartment.
//
ID   Prevacuolar compartment lumen.
AC   SL-0343
DE   The PVC compartment bounded by the membrane of the PVC.
SY   PVC lumen.
SL   Prevacuolar compartment lumen.
HP   Prevacuolar compartment.
//
ID   Prevacuolar compartment membrane.
AC   SL-0224
DE   The membrane surrounding the prevacuolar compartment.
SY   PVC membrane.
SL   Prevacuolar compartment membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Prevacuolar compartment.
//
ID   Primary cell wall.
AC   SL-0225
DE   Trimary cell wall is the first-formed wall layer of still growing
DE   plant cells (at least potentially). This wall is part of the apoplast
DE   which itself is largely self-contiguous and contains everything that
DE   is located between the plasma membrane and the cuticle. Primary walls
DE   are composed predominantly of polysaccharides, smaller proportions of
DE   glycoproteins and, in some specialized cell types, various
DE   noncarbohydrate substances such as lignin, suberin, cutin, cutan or
DE   silica. It is strong but usually thin, flexible, and capable of both
DE   plastic and elastic extension. It governs the rate and direction of
DE   cell expansion, and thus the ultimate size and shape of the cell.
SL   Secreted, primary cell wall.
HI   Cell wall.
GO   GO:0009530; primary cell wall
//
ID   Prolamellar body.
AC   SL-0226
DE   The prolamellar body is a paracrystalline lattice found in the
DE   plastids of etiolated plants (etioplasts). Upon greening it gives rise
DE   to thylakoids.
SY   Etioplast prolamellar body.
SL   Plastid, etioplast, prolamellar body.
HP   Etioplast.
GO   GO:0009541; etioplast prolamellar body
//
ID   Prospore.
AC   SL-0369
DE   The prospore or immature spore is formed during sporulation by the
DE   engulfment of the post-meiotic nuclei by the prospore double membrane.
DE   These prospores are then maturated into spores with the synthesis of
DE   the spore wall.
SY   Prespore.
SL   Prospore.
GO   GO:0042764; ascospore-type prospore
//
ID   Prospore membrane.
AC   SL-0368
DE   The prospore membrane is a double membrane which forms at the spindle
DE   pole body outer plaque during the second meiotic division of the
DE   sporulation process. The prospore membrane grows larger and finally
DE   engulfs the post-meiotic nuclei to form immature spores called
DE   prospores. The de novo synthesis of the spore wall occurs in the
DE   prospore intermembrane space and leads to mature spores.
SY   Prespore membrane.
SL   Prospore membrane.
HI   Membrane.
HP   Prospore.
GO   GO:0005628; prospore membrane
//
ID   Protein storage vacuole.
AC   SL-0228
DE   The protein storage vacuole (PSV) is a specialized vacuole where
DE   storage proteins accumulate. These act as a source of amino acids for
DE   various SYnthetic activities.
SY   PSV; Storage vacuole.
SL   Protein storage vacuole.
HI   Vacuole.
GO   GO:0000326; protein storage vacuole
//
ID   Protein storage vacuole lumen.
AC   SL-0344
DE   The protein storage vacuolar compartment bounded by the membrane of
DE   the protein storage vacuole.
SY   Protein storage vacuolar lumen.
SL   Protein storage vacuole lumen.
HI   Vacuole lumen.
HP   Protein storage vacuole.
GO   GO:0034495; protein storage vacuole lumen
//
ID   Protein storage vacuole membrane.
AC   SL-0227
DE   The membrane surrounding a protein storage vacuole.
SY   Protein storage vacuolar membrane.
SL   Protein storage vacuole membrane.
HI   Vacuole membrane.
HP   Protein storage vacuole.
GO   GO:0032586; protein storage vacuole membrane
//
ID   Protoplasm.
AC   SL-0229
DE   The protoplasm is the viscid, translucent, polyphasic colloid with
DE   water as the continuous phase that makes up the essential material of
DE   all plant and animal cells. It is composed mainly of nucleic acids,
DE   proteins, lipids, carbohydrates, and inorganic salts. The protoplasm
DE   surrounding the nucleus is known as the cytoplasm and that composing
DE   the nucleus is the nucleoplasm.
SL   Protoplasm.
GO   GO:0005622; intracellular anatomical structure
AN   Not used.
//
ID   Pseudopodium.
AC   SL-0298
DE   The pseudopodium is a thick knobby cell protrusion. Pseudopodia are
DE   produced by polymerization of extensive dendritic meshwork of actin
DE   filaments along broad sectors of the cell surface. These temporary
DE   irregular and dynamic protrusion or retractile processes of a cell,
DE   are associated with ameboid movement (crawling). Pseudopodium, or
DE   "false foot", mostly used for motile protozoans is comparable to the
DE   'lamellipodium' in vertebrate cells.
SY   Pseudopod; Pseudopodia.
SL   Cell projection, pseudopodium.
HI   Cell projection.
GO   GO:0031143; pseudopodium
//
ID   Pseudopodium membrane.
AC   SL-0299
DE   The portion of the cell membrane surrounding a pseudopodium.
SL   Cell projection, pseudopodium membrane.
HP   Cell membrane.
HP   Pseudopodium.
GO   GO:0031260; pseudopodium membrane
//
ID   Pseudopodium tip.
AC   SL-0471
DE   The end of the pseudopodium distal to the body of the cell.
SL   Cell projection, pseudopodium tip.
HP   Pseudopodium.
//
ID   Recycling endosome.
AC   SL-0232
DE   The recycling endosome is a membrane network composed of narrow
DE   diameters tubules which concentrate in the vicinity of the microtubule
DE   organizing center. Recycling receptors after release of their ligands
DE   accumulate in those membranes which are devoid of fluid markers.
DE   Recycling endosomes may be an intermediate station for receptors
DE   before recycling back to the cell surface.
SY   Endosomal recycling compartment; ERC.
SL   Recycling endosome.
HP   Endosome.
GO   GO:0055037; recycling endosome
AN   Compartment specific marker: Rab11.
//
ID   Recycling endosome lumen.
AC   SL-0345
DE   The recycling endosomal compartment bounded by the membrane of the
DE   recycling endosome.
SY   Recycling endosomal lumen.
SL   Recycling endosome lumen.
HI   Endosome lumen.
HP   Recycling endosome.
GO   GO:0034777; recycling endosome lumen
//
ID   Recycling endosome membrane.
AC   SL-0231
DE   The membrane surrounding the recycling endosomes.
SY   Recycling endosomal membrane.
SL   Recycling endosome membrane.
HI   Endosome membrane.
HP   Recycling endosome.
GO   GO:0055038; recycling endosome membrane
//
ID   Rhoptry.
AC   SL-0233
DE   The rhoptry is an Apicomplexan parasite organelle. Apicomplexa are
DE   named for the unique set of morphologically distinct secretory
DE   organelles (refered to as the apical complex)- micronemes, rhoptries
DE   and dense granules - whose sequential secretion is required for the
DE   invasion of host cells. Rhoptries are twin, membrane-bound, pear-
DE   shaped organelles that secrete proteins through their elongated necks
DE   at the apical tip of the parasite.
SY   Rhoptries.
SL   Cytoplasmic vesicle, secretory vesicle, rhoptry.
HI   Secretory vesicle.
GO   GO:0020008; rhoptry
//
ID   Rhoptry lumen.
AC   SL-0346
DE   The rhoptry compartment bounded by the membrane of a rhoptry.
SL   Cytoplasmic vesicle, secretory vesicle, rhoptry lumen.
HI   Secretory vesicle lumen.
HP   Rhoptry.
GO   GO:0034591; rhoptry lumen
//
ID   Rhoptry membrane.
AC   SL-0234
DE   The membrane surrounding a rhoptry.
SL   Cytoplasmic vesicle, secretory vesicle, rhoptry membrane.
HI   Secretory vesicle membrane.
HP   Rhoptry.
GO   GO:0033016; rhoptry membrane
//
ID   Rough endoplasmic reticulum.
AC   SL-0235
DE   The rough endoplasmic reticulum (RER) is the portion of the ER which
DE   is covered with ribosomes.
SY   RER; Rough ER.
SL   Rough endoplasmic reticulum.
HP   Endoplasmic reticulum.
GO   GO:0005791; rough endoplasmic reticulum
//
ID   Rough endoplasmic reticulum lumen.
AC   SL-0236
DE   The rough endoplasmic reticulum lumen is the area enclosed by the
DE   rough endoplasmic reticulum membrane.
SL   Rough endoplasmic reticulum lumen.
HI   Endoplasmic reticulum lumen.
HP   Rough endoplasmic reticulum.
GO   GO:0048237; rough endoplasmic reticulum lumen
//
ID   Rough endoplasmic reticulum membrane.
AC   SL-0237
DE   The membrane surrounding the rough endoplasmic reticulum.
SL   Rough endoplasmic reticulum membrane.
HI   Endoplasmic reticulum membrane.
HP   Rough endoplasmic reticulum.
GO   GO:0030867; rough endoplasmic reticulum membrane
//
ID   Ruffle.
AC   SL-0300
DE   A ruffle is a cell protrusion at the leading edge of a crawling cell.
DE   Ruffles are supported by a microfilament meshwork.
SL   Cell projection, ruffle.
HI   Cell projection.
GO   GO:0001726; ruffle
//
ID   Ruffle membrane.
AC   SL-0301
DE   The portion of the cell membrane surrounding a ruffle.
SL   Cell projection, ruffle membrane.
HP   Cell membrane.
HP   Ruffle.
GO   GO:0032587; ruffle membrane
//
ID   S-layer.
AC   SL-0262
DE   The S-layer is a paracrystalline protein thin layer attached to the
DE   outermost portion of the cell wall. Found in some bacteria and common
DE   in archaea where it can constitute the only cell wall structure
DE   outside the plasma membrane. In Gram-negative bacteria, the S-layer is
DE   directly attached to the outer membrane. In Gram-positive bacteria,
DE   the S-layer is attached to the peptidoglycan layer. The S-layer may
DE   protect the cell from aggressions such as phagocytosis, harmful
DE   enzymes, etc. It also allows bacteria to adhere to host cells or other
DE   environmental surfaces and to maintain shape and envelope rigidity.
SL   Secreted, cell wall, S-layer.
HP   Cell wall.
KW   KW-0701
GO   GO:0030115; S-layer
//
ID   Sarcolemma.
AC   SL-0238
DE   The sarcolemma is a specialized membrane which surrounds striated
DE   muscle fiber cells. It consists of a lipid bilayer typical of a plasma
DE   membrane and a thin outer coat of polysaccharide material, called
DE   glycocalyx, that contacts the basement membrane and allows the cell to
DE   anchor into the tissues that build and support muscle fibers.
SY   Myolemma.
SL   Cell membrane, sarcolemma.
HI   Cell membrane.
GO   GO:0042383; sarcolemma
//
ID   Sarcomere.
AC   SL-0313
DE   The sarcomere represents the basal contractile unit of striated
DE   muscles. A single myofibril is composed of these short structural
DE   units arranged end to end, which contract due to the relative sliding
DE   of thick (myosin) over thin (actin) filaments. The mammalian sarcomere
DE   is ~ 2 mm in length, and can shorten to ~ 70% of its original length
DE   during contraction. Structural features of the sarcomere include
DE   bundles of parallel thick and thin filaments assembled by two
DE   transverse structures, the Z lines and M lines. The Z lines and the M
DE   lines are connected by transverse filaments to the sarcolemma or to
DE   the neighboring myofibrils. Sarcomeres give to skeletal and cardiac
DE   muscles their striated appearance with I bands surrounding the Z
DE   lines, followed by A bands. The A bands contain a paler region called
DE   the H zone and in the middle the M line.
SL   Cytoplasm, myofibril, sarcomere.
HP   Myofibril.
GO   GO:0030017; sarcomere
WW   http://www.sarcomere.org/
//
ID   Sarcoplasm.
AC   SL-0311
DE   The sarcoplasm is the cytoplasm of a muscle fiber or muscle cell or
DE   myofiber.
SL   Cytoplasm, sarcoplasm.
HI   Cytoplasm.
GO   GO:0016528; sarcoplasm
//
ID   Sarcoplasmic reticulum.
AC   SL-0239
DE   The sarcoplasmic reticulum (SR) is a highly specialized form of the
DE   smooth endoplasmic reticulum which is dedicated to the regulation of
DE   intracellular calcium homeostasis. The SR can be subdivided in at
DE   least two well-characterized regions: the terminal cisternae, where
DE   the calcium ions are released, and the longitudinal tubules
DE   specialized in the uptake of the calcium ions.
SL   Sarcoplasmic reticulum.
KW   KW-0703
GO   GO:0016529; sarcoplasmic reticulum
AN   Not ok: HI   Endoplasmic reticulum.
//
ID   Sarcoplasmic reticulum lumen.
AC   SL-0240
DE   The lumen of the sarcoplasmic reticulum is the area enclosed by the
DE   sarcoplasmic reticulum membrane.
SL   Sarcoplasmic reticulum lumen.
HP   Sarcoplasmic reticulum.
GO   GO:0033018; sarcoplasmic reticulum lumen
//
ID   Sarcoplasmic reticulum membrane.
AC   SL-0241
DE   The membrane surrounding the sarcoplasmic reticulum (SR).
SL   Sarcoplasmic reticulum membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Sarcoplasmic reticulum.
GO   GO:0033017; sarcoplasmic reticulum membrane
//
ID   Secondary cell wall.
AC   SL-0242
DE   In some plants, and cell types after a maximum size or point in
DE   development has been reached, a secondary wall, often layered, is
DE   constructed below the primary wall. Unlike the primary wall, it losts
DE   plasticity and is made usually of cellulose, hemicellulose and lignin.
SL   Secreted, secondary cell wall.
HI   Cell wall.
GO   GO:0009531; secondary cell wall
//
ID   Secreted.
AC   SL-0243
DE   Protein located outside the cell membrane(s).
SL   Secreted.
KW   KW-0964
GO   GO:0005576; extracellular region
//
ID   Secretory vesicle.
AC   SL-0244
DE   The secretory vesicle is a vesicle that mediates the vesicular
DE   transport of cargo - e.g. hormones or neurotransmitters - from an
DE   organelle to specific sites at the cell membrane, where it docks and
DE   fuses to release its content. It has been demonstrated that membrane-
DE   bound secretory vesicles dock and fuse at porosomes, which are
DE   specialized supramolecular structures at the cell membrane.
SY   Secretory granule.
SL   Cytoplasmic vesicle, secretory vesicle.
HI   Cytoplasmic vesicle.
GO   GO:0030133; transport vesicle
//
ID   Secretory vesicle lumen.
AC   SL-0347
DE   The secretory vesicle compartment bounded by the membrane of the
DE   secretory vesicle.
SY   Secretory granule lumen.
SL   Cytoplasmic vesicle, secretory vesicle lumen.
HI   Cytoplasmic vesicle lumen.
HP   Secretory vesicle.
//
ID   Secretory vesicle membrane.
AC   SL-0245
DE   The membrane surrounding secretory vesicles.
SY   Secretory granule membrane.
SL   Cytoplasmic vesicle, secretory vesicle membrane.
HI   Cytoplasmic vesicle membrane.
HP   Secretory vesicle.
GO   GO:0030658; transport vesicle membrane
//
ID   Septate junction.
AC   SL-0246
DE   The septate junction (SJ) in invertebrates is an occluding complex
DE   located basolateral to the adherens junction which have regularly
DE   spaced septa bridging a circa 15-nm intercellular space. SJs form the
DE   paracellular barrier that regulates passage of solutes through the
DE   spaces between adjacent cells in an epithelium for proper nutrient
DE   absorption or secretion.
SY   Paired septate junction; Pleated septate junction; SJ.
SL   Cell junction, septate junction.
HI   Cell junction.
GO   GO:0005918; septate junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
//
IT   Single-pass membrane protein.
AC   SL-9904
DE   Protein spanning the membrane once.
SY   Singlepass; Single pass; Single-pass; Singlespan; Single span.
SL   Single-pass membrane protein.
HI   Membrane.
//
IT   Single-pass type I membrane protein.
AC   SL-9905
DE   Protein spanning the membrane once, with its N-terminus on the
DE   extracellular side of the membrane and removal of its signal sequence.
SY   Singlepass; Single pass; Single-pass; Singlespan; Single span.
SL   Single-pass type I membrane protein.
HI   Single-pass membrane protein.
//
IT   Single-pass type II membrane protein.
AC   SL-9906
DE   Protein spanning the membrane once, with its N-terminus on the
DE   cytoplasmic side of the membrane. The transmembrane domain is located
DE   close to the N-terminus and it functions as an anchor.
SY   Singlepass; Single pass; Single-pass; Singlespan; Single span.
SL   Single-pass type II membrane protein.
HI   Single-pass membrane protein.
//
IT   Single-pass type III membrane protein.
AC   SL-9907
DE   Protein spanning the membrane once, with its N-terminus on the
DE   extracellular side of the membrane and no signal sequence.
SY   Singlepass; Single pass; Single-pass; Singlespan; Single span.
SL   Single-pass type III membrane protein.
HI   Single-pass membrane protein.
//
IT   Single-pass type IV membrane protein.
AC   SL-9908
DE   Protein spanning the membrane once, with its N-terminus on the
DE   cytoplasmic side of the membrane. The transmembrane domain is located
DE   close to the C-terminus and it functions as an anchor.
SY   Singlepass; Single pass; Single-pass; Singlespan; Single span.
SL   Single-pass type IV membrane protein.
HI   Single-pass membrane protein.
//
ID   Slime layer.
AC   SL-0247
DE   The slime layer is an easily removed, diffuse, unorganized layer of
DE   extracellular material which surrounds the bacterial cell. It is
DE   usually composed of polysaccharides and it may serve to trap
DE   nutrients, to aid in cell motility, to bind cells together or to
DE   adhere to smooth surfaces. Slime layers are a more-diffuse glycocalyx
DE   than capsules.
SL   Secreted, slime layer.
HP   Secreted.
GO   GO:0030114; slime layer
//
ID   Smooth endoplasmic reticulum.
AC   SL-0248
DE   The smooth endoplasmic reticulum (SER) is the portion of the ER which
DE   is free of ribosomes.
SY   SER; Smooth ER.
SL   Smooth endoplasmic reticulum.
HP   Endoplasmic reticulum.
GO   GO:0005790; smooth endoplasmic reticulum
//
ID   Smooth endoplasmic reticulum lumen.
AC   SL-0249
DE   The smooth endoplasmic reticulum lumen is the area enclosed by the
DE   smooth endoplasmic reticulum membrane.
SL   Smooth endoplasmic reticulum lumen.
HI   Endoplasmic reticulum lumen.
HP   Smooth endoplasmic reticulum.
GO   GO:0048238; smooth endoplasmic reticulum lumen
//
ID   Smooth endoplasmic reticulum membrane.
AC   SL-0250
DE   The membrane surrounding the smooth endoplasmic reticulum.
SL   Smooth endoplasmic reticulum membrane.
HI   Endoplasmic reticulum membrane.
HP   Smooth endoplasmic reticulum.
GO   GO:0030868; smooth endoplasmic reticulum membrane
//
ID   Spindle.
AC   SL-0251
DE   The spindle is a specialized microtubule structure designed to attach
DE   and capture chromosomes in order to partition them evenly to each
DE   daughter cells.
SY   Meiotic spindle; Mitotic apparatus; Mitotic spindle.
SL   Cytoplasm, cytoskeleton, spindle.
HP   Cytoskeleton.
GO   GO:0005819; spindle
//
ID   Spindle pole.
AC   SL-0448
DE   Either of the ends of a spindle, a specialized microtubule structure
DE   designed to attach and capture chromosomes in order to partition them
DE   evenly to each daughter cells.
SL   Cytoplasm, cytoskeleton, spindle pole.
HP   Spindle.
GO   GO:0000922; spindle pole
//
ID   Spindle pole body.
AC   SL-0252
DE   The spindle pole body is the microtubule organizing center (MTOC) in
DE   fungi, functionally equivalent to the animal cell centrosome. The SPB
DE   is responsible for the nucleation and organisation of microtubules.
DE   This may include the spindle microtubules required for chromosome
DE   segregation in mitosis and meiosis as well as the cytoplasmic
DE   interphase microtubules.
SY   SPB; Spindle polar body.
SL   Cytoplasm, cytoskeleton, microtubule organizing center, spindle pole body.
HP   Microtubule organizing center.
GO   GO:0005816; spindle pole body
//
ID   Spine apparatus.
AC   SL-0530
DE   Specialized form of endoplasmic reticulum found in a subpopulation of
DE   dendritic spines in central neurons consisting of two or more closely
DE   apposed lamellae with interspersed electron dense material.
SL   Endoplasmic reticulum, spine apparatus.
HI   Endoplasmic reticulum.
HP   Dendritic spine.
HP   Postsynapse.
GO   GO:0097444; spine apparatus
//
ID   Spore.
AC   SL-0539
DE   Spores are hardy unicellular units used by various bacteria, fungi,
DE   plants and protozoa to allow them to remain dormant during long
DE   periods of time and under often unfavorable conditions.
SY   Ascospore; Basidiospore; Chlamydospore; Megaspore; Microspore;
SY   Teliospore; Tetraspore; Zoospore.
SL   Spore.
//
ID   Spore coat.
AC   SL-0366
DE   Protein found in the spore coat. The spore coat is the thick layer
DE   found beneath the perispore of some eukaryotic spores and bacterial
DE   mature spores. It is made up of highly cross-linked keratin and layers
DE   of specific proteins. The coat is composed of several electron-dense
DE   and lamella-like layers, differing between species.
SL   Spore coat.
HP   Spore.
//
ID   Spore core.
AC   SL-0253
DE   Protein found in the spore core. The core also called spore matrix is
DE   the central part of the spore and contains normal cell structures,
DE   such as DNA, proteins and ribosomes, but is metabolically inactive.
SL   Spore core.
HP   Spore.
//
ID   Spore cortex.
AC   SL-0364
DE   Protein found in the spore cortex. The spore cortex is a loosely
DE   cross-linked peptidoglycan layer localized between the spore core and
DE   the outer membrane or cortex membrane of bacterial mature spores. The
DE   cortex maintains heat resistance and dormancy.
SL   Spore cortex.
HP   Spore.
GO   GO:0043595; endospore cortex
//
ID   Spore membrane.
AC   SL-0363
DE   Protein associated with the membrane that surrounds the center or core
DE   of a spore, often called spore inner membrane in bacterial spores.
SY   Spore inner membrane.
SL   Spore membrane.
HI   Membrane.
HP   Spore.
//
ID   Spore outer membrane.
AC   SL-0365
DE   Protein associated with the spore outer membrane. The outer membrane,
DE   also called the cortex membrane, is a membrane localized between the
DE   cortex and the inner layer of the coat of bacterial mature spores.
SL   Spore outer membrane.
HI   Membrane.
HP   Spore.
GO   GO:0043594; outer endospore membrane
//
ID   Spore polar tube.
AC   SL-0436
DE   The polar tube is a highly specialised structure unique to
DE   Microsporidia and required for host cell invasion. In the spore, the
DE   polar tube is connected at the anterior end, and then coils around the
DE   sporoplasm. Upon appropriate environmental stimulation, the polar tube
DE   rapidly discharges out of the spore, pierces a cell membrane and
DE   serves as a conduit for sporoplasm passage into the new host cell.
SL   Spore polar tube.
HP   Spore.
GO   GO:0044099; polar tube
//
ID   Spore wall.
AC   SL-0254
DE   Protein found in the spore wall. The spore wall is the main element of
DE   the spore's resistance to environmental stress. It is usually composed
DE   of several layers of different sugar polymers like mannans and glucans
DE   which are associated to glycoproteins. The composition, structure and
DE   number of layers are very different between bacteria, plants,
DE   protozoans or fungi.
SL   Spore wall.
HP   Spore.
GO   GO:0031160; spore wall
//
ID   Stereocilium.
AC   SL-0302
DE   The stereocilium is a finger-like projection forming the hair bundle
DE   on the apical surface of sensory hair cells in the cochlea.
DE   Stereocilia stiffness and function depend on the several hundreds of
DE   uniformly polarized and tightly cross-linked actin filaments.
DE   Stereocilia cytoskeleton shows continuous turnover with actin filament
DE   assembly occuring at the stereocilium tip and its disassembly at the
DE   base so that stereocilium length is maintained in a dynamic steady-
DE   state. This staircase-like bundle of stereocilia is responsible for
DE   mechanosensation and ultimately the perception of sound.
SY   Stereocilia.
SL   Cell projection, stereocilium.
HI   Cell projection.
GO   GO:0032420; stereocilium
RX   PubMed=17326148; DOI=10.1002/cm.20199;
//
ID   Stereocilium membrane.
AC   SL-0303
DE   The stereocilium membrane is the portion of the cell membrane
DE   surrounding a stereocilium.
SY   Stereocilia membrane.
SL   Cell projection, stereocilium membrane.
HP   Cell membrane.
HP   Stereocilium.
GO   GO:0060171; stereocilium membrane
//
ID   Stress fiber.
AC   SL-0501
DE   Stress fibers are contractile actomyosin bundles found in non-muscle
DE   cells, in eukaryotes, mostly in animals. They are composed of bundles
DE   of 10 to 30 actin filaments (microfilaments), crosslinked by alpha-
DE   actinin, and non-muscle myosin. They are often anchored to focal
DE   adhesions, that connect the extracellular matrix to the actin
DE   cytoskeleton. Stress fibers play an essential role in cell
DE   contractility, governing cell morphology, adhesion, and migration. In
DE   non-motile cells, stress fibers are usually thick and relatively
DE   stable. By contrast, highly motile cells typically contain fewer,
DE   thinner and more dynamic stress fibers. Stress fibers can be divided
DE   into at least 4 different categories : dorsal and ventral stress
DE   fibers, transverse arcs and the perinuclear actin cap.
SL   Cytoplasm, cytoskeleton, stress fiber.
HP   Cytoskeleton.
AN   Mostly in animal, non-muscle cells.
//
ID   Stress granule.
AC   SL-0496
DE   Stress granules are dense non-membrane bound aggregations in the
DE   cytosol composed of proteins and RNAs that appear when the cell is
DE   under stress. The aggregates are mostly composed of stalled
DE   translation initiation complexes. They are 100-200 nm in size. Stress
DE   granules can also precipitate the formation of toxic protein
DE   aggregates such as those seen during the progression of certain types
DE   of neurological disease.
SL   Cytoplasm, Stress granule.
HI   Cytoplasmic ribonucleoprotein granule.
GO   GO:0010494; cytoplasmic stress granule
//
IO   Stromal side.
AC   SL-9917
DE   Protein found mostly on the stromal side of the membrane.
SL   Stromal side.
//
ID   Surface film.
AC   SL-0255
DE   The film of pulmonary surfactants which cover the alveolar surface of
DE   the mammalian lung. These surfactants are composed of 90%
DE   phospholipids and 10% proteins.
SL   Secreted, extracellular space, surface film.
HP   Extracellular space.
KW   KW-0767
//
ID   Symbiosome.
AC   SL-0256
DE   Symbiosis lead to the formation of a new compartment in the plant cell
DE   when bacteria enter the plant cell by endocytosis, the symbiosome.
DE   This compartment harbours the bacteroids surrounded by a peribacteroid
DE   membrane (PMB) originating from the plant plasma membrane. The space
DE   between this membrane and the bacteroid membrane is called the
DE   peribacteroid space.
SL   Symbiosome.
GO   GO:0043659; symbiosome
//
ID   Symplast.
AC   SL-0257
DE   The symplast is a highly ordered and connected space within plants
DE   formed by the cytoplasms of individual cells connected by
DE   plasmodesmata. The symplast is held in place by a rigid framework, the
DE   apoplast.
SL   Symplast.
GO   GO:0055044; symplast
//
ID   Synapse.
AC   SL-0258
DE   Synapses are the communicating cell-cell junctions that allow signals
DE   to pass from a nerve cell to a target cell. In a chemical synapse, the
DE   signal is carried by a neurotransmitter which diffuses across a narrow
DE   synaptic cleft and activates a receptor on the postsynaptic membrane
DE   of the target cell. The target may be a dendrite, cell body, neuronal
DE   axon, a specialized region of a muscle or a secretory cell. In an
DE   electrical synapse, a direct connection is made between the cytoplasms
DE   of two cells via gap junctions.
SL   Synapse.
KW   KW-0770
GO   GO:0045202; synapse
//
ID   Synaptic cell membrane.
AC   SL-0531
DE   A specialized area of membrane on either the presynaptic or the
DE   postsynaptic side of a synapse, the junction between a nerve fiber of
DE   one neuron and another neuron or muscle fiber or glial cell.
SL   Synaptic cell membrane.
HI   Cell membrane.
HP   Synapse.
GO   GO:0097060; synaptic membrane
//
ID   Synaptic cleft.
AC   SL-0517
DE   The narrow space between the presynaptic and postsynaptic membranes
DE   into which neurotransmitters are released by synaptic vesicles through
DE   exocytosis and diffuse to activate receptors on post-synaptic
DE   membrane.
SL   Synaptic cleft.
HP   Extracellular space.
HP   Synapse.
GO   GO:0043083; synaptic cleft
//
ID   Synaptic vesicle.
AC   SL-0259
DE   The synaptic vesicles mediate the exocytosis of neurotransmitters and
DE   subsequent re-uptake by endocytosis of vesicular components. Re-uptake
DE   is a crucial element in the maintenance of synaptic transmission in
DE   the nervous system.
SL   Cytoplasmic vesicle, secretory vesicle, synaptic vesicle.
HI   Secretory vesicle.
HP   Synapse.
GO   GO:0008021; synaptic vesicle
//
ID   Synaptic vesicle lumen.
AC   SL-0348
DE   The synaptic vesicle compartment bounded by the membrane of a synaptic
DE   vesicle.
SY   Synaptic vesicular lumen.
SL   Cytoplasmic vesicle, secretory vesicle, synaptic vesicle lumen.
HI   Secretory vesicle lumen.
HP   Synaptic vesicle.
GO   GO:0034592; synaptic vesicle lumen
//
ID   Synaptic vesicle membrane.
AC   SL-0260
DE   The membrane surrounding a synaptic vesicle.
SY   Synaptic vesicular membrane.
SL   Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane.
HI   Secretory vesicle membrane.
HP   Synaptic vesicle.
GO   GO:0030672; synaptic vesicle membrane
//
ID   Synaptosome.
AC   SL-0261
DE   Synaptosomes are the pinched-off nerve endings and their contents of
DE   vesicles and cytoplasm together with the attached subsynaptic area of
DE   the membrane of the postsynaptic cell. They are largely artificial
DE   structures produced by fractionation after selective centrifugation of
DE   nervous tissue homogenates.
SL   Synapse, synaptosome.
HP   Synapse.
KW   KW-0771
//
ID   T-tubule.
AC   SL-0505
DE   T-tubules are invaginations of the sarcolemma penetrating into the
DE   myocyte interior, forming a highly branched and interconnected network
DE   that makes junctions with the sarcoplasmic reticulum. T-tubules are
DE   selectively enriched with specific ion channels and proteins crucial
DE   in the development of calcium transients necessary in excitation-
DE   contraction coupling, thereby facilitating a fast and synchronous
DE   contraction across the entire cell volume. T-tubules are unique to
DE   striated muscle cells, i.e. skeletal and cardiac muscle cells.
SY   Transverse-axial tubular system; Transverse tubule.
SL   Cell membrane, sarcolemma, T-tubule.
HP   Sarcolemma.
GO   GO:0030315; T-tubule
//
ID   Target cell.
AC   SL-0487
DE   A cell including the cell membrane and any external encapsulating of
DE   another cell. This term is used to describe a toxin located in the
DE   structures such as the cell wall and cell envelope that is the target.
SL   Target cell.
GO   GO:0044216; obsolete other organism cell
//
ID   Target cell cytoplasm.
AC   SL-0486
DE   The contents of a target cell within the plasma membrane and which, in
DE   eukaryotic cells, surrounds the host nucleus. This term is used to
DE   describe a toxin located in the cytoplasm of a target cell.
SY   Target cytoplasm.
SL   Target cell, target cell cytoplasm.
HI   Target cell.
KW   KW-1266
//
ID   Target cell membrane.
AC   SL-0451
DE   The target cell membrane is the selectively permeable membrane which
DE   separates the target cell cytoplasm from its surroundings. This term
DE   is used to describe a toxin located to the cell membrane of a target
DE   cell.
SY   Target cytoplasmic membrane; Target plasmalemma;
SY   Target plasma membrane.
SL   Target cell membrane.
HI   Target membrane.
KW   KW-1052
//
ID   Target membrane.
AC   SL-0452
DE   A target membrane is a lipid bilayer which surrounds target cell
DE   enclosed spaces and compartments. This selectively permeable structure
DE   is essential for effective separation of a target cell or target cell
DE   organelle from its surroundings. This term is used to describe a toxin
DE   located to a membrane of a target cell.
SL   Target cell, Membrane, target membrane.
HI   Membrane.
HI   Target cell.
KW   KW-1053
//
ID   Tegument.
AC   SL-0263
DE   The tegument of schistosomes is an outer-surface covering blood-
DE   dwelling flatworms. This unique structure consists of a double
DE   phospholipid bilayer (also known as the heptalaminar outer-surface
DE   structure) that ovelay a syncytium of fused cells surrounding the
DE   entire worm. These outer-tegumental membranes form many surface pits
DE   that substantially increase the surface area of the schistosome. The
DE   underlying syncytial-matrix contains some mitochondria, many vesicular
DE   structures and an extensive cytoskeleton. A basal lamina separates the
DE   syncytium from a layer of muscle cells. Nuclei and ribosomes are
DE   located in cytons, which are located underneath the muscle layer and
DE   connected by microtubule-lined cytoplasmic connections.
SL   Tegument.
//
ID   Tegument membrane.
AC   SL-0264
DE   The membrane suroounding the tegument of schistosomes.
SY   Tegumental membrane.
SL   Tegument membrane.
HI   Membrane.
HP   Tegument.
//
ID   Telomere.
AC   SL-0276
DE   The telomere is a nucleoprotein structure comprising the terminal
DE   section of a eukaryotic chromosome. It has a specialized structure
DE   which is replicated by a special process, thereby counteracting the
DE   tendency of a chromosome to be shortened during each round of
DE   replication.
SY   Chromosome, telomeric region.
SL   Chromosome, telomere.
HP   Chromosome.
KW   KW-0779
GO   GO:0000781; chromosome, telomeric region
//
ID   Thylakoid.
AC   SL-0450
DE   The thylakoid is a membranous cellular structure containing the
DE   photosynthetic pigments, reaction centers and electron-transport
DE   chain. In chloroplast, thylakoids stack up to form the grana or stay
DE   as single cisternae and interconnect the grana. Thylakoid, where
DE   photosynthesis occurs, are found in chloroplasts, cyanelles and in
DE   photosynthetic bacteria where they are the extensive invaginations of
DE   the plasma membrane.
SL   Thylakoid.
KW   KW-0793
GO   GO:0009579; thylakoid
//
ID   Tight junction.
AC   SL-0265
DE   The tight junction (TJ) is a dynamic, multifunctional complex which,
DE   together with adherens junctions and desmosomes, maintains the
DE   integrity of the epithelial cell layer(s) that protects multicellular
DE   organisms. TJ is located at the apical-most portion of the
DE   intercellular junction. It separates the apical and basolateral
DE   compartments of epithelia (preventing the lateral diffusion of lipids
DE   and proteins between the apical and basolateral domains of plasma
DE   membrane) and plays a key role in limiting paracellular permeability
DE   to ions and solutes in a charge and size selective manner. TJs appear
DE   as multiple strands of fibrils forming a continuous circumferential
DE   seal around cells.
SY   TJ; Zonula occludens.
SL   Cell junction, tight junction.
HI   Cell junction.
KW   KW-0796
GO   GO:0005923; bicellular tight junction
AN   Add "Cell membrane" if the protein is clearly associated with the
AN   membrane.
WW   http://celljunctions.med.nyu.edu/desmosomes/desframe.html
//
ID   trans-Golgi network.
AC   SL-0266
DE   The trans-Golgi network is a highly dynamic series of interconnected
DE   tubules and vesicles at the trans face of the Golgi stack. The trans-
DE   Golgi network functions in the processing and sorting of glycoproteins
DE   and glycolipids at the interface of the biosynthetic and endosomal
DE   pathways. The generation and maintenance of apical and basolateral
DE   membranes rely on sorting events that occur in the TGN.
SY   Golgi trans-face; TGN; trans-Golgi; trans-Golgi complex.
SL   Golgi apparatus, trans-Golgi network.
HP   Golgi apparatus.
GO   GO:0005802; trans-Golgi network
AN   The TGN is different from the trans-cisternae of the Golgi stack.
AN   Compartment specific marker: TGOLN2/TGN46.
//
ID   trans-Golgi network membrane.
AC   SL-0267
DE   The membrane surrounding the trans-Golgi network.
SY   Golgi trans-face membrane; TGN membrane; trans-Golgi complex membrane;
SY   trans-Golgi membrane.
SL   Golgi apparatus, trans-Golgi network membrane.
HI   Golgi apparatus membrane.
HP   trans-Golgi network.
GO   GO:0032588; trans-Golgi network membrane
//
ID   Trichocyst.
AC   SL-0268
DE   The trichocyst is an architecturally complex secretory granule having
DE   a highly constrained shape docked at specialized cortical sites in
DE   Paramecium and other ciliates. Each cell bears about 1'000
DE   trichocysts, which are supposed to be defensive organelles against
DE   predators. Trichocyst consists of a spindle-shaped body bearing at its
DE   wide end a tip often compared to an inverted golf tee. An external
DE   stimulus can trigger massive and synchronous exocytosis. After
DE   exocytotic membrane fusion, contact with the H2O and calcium ions in
DE   the external medium leads to an extremely rapid (< 50 ms) and
DE   irreversible expansion of the trichocyst contents, to yield a second,
DE   needle-shaped form which remains insoluble.
SL   Trichocyst.
GO   GO:0055039; trichocyst
RX   PubMed=10865117; DOI=10.1016/s0300-9084(00)00201-7;
//
ID   Uropodium.
AC   SL-0141
DE   The uropodium is a rigid membrane projection with related cytoskeletal
DE   components at the trailing edge of a lymphocyte or other cell in the
DE   process of migrating or being activated, found on the opposite side of
DE   the cell from the lamellipodium or immunological synapse,
DE   respectively.
SY   Uropod; Uropodia.
SL   Cell projection, uropodium.
HI   Cell projection.
GO   GO:0001931; uropod
//
ID   Vacuole.
AC   SL-0272
DE   The vacuole is a generally large fluid-filled membrane-bound
DE   compartment in the cytoplasm. The precise form and function of
DE   vacuoles may vary between phyla. Plant vacuoles are among the best
DE   characterized. They differ in terms of their lumenal contents and
DE   processing enzymes, as well as on the basis of the type of integral
DE   proteins in their membranes (tonoplast intrinsic proteins, TIPs).
DE   Examples include the lytic vacuole, the storage vacuole and the
DE   lutoid. One important function of plant vacuoles is the maintenance of
DE   hydrostatic pressure. Other eukaryotes employ vacuoles for a variety
DE   of purposes, including storage (as in the yeast lysosome/vacuole),
DE   secretion and phagocytosis. In Protozoa, contractile vacuoles can be
DE   used to discharge water from the cytoplasm to the external
DE   environment. Aquatic microorganisms may employ gas vacuoles (composed
DE   of clusters of inert gas vesicles) to provide buoyancy.
SL   Vacuole.
KW   KW-0926
GO   GO:0005773; vacuole
//
ID   Vacuole lumen.
AC   SL-0270
DE   The lumen of a vacuole is the area enclosed by the vacuolar membrane.
SY   Vacuolar lumen.
SL   Vacuole lumen.
HP   Vacuole.
GO   GO:0005775; vacuolar lumen
//
ID   Vacuole membrane.
AC   SL-0271
DE   The membrane surrounding a vacuole.
SY   Vacuolar membrane.
SL   Vacuole membrane.
HI   Membrane.
HP   Endomembrane system.
HP   Vacuole.
GO   GO:0005774; vacuolar membrane
//
ID   Vesicle.
AC   SL-0498
DE   A vesicle is a small structure consisting of fluid enclosed by a lipid
DE   bilayer. Vesicles form naturally during the processes of secretion
DE   (exocytosis), uptake (endocytosis) and transport of materials within
DE   the cytoplasm or between cells, and exist both within the cell and in
DE   the extracellular space.
SL   Vesicle.
RX   PubMed=24769233; DOI=10.1016/j.jprot.2014.04.028;
//
ID   Virion.
AC   SL-0274
DE   The virion is the complete fully infectious extracellular virus
DE   particle.
SL   Virion.
KW   KW-0946
//
ID   Virion membrane.
AC   SL-0275
DE   The membrane surrounding the virion.
SL   Virion membrane.
HI   Membrane.
HP   Virion.
GO   GO:0055036; virion membrane
//
ID   Virion tegument.
AC   SL-0273
DE   The viral tegument is a protein structure that resides between the
DE   capsid and envelope of herpesviruses and which appears amorphous in
DE   electron micrographs.
SY   Viral tegument.
SL   Virion tegument.
HP   Virion.
KW   KW-0920
GO   GO:0019033; viral tegument
//
ID   Z line.
AC   SL-0314
DE   Z-disks are the lateral boundaries of a single sarcomere. In electron
DE   micrographs of cross striated muscle the Z line appears as a series of
DE   dark lines. They represent a key interface between the contractile
DE   apparatus and the cytoskeleton. The Z line (from the German
DE   "Zwischen") largely consists of alpha-actinin homodimers organized in
DE   an antiparallel fashion, thereby providing a backbone for the
DE   insertions of actin-based thin filaments, as well as titin and
DE   nebulin/nebulette. Z line of neighbouring sarcomeres are aligned in
DE   parallel and connected via the intermediate filament protein desmin.
DE   They maintain the actin filaments in a tetragonal lattice.
SY   Z-band; Z bodies; Z body; Z disc; Z-disc; Z disk; Z-disk; Z-line.
SL   Cytoplasm, myofibril, sarcomere, Z line.
HP   I band.
GO   GO:0030018; Z disc
//
ID   Zona pellucida.
AC   SL-0540
DE   Zona pellucida is a specialized extracellular matrix that surrounds
DE   the plasma membrane of mammalian oocytes. It is required for
DE   successful fertilization. Zona pellucida allows species-specific
DE   fertilization, prevents polyspermy, and enables acrosomal reaction for
DE   the successful adhesion and penetration of the sperm cell.
SY   Egg coat; Pellucid zone; Vitelline membrane.
SL   Zona pellucida.
HP   Extracellular matrix.
KW   KW-0272
GO   GO:0035805; egg coat
//
ID   Zymogen granule.
AC   SL-0545
DE   A membrane-bounded, cytoplasmic secretory granule found in enzyme-
DE   secreting cells that allows the sorting, packaging and regulated
DE   apical secretion of digestive enzymes. Enzymes are packaged in these
DE   granules as zymogen or proenzyme, their inactive precursor form.
SL   Zymogen granule.
HI   Secretory vesicle.
GO   GO:0042588; zymogen granule
RX   PubMed=1191276; DOI=10.1016/0006-2944(75)90154-4;
//
ID   Zymogen granule lumen.
AC   SL-0548
DE   The zymogen granule compartment bounded by the membrane of the
DE   secretory vesicle.
SL   Zymogen granule lumen.
HI   Secretory vesicle lumen.
HP   Zymogen granule.
//
ID   Zymogen granule membrane.
AC   SL-0549
DE   The membrane surrounding zymogen granules.
SL   Zymogen granule membrane.
HI   Secretory vesicle membrane.
HP   Zymogen granule.
//
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