Mouse Gene Polr2a (ENSMUST00000058470.15) Description and Page Index
  Description: Mus musculus polymerase (RNA) II (DNA directed) polypeptide A (Polr2a), mRNA. (from RefSeq NM_001291068)
Gencode Transcript: ENSMUST00000058470.15
Gencode Gene: ENSMUSG00000005198.15
Transcript (Including UTRs)
   Position: mm10 chr11:69,733,997-69,758,637 Size: 24,641 Total Exon Count: 29 Strand: -
Coding Region
   Position: mm10 chr11:69,734,410-69,758,223 Size: 23,814 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:69,733,997-69,758,637)mRNA (may differ from genome)Protein (1970 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RPB1_MOUSE
DESCRIPTION: RecName: Full=DNA-directed RNA polymerase II subunit RPB1; Short=RNA polymerase II subunit B1; EC=2.7.7.6; AltName: Full=DNA-directed RNA polymerase II subunit A; AltName: Full=DNA-directed RNA polymerase III largest subunit;
FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. During transcription elongation, Pol II moves on the template as the transcript elongates. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing (By similarity).
CATALYTIC ACTIVITY: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. The phosphorylated C-terminal domain interacts with FNBP3 and SYNCRIP. Interacts with SAFB/SAFB1. Interacts with CCNL1, CCNL2 and SFRS19. Component of a complex which is at least composed of HTATSF1/Tat-SF1, the P-TEFb complex components CDK9 and CCNT1, RNA polymerase II, SUPT5H, and NCL/nucleolin. Hyperphosphorylated form on tandem 7 residues repeats specifically interacts with SETD2 (By similarity). Interacts with PAF1. Interacts (via C-terminus) with FTSJD2 and CTDSP1 (By similarity). Interacts with MYO1C. Interacts (via C- terminus) with SCAF8. Interacts via the phosphorylated C-terminal domain with WDR82 and with SETD1A and SETD1B only in the presence of WDR82 (By similarity). Interacts with ATF7IP (By similarity). When phosphorylated at 'Ser-5', interacts with MEN1; the unphosphorylated form, or phosphorylated at 'Ser-2' does not interact. Interacts with DDX5 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapepdtide repeat and is mediated, at least, by CDK7 and CDK9. CDK7 phosphorylation of POLR2A associated with DNA promotes transcription initiation by triggering dissociation from DNA. Phosphorylation also takes place at 'Ser-7' of the heptapepdtide repeat, which is required for efficient transcription of snRNA genes and processing of the transcripts. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed (By similarity).
PTM: Dephosphorylated by the protein phosphatase CTDSP1 (By similarity).
PTM: Following UV treatment, the elongating form of RNA polymerase II (RNA pol IIo) is ubiquitinated UV damage sites without leading to degradation: ubiquitination is facilitated by KIAA1530/UVSSA and promotes RNA pol IIo backtracking to allow access to the nucleotide excision repair machinery (By similarity.) Ubiquitinated by WWP2 leading to proteasomal degradation.
PTM: Methylated at Arg-1810 by CARM1. Methylation occurs only when the CTD is hypophosphorylated, and phosphorylation at Ser-1805 and Ser-1808 prevent methylation (in vitro). It is assumed that methylation occurs prior to phosphorylation and transcription initiation. CTD methylation may facilitate the expression of select RNAs (By similarity).
MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two- step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.
SIMILARITY: Belongs to the RNA polymerase beta' chain family.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -157.77414-0.381 Picture PostScript Text
3' UTR -118.20413-0.286 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000722 - RNA_pol_asu
IPR000684 - RNA_pol_II_repeat_euk
IPR006592 - RNA_pol_N
IPR007080 - RNA_pol_Rpb1_1
IPR007066 - RNA_pol_Rpb1_3
IPR007083 - RNA_pol_Rpb1_4
IPR007081 - RNA_pol_Rpb1_5
IPR007075 - RNA_pol_Rpb1_6
IPR007073 - RNA_pol_Rpb1_7

Pfam Domains:
PF00623 - RNA polymerase Rpb1, domain 2
PF04983 - RNA polymerase Rpb1, domain 3
PF04990 - RNA polymerase Rpb1, domain 7
PF04992 - RNA polymerase Rpb1, domain 6
PF04997 - RNA polymerase Rpb1, domain 1
PF04998 - RNA polymerase Rpb1, domain 5
PF05000 - RNA polymerase Rpb1, domain 4
PF05001 - RNA polymerase Rpb1 C-terminal repeat

SCOP Domains:
82714 - Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
64484 - beta and beta-prime subunits of DNA dependent RNA-polymerase

ModBase Predicted Comparative 3D Structure on P08775
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
      
      
 RGDEnsemblEnsemblWormBase 
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001047 core promoter binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0046872 metal ion binding
GO:1990841 promoter-specific chromatin binding
GO:0001055 RNA polymerase II activity

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006353 DNA-templated transcription, termination
GO:0006366 transcription from RNA polymerase II promoter
GO:0014070 response to organic cyclic compound
GO:0033120 positive regulation of RNA splicing
GO:0071453 cellular response to oxygen levels

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 DNA-directed RNA polymerase II, core complex
GO:0005719 nuclear euchromatin
GO:0005737 cytoplasm
GO:0000974 Prp19 complex
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  LF198614 - JP 2014500723-A/6117: Polycomb-Associated Non-Coding RNAs.
LF198615 - JP 2014500723-A/6118: Polycomb-Associated Non-Coding RNAs.
U37500 - Mus musculus RNA polymerase II largest subunit (RPB1) mRNA, complete cds.
LF228463 - JP 2014500723-A/35966: Polycomb-Associated Non-Coding RNAs.
BC114996 - Mus musculus cDNA clone IMAGE:40087250.
LF228464 - JP 2014500723-A/35967: Polycomb-Associated Non-Coding RNAs.
LF228465 - JP 2014500723-A/35968: Polycomb-Associated Non-Coding RNAs.
LF228466 - JP 2014500723-A/35969: Polycomb-Associated Non-Coding RNAs.
LF228467 - JP 2014500723-A/35970: Polycomb-Associated Non-Coding RNAs.
LF228468 - JP 2014500723-A/35971: Polycomb-Associated Non-Coding RNAs.
LF228469 - JP 2014500723-A/35972: Polycomb-Associated Non-Coding RNAs.
LF228470 - JP 2014500723-A/35973: Polycomb-Associated Non-Coding RNAs.
LF228471 - JP 2014500723-A/35974: Polycomb-Associated Non-Coding RNAs.
LF228472 - JP 2014500723-A/35975: Polycomb-Associated Non-Coding RNAs.
AK154270 - Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630014B05 product:polymerase (RNA) II (DNA directed) polypeptide A, full insert sequence.
AK154389 - Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630026F16 product:polymerase (RNA) II (DNA directed) polypeptide A, full insert sequence.
AK155391 - Mus musculus NOD-derived CD11c +ve dendritic cells cDNA, RIKEN full-length enriched library, clone:F630223N03 product:polymerase (RNA) II (DNA directed) polypeptide A, full insert sequence.
LF228474 - JP 2014500723-A/35977: Polycomb-Associated Non-Coding RNAs.
LF228475 - JP 2014500723-A/35978: Polycomb-Associated Non-Coding RNAs.
LF228477 - JP 2014500723-A/35980: Polycomb-Associated Non-Coding RNAs.
LF228478 - JP 2014500723-A/35981: Polycomb-Associated Non-Coding RNAs.
LF228479 - JP 2014500723-A/35982: Polycomb-Associated Non-Coding RNAs.
LF228480 - JP 2014500723-A/35983: Polycomb-Associated Non-Coding RNAs.
LF228481 - JP 2014500723-A/35984: Polycomb-Associated Non-Coding RNAs.
LF228483 - JP 2014500723-A/35986: Polycomb-Associated Non-Coding RNAs.
LF228484 - JP 2014500723-A/35987: Polycomb-Associated Non-Coding RNAs.
LF228485 - JP 2014500723-A/35988: Polycomb-Associated Non-Coding RNAs.
AK051012 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030054J22 product:unclassifiable, full insert sequence.
LF228488 - JP 2014500723-A/35991: Polycomb-Associated Non-Coding RNAs.
MA434191 - JP 2018138019-A/6117: Polycomb-Associated Non-Coding RNAs.
MA434192 - JP 2018138019-A/6118: Polycomb-Associated Non-Coding RNAs.
MA464040 - JP 2018138019-A/35966: Polycomb-Associated Non-Coding RNAs.
MA464041 - JP 2018138019-A/35967: Polycomb-Associated Non-Coding RNAs.
MA464042 - JP 2018138019-A/35968: Polycomb-Associated Non-Coding RNAs.
MA464043 - JP 2018138019-A/35969: Polycomb-Associated Non-Coding RNAs.
MA464044 - JP 2018138019-A/35970: Polycomb-Associated Non-Coding RNAs.
MA464045 - JP 2018138019-A/35971: Polycomb-Associated Non-Coding RNAs.
MA464046 - JP 2018138019-A/35972: Polycomb-Associated Non-Coding RNAs.
MA464047 - JP 2018138019-A/35973: Polycomb-Associated Non-Coding RNAs.
MA464048 - JP 2018138019-A/35974: Polycomb-Associated Non-Coding RNAs.
MA464049 - JP 2018138019-A/35975: Polycomb-Associated Non-Coding RNAs.
MA464051 - JP 2018138019-A/35977: Polycomb-Associated Non-Coding RNAs.
MA464052 - JP 2018138019-A/35978: Polycomb-Associated Non-Coding RNAs.
MA464054 - JP 2018138019-A/35980: Polycomb-Associated Non-Coding RNAs.
MA464055 - JP 2018138019-A/35981: Polycomb-Associated Non-Coding RNAs.
MA464056 - JP 2018138019-A/35982: Polycomb-Associated Non-Coding RNAs.
MA464057 - JP 2018138019-A/35983: Polycomb-Associated Non-Coding RNAs.
MA464058 - JP 2018138019-A/35984: Polycomb-Associated Non-Coding RNAs.
MA464060 - JP 2018138019-A/35986: Polycomb-Associated Non-Coding RNAs.
MA464061 - JP 2018138019-A/35987: Polycomb-Associated Non-Coding RNAs.
MA464062 - JP 2018138019-A/35988: Polycomb-Associated Non-Coding RNAs.
MA464065 - JP 2018138019-A/35991: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu00230 - Purine metabolism
mmu00240 - Pyrimidine metabolism
mmu01100 - Metabolic pathways
mmu03020 - RNA polymerase
mmu05016 - Huntington's disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001291068, P08775, Q5F298, RPB1_MOUSE, Rpii215, Rpo2-1, uc007jrk.1, uc007jrk.2, uc007jrk.3, uc007jrk.4
UCSC ID: uc007jrk.4
RefSeq Accession: NM_001291068
Protein: P08775 (aka RPB1_MOUSE)
CCDS: CCDS70217.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.