# HISTORY 07 May 2016: Updated by: TOUCHUP-v1.18 17 Mar 2016: Updated by: TOUCHUP-v1.14 18 Nov 2015: redistribution of PTN000602008 from PTHR23413 to PTHR23431 27 Mar 2016: Updated by: TOUCHUP-v1.15 # molecular_function 20131030: cellular organisms_PTN000602007 has function zinc ion binding (GO:0008270) 20131030: cellular organisms_PTN000602007 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 20131030: Eukaryota_PTN000602008 contributes to function RNA polymerase I activity (GO:0001054) 20131030: Eukaryota_PTN000602008 contributes to function RNA polymerase III activity (GO:0001056) 20131030: Eukaryota_PTN000602008 contributes to function RNA polymerase II activity (GO:0001055) # cellular_component 20131030: cellular organisms_PTN000602007 is found in DNA-directed RNA polymerase complex (GO:0000428) 20131030: Eukaryota_PTN000602008 is found in DNA-directed RNA polymerase III complex (GO:0005666) 20131030: Eukaryota_PTN000602008 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 20131030: Eukaryota_PTN000602008 is found in DNA-directed RNA polymerase I complex (GO:0005736) # biological_process # WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED # NOTES this tree has two different families stuck together inappropriately through a duplication node. 1. L32 cytosolic ribosome protein - The family with cellular_organisms_PTN000601894 as its upper node comprises the conserved subunit L32 of the cytosolic large ribosomal subunit. Annotation Comment ----------------- Only the CC term "cytosolic large ribosomal subunit" was propagated. No MF or BP annotations were made for this family due to lack of experimental evidence codes for appropriate terms. 2. RPABC5 RNA polymerase subunit - The family with cellular_organisms_PTN000602007 as its upper node comprises a conserved subunit of the multisubunit DNA-dependent RNA polymerases in eukaryotes and archaea, though not in the bacteria. Archaeal RNA polymerases ----------------------------- In the Archaea, which have a single multisubunit RNA polymerase which is more similar to that of eukarya than to that of prokarya, this family contains sequences for subunit N (PMID:23768203). Eukaryotic nuclear RNA polymerases ----------------------------- In the true eukaryotes, which have three conserved nuclear multisubunit RNA polymerases as well as two additional ones in plants, this is the family of the RPABC5 (aka Rpb10, POLR2L) of the multisubunit DNA-directed RNA polymerases. In those eukaryotes which have only the three standard nuclear RNA polymerases (I, II, and III), this subunit is found in all three of these RNAPs (PMID:18573085). In Arabidopsis thaliana, which has two additional nuclear RNA polymerases, RNAPs IV and V (both of which appear to be derived from RNAP II; PMID:19110459), there is a duplication of this subunit and the two genes may or not be completely redundant as only one subunit has been shown to be present in RNAPs IV and V, though RNAP II is found to contain either of the two RPB6 homologs (PMID:19110459). While there are also two copies of this gene in Oryza sativa (rice), the structure of the tree within plants suggests that the duplications in Arabidopsis and rice have arisen separately, so it is not possible to propagate the RNAP IV or V annotations from ARATH_Q8LFJ6 within the plant clade since it isn't possible to tell which rice subunit is most closely related to which Arabidopsis subunit. Annotation Comment ----------------- No direct propagations were made for BP terms since the appropriate terms can all be inferred by the Function-Process links from the propagated MF terms. Pruned sequences --------------- The mouse sequence E9Q3B5 was pruned because it has been curated as a pseudogene at MGI. # 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).