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    Polr2a polymerase (RNA) II (DNA directed) polypeptide A [ Mus musculus (house mouse) ]

    Gene ID: 20020, updated on 9-Dec-2024

    Summary

    Official Symbol
    Polr2aprovided by MGI
    Official Full Name
    polymerase (RNA) II (DNA directed) polypeptide Aprovided by MGI
    Primary source
    MGI:MGI:98086
    See related
    Ensembl:ENSMUSG00000005198 AllianceGenome:MGI:98086
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Rpb1; 220kDa; Rpo2-1
    Summary
    Enables core promoter sequence-specific DNA binding activity. Predicted to be involved in DNA-templated transcription termination; positive regulation of RNA splicing; and transcription by RNA polymerase II. Located in euchromatin and nucleus. Is expressed in several structures, including alimentary system; genitourinary system; integumental system; nervous system; and sensory organ. Orthologous to human POLR2A (RNA polymerase II subunit A). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 39.8), limb E14.5 (RPKM 30.7) and 28 other tissues See more
    Orthologs
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    Genomic context

    See Polr2a in Genome Data Viewer
    Location:
    11 B3; 11 42.86 cM
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (69624823..69649459, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (69733997..69758633, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene tumor necrosis factor (ligand) superfamily, member 13, opposite strand Neighboring gene tumor necrosis factor (ligand) superfamily, membrane-bound member 13 Neighboring gene tumor necrosis factor (ligand) superfamily, member 13 Neighboring gene tumor necrosis factor (ligand) superfamily, member 12 Neighboring gene STARR-seq mESC enhancer starr_29859 Neighboring gene STARR-seq mESC enhancer starr_29860 Neighboring gene STARR-positive B cell enhancer ABC_E3966 Neighboring gene STARR-positive B cell enhancer ABC_E1830 Neighboring gene solute carrier family 35, member G3 Neighboring gene zinc finger and BTB domain containing 4

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-directed 5'-3' RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-directed 5'-3' RNA polymerase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables RNA polymerase I activity IEA
    Inferred from Electronic Annotation
    more info
     
    contributes_to RNA polymerase II activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase III activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase IV activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase V activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA-dependent RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables core promoter sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables magnesium ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables microfibril binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables mitochondrial single subunit type RNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables plastid single subunit type RNA polymerase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables promoter-specific chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in DNA-templated transcription termination ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA-templated transcription termination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to oxygen levels IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mitochondrial transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in plastid transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of RNA splicing ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of RNA splicing ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to organic cyclic compound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase I IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transcription by RNA polymerase III IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase IV IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transcription by RNA polymerase V IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of Prp19 complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of Prp19 complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of RNA polymerase II, core complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of RNA polymerase II, core complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of RNA polymerase II, core complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in euchromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    DNA-directed RNA polymerase II subunit RPB1
    Names
    3'-5' exoribonuclease
    DNA-directed RNA polymerase II subunit A
    DNA-directed RNA polymerase III largest subunit
    RNA polymerase II 1
    RNA polymerase II subunit B1
    RNA-directed RNA polymerase II subunit RPB1
    NP_001277997.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001291068.1NP_001277997.1  DNA-directed RNA polymerase II subunit RPB1

      See identical proteins and their annotated locations for NP_001277997.1

      Status: VALIDATED

      Source sequence(s)
      AL603707
      Consensus CDS
      CCDS70217.1
      UniProtKB/Swiss-Prot
      P08775, Q5F298
      UniProtKB/TrEMBL
      O08847
      Related
      ENSMUSP00000050771.10, ENSMUST00000058470.16
      Conserved Domains (5) summary
      cd02584
      Location:10581476
      RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain
      smart01104
      Location:14911610
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
      cd02733
      Location:19876
      RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain
      pfam04992
      Location:8961079
      RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6
      cl25496
      Location:18571961
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      69624823..69649459 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_009089.2: Suppressed sequence

      Description
      NM_009089.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.