# HISTORY
24 Mar 2016: Updated by: TOUCHUP-v1.15
14 Mar 2016: Updated by: TOUCHUP-v1.14

# molecular_function
20140102: cellular organisms_PTN000133051 contributes to function DNA-directed RNA polymerase activity (GO:0003899) 
20140102: Eukaryota_PTN000133053 contributes to function RNA polymerase I activity (GO:0001054) 
20140102: Eukaryota_PTN000133175 contributes to function RNA polymerase III activity (GO:0001056) 

# cellular_component
20140102: cellular organisms_PTN000133051 is found in DNA-directed RNA polymerase complex (GO:0000428) 
20140102: Eukaryota_PTN000133053 is found in DNA-directed RNA polymerase I complex (GO:0005736) 
20140102: Eukaryota_PTN000133107 is found in DNA-directed RNA polymerase II, core complex (GO:0005665) 
20140102: Eukaryota_PTN000133175 is found in DNA-directed RNA polymerase III complex (GO:0005666) 

# biological_process
20140102: Eukaryota_PTN000133053 participates in termination of RNA polymerase I transcription (GO:0006363) 
20140102: Eukaryota_PTN000133107 participates in maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter (GO:0001193) 
20140102: Eukaryota_PTN000133107 participates in transcription-coupled nucleotide-excision repair (GO:0006283) 
20140102: Eukaryota_PTN000133107 participates in transcription initiation from RNA polymerase II promoter (GO:0006367) 
20140102: Eukaryota_PTN000133175 participates in termination of RNA polymerase III transcription (GO:0006386) 

# WARNINGS - THE FOLLOWING HAVE BEEN REMOVED FOR THE REASONS NOTED

# NOTES
Background & Phylogeny
This family comprises a small subunit conserved in the Archaeal and in the eukaryotic nuclear multisubunit DNA-dependent RNA polymerases. It is not present in the bacterial multisubunit RNA polymerases.
Archaeal RNA polymerases
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Within the Archaea (Archaea_PTN000133236), this tree contains the M subunit (PMID:23768203).
Eukaryotic nuclear RNA polymerases
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Within the eukaryota, there are three large subgroupings for subunits of each of the three types of nuclear RNAPs:
- RNAP I ( Eukaryota_PTN000133053)
- RNAP II (Eukaryota_PTN000133107),  including plant RNAP IV (or RNAP D) and RNAP V (or RNAP E), both of which are thought to be derived from RNAP II (PMID:19110459).
- RNAP III (Eukaryota_PTN000133175)
Comments and issues with the tree
---------------------------------
Eubacterial sequences:
- The tree contains two sequences from the eubacterium Thermotoga maritima. However, there aren't supposed to be any bacterial sequences in this tree. Additionally, the sequences are labelled as "Transposase, putative" and "Transposase-related protein" and the MSA strongly suggests that these two sequences do not belong here.
RNAP IV and RNAP V:
- 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). In this tree, there are two subunits within the RNAP II clade, ARATH_NRPB9A and ARATH_NRPB9B, both of which are thought to be present in both RNAP IV and RNAP V as well as RNAP II.
RNAP II clade:
- No MF propagations were made for the RPB9 subunit within the RNAP II clade because in the yeast S. cerevisiae, the Rpb9 subunit can be deleted without eliminating RNAP II activity.

# 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).