UniGene
FILES IN THIS DIRECTORY
=======================
NOTE: The files in this directory have been renamed with "Hs"
(for Homo sapiens) appearing somewhere in the filename.
Other organisms are abbreviated:
Below is the abbreviation used as a
prefix for naming files within the organism's subdirectory,
the numerical identifier of the taxon,
and the organism's name for each organism
for which UniGene datasets ar provided.
Aae:7159:Aedes aegypti
Afp:338618:Aquilegia formosa x Aquilegia pubescens
Aga:7165:Anopheles gambiae
Ame:7460:Apis mellifera
At:3702:Arabidopsis thaliana
Bfl:7739:Branchiostoma floridae
Bmo:7091:Bombyx mori
Bna:3708:Brassica napus
Bt:9913:Bos taurus
Cel:6239:Caenorhabditis elegans
Cfa:9615:Canis familiaris
Cin:7719:Ciona intestinalis
Cpo:199306:Coccidioides posadasii
Cre:3055:Chlamydomonas reinhardtii
Csa:51511:Ciona savignyi
Csi:2711:Citrus sinensis
Ddi:44689:Dictyostelium discoideum
Dm:7227:Drosophila melanogaster
Dr:7955:Danio rerio
Fhe:8078:Fundulus heteroclitus
Fne:5207:Filobasidiella neoformans
Gac:69293:Gasterosteus aculeatus
Gga:9031:Gallus gallus
Ghi:3635:Gossypium hirsutum
Gma:3847:Glycine max
Gmo:117187:Gibberella moniliformis
Gra:29730:Gossypium raimondii
Han:4232:Helianthus annuus
Hma:6085:Hydra magnipapillata
Hs:9606:Homo sapiens
Hv:4513:Hordeum vulgare
Lco:47247:Lotus corniculatus
Les:4081:Lycopersicon esculentum
Lsa:4236:Lactuca sativa
Mdo:3750:Malus x domestica
Mfa:9541:Macaca fascicularis
Mgr:148305:Magnaporthe grisea
Mm:10090:Mus musculus
Mmu:9544:Macaca mulatta
Mte:30286:Molgula tectiformis
Mtr:3880:Medicago truncatula
Ncr:5141:Neurospora crassa
Oar:9940:Ovis aries
Ocu:9986:Oryctolagus cuniculus
Ola:8090:Oryzias latipes
Omy:8022:Oncorhynchus mykiss
Os:4530:Oryza sativa
Pba:73824:Populus balsamifera
Pgl:3330:Picea glauca
Pin:4787:Phytophthora infestans
Ppa:3218:Physcomitrella patens
Psi:3332:Picea sitchensis
Pta:3352:Pinus taeda
Ptp:47664:Populus tremula x Populus tremuloides
Rn:10116:Rattus norvegicus
Sbi:4558:Sorghum bicolor
Sja:6182:Schistosoma japonicum
Sma:6183:Schistosoma mansoni
Sof:4547:Saccharum officinarum
Spu:7668:Strongylocentrotus purpuratus
Ssa:8030:Salmo salar
Ssc:9823:Sus scrofa
Str:8364:Xenopus tropicalis
Stu:4113:Solanum tuberosum
Ta:4565:Triticum aestivum
Tca:7070:Tribolium castaneum
Tgo:5811:Toxoplasma gondii
Tru:31033:Takifugu rubripes
Vvi:29760:Vitis vinifera
Xl:8355:Xenopus laevis
Zm:4577:Zea mays
The files in each subdirectory are as follows, with
each organism's filename beginning with the organism abbreviation:
Hs.info
Some statistics for the current build
Hs.seq.all.Z
Human transcript sequences derived both known genes and ESTs that
have been partitioned into clusters. The lines beginning with the
# character delimit the clusters. The cluster identifier,
which is NOT guaranteed to remain stable across UG builds,
appears as Xx.99999, with Xx the two-letter organism abbreviation.
The extent of the coding sequence is indicated with /cds=[p,m](x,y)
with p incating a CDS annotated on the plus strand (the usual case) and
m indicating a CDS on the minus strand.
Otherwise, the sequences are
shown in FASTA-style. The number following the # is the UniGene
sequence ID; This number won't change from UG build to build, though
the sequence may not remain in the same (or in any) cluster across UG builds.
If the GB or dbEST sequence is updated, the UG sid remains the same.
Note that individual clusters may be downloaded from the main
UniGene website.
Hs.seq.uniq.Z
One sequence selected from each UniGene cluster (the one with the
longest region of high-quality sequence data). This file was
intended to be used for BLAST/FASTA searching.
Hs.data.Z
Send comments to Lukas Wagner (wagner@ncbi.nlm.nih.gov).
Line types/qualifiers:
ID UniGene cluster ID
TITLE Title for the cluster
GENE Gene symbol
CYTOBAND Cytological band
EXPRESS Tissues of origin for ESTs in cluster
RESTR_EXPR Single tissue or development stage contributes
more than half the total EST frequency for this gene.
GNM_TERMINUS genomic confirmation of presence of a 3' terminus;
T if a non-templated polyA tail is found among
a cluster's sequences; else
I if templated As are found in genomic sequence or
S if a canonical polyA signal is found on
the genomic sequence
GENE_ID Entrez gene identifier associated with at least one sequence in this cluster;
to be used instead of LocusLink.
LOCUSLINK LocusLink identifier associated with at least one sequence in this cluster;
deprecated in favor of GENE_ID
CHROMOSOME Chromosome. For plants, CHROMOSOME refers to mapping on the arabidopsis genome.
STS STS
NAME= Name of STS
ACC= GenBank/EMBL/DDBJ accession number of STS [optional field]
DSEG= GDB Dsegment number [optional field]
UNISTS= identifier in NCBI's UNISTS database
TXMAP Transcript map interval
MARKER= Marker found on at least one sequence in this cluster
RHPANEL= Radiation Hybrid panel used to place marker
PROTSIM Protein Similarity data for the sequence with highest-scoring protein similarity in this cluster
ORG= Organism
PROTGI= Sequence GI of protein
PROTID= Sequence ID of protein
PCT= Percent alignment
ALN= length of aligned region (aa)
SCOUNT Number of sequences in the cluster
SEQUENCE Sequence
ACC= GenBank/EMBL/DDBJ accession number of sequence
NID= Unique nucleotide sequence identifier (gi)
PID= Unique protein sequence identifier (used for non-ESTs)
CLONE= Clone identifier (used for ESTs only)
END= End (5'/3') of clone insert read (used for ESTs only)
LID= Library ID; see Hs.lib.info for library name and tissue
MGC= 5' CDS-completeness indicator; if present,
the clone associated with this sequence
is believed CDS-complete. A value greater than 511
is the gi of the CDS-complete mRNA matched by the EST,
otherwise the value is an indicator of the reliability
of the test indicating CDS comleteness;
higher values indicate more reliable CDS-completeness predictions.
SEQTYPE= Description of the nucleotide sequence. Possible values are
mRNA, EST and HTC.
TRACE= The Trace ID of the EST sequence, as provided by NCBI Trace Archive
PERIPHERAL= Indicator that the sequence is a suboptimal
representative of the gene represented by this cluster.
Peripheral sequences are those that are in a cluster
which represents a spliced gene without sharing a
splice junction with any other sequence. In many
cases, they are unspliced transcripts originating
from the gene.
// End of record
Hs.lib.info.Z
additional information regarding the LID field. Note that
libraries may be browsed and downloaded via the Library Browser
page, accessible through the main UniGene website.
Hs.retired.lst.Z
This file allows a comparison of the current UniGene release
with the previous version. It is a list of the previous UniGene
clusters, their composite sequences, and the current UniGene cluster
for each sequence.
As of April 30, 2001, the file will include a header with the organism
name and UniGene release number and date. The data will be in 4
columns. the first column will be the previous UniGene cluster ID,
the second colum will indicate the current UniGene cluster ID. The
third column is the UniGene sequence ID, and the fourth column is the
GenBank accession ID of the sequence.
Previously, the file had 3 columns, the first being the original
UniGene cluster number, the second being the GenBank accession code of
the sequence, the third column is the current UniGene cluster ID.
Hs.profiles.gz
This file summarizes the expression profile of ESTs in
each cluster from libraries with curated controlled-vocabulary
tissue, organ, or developmental stage of origin. Libraries
derived by normalized or subtracted laboratory protocols are not
used for the expression profiles because they could bias the
results. Clusters with 10 or more classified ESTs are reported.
The figures reported are fractions, with the numerator being the
number of ESTs in the cluster from all qualifying RNA sources and
denominator being the total number of ESTs from the same set of
RNA sources. By reporting both, absolute and relative expression
levels can be assessed. Where possible, separate classifications
for, e.g., tissue of origin and developmental stage are
expressed.