# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 15 Mar 2016: Updated by: TOUCHUP-v1.14 25 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20140211: cellular organisms_PTN000295288 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 20140211: Eukaryota_PTN001398707 contributes to function RNA polymerase I activity (GO:0001054) 20140211: Eukaryota_PTN000295290 has function single-stranded RNA binding (GO:0003727) 20140211: Eukaryota_PTN000295290 has function single-stranded DNA binding (GO:0003697) 20140211: Eukaryota_PTN000295290 has function translation initiation factor binding (GO:0031369) 20140211: Eukaryota_PTN000295357 contributes to function RNA polymerase III activity (GO:0001056) 20140211: Magnoliophyta_PTN000295348 has LOST/MODIFIED function translation initiation factor binding (GO:0031369) # cellular_component 20140211: cellular organisms_PTN000295288 is found in DNA-directed RNA polymerase complex (GO:0000428) 20140211: Eukaryota_PTN001398707 is found in DNA-directed RNA polymerase I complex (GO:0005736) 20140211: Eukaryota_PTN000295290 is found in cytoplasmic mRNA processing body (GO:0000932) 20140211: Eukaryota_PTN000295290 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20140211: Eukaryota_PTN000295357 is found in DNA-directed RNA polymerase III complex (GO:0005666) 20140211: Magnoliophyta_PTN000295348 is NOT found in cytoplasmic mRNA processing body (GO:0000932) 20140211: Magnoliophyta_PTN000295348 is NOT found in DNA-directed RNA polymerase II, core complex (GO:0005665) # biological_process 20140211: Eukaryota_PTN000295290 participates in positive regulation of translational initiation (GO:0045948) 20140211: Eukaryota_PTN000295290 participates in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213) 20140211: Eukaryota_PTN000295290 participates in transcription initiation from RNA polymerase II promoter (GO:0006367) 20140211: Eukaryota_PTN000295290 participates in nuclear-transcribed mRNA catabolic process, exonucleolytic (GO:0000291) 20140211: Eukaryota_PTN000295357 participates in transcription initiation from RNA polymerase III promoter (GO:0006384) 20140211: Magnoliophyta_PTN000295348 does NOT participate in positive regulation of translational initiation (GO:0045948) 20140211: Magnoliophyta_PTN000295348 does NOT participate in positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213) 20140211: Magnoliophyta_PTN000295348 does NOT participate in transcription initiation from RNA polymerase II promoter (GO:0006367) 20140211: Magnoliophyta_PTN000295348 does NOT participate in nuclear-transcribed mRNA catabolic process, exonucleolytic (GO:0000291) # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES Background & Phylogeny - This family comprises a highly conserved small subunit of multisubunit DNA-dependent RNA polymerases in the Archaea and Eukaryota. Archaeal RNA polymerases ----------------------------- Within the Archaea (Archaea_PTN000295420), this tree contains the E' subunits (PMID:23768203, PMID:19419240). Eukaryotic nuclear RNA polymerases --------------------------------- Within the eukaryota, this family contains a small subunit that is conserved across the multisubunit eukaryotic RNA polymerases, but which is encoded by separate genes for the RNAP I, RNAP II, and RNAP III clades (PMID:18573085): - the RPA43 (aka TWISTNB) subunits (Eukaryota)PTN1398707), which are found in RNA polymerase I - the RPB7 (aka POLR2G) subunits (Eukaryota_PTN000295290), which are found in RNA polymerase II - the RPC25 (aka POLR2H) subunits (Eukaryota_PTN000295357), which are found in RNA polymerase III Comments and issues with the tree --------------------------------- In plants, there are two additional nuclear RNA polymerases called RNAP IV and RNAP V, both of which are thought to be derived from RNAP II (PMID:19110459). Based on the annotation of the A. thaliana sequences NRPB7 (RNAP II), NRPD7 (RNAP IV), and NRPE7 (RNAP V), it looks like there is a unique gene encoding the each of the subunits for RNAPs II, IV, and V. Therefore, I have blocked annotation of all RNAP II specific annotations to the branch of the plants (Magnoliophyta_PTN295348) that contains the subunits for the RNAP IV and RNAP V enzymes. # REFERENCE Annotation inferences using phylogenetic trees The goal of the GO Reference Genome Project, described in PMID 19578431, is to provide accurate, complete and consistent GO annotations for all genes in twelve model organism genomes. To this end, GO curators are annotating evolutionary trees from the PANTHER database with GO terms describing molecular function, biological process and cellular component. GO terms based on experimental data from the scientific literature are used to annotate ancestral genes in the phylogenetic tree by sequence similarity (ISS), and unannotated descendants of these ancestral genes are inferred to have inherited these same GO annotations by descent. The annotations are done using a tool called PAINT (Phylogenetic Annotation and INference Tool).