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    Polr2a RNA polymerase II subunit A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363633, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Polr2aprovided by RGD
    Official Full Name
    RNA polymerase II subunit Aprovided by RGD
    Primary source
    RGD:1587326
    See related
    Ensembl:ENSRNOG00000028834 AllianceGenome:RGD:1587326
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Rpo2-1
    Summary
    Predicted to enable several functions, including enzyme binding activity; promoter-specific chromatin binding activity; and protein C-terminus binding activity. Predicted to contribute to RNA polymerase II activity. Involved in cellular response to oxygen levels and response to organic cyclic compound. Located in nucleus. Orthologous to human POLR2A (RNA polymerase II subunit A). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 178.4), Adrenal (RPKM 169.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Polr2a in Genome Data Viewer
    Location:
    10q24
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (54951162..54977179, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (54452438..54478486, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (56339277..56364888, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4A1 like Neighboring gene TNF superfamily member 12 Neighboring gene ribosomal protein L13, pseudogene 19 Neighboring gene solute carrier family 35, member G3 Neighboring gene zinc finger and BTB domain containing 4 Neighboring gene cholinergic receptor nicotinic beta 1 subunit

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The effect of aryl hydrocarbon receptor ligands on the expression of polymerase (DNA directed) kappa (Polκ), polymerase RNA II (DNA directed) polypeptide A (PolR2a), CYP1B1 and CYP1A1 genes in rat liver. Brauze D, et al. Environ Toxicol Pharmacol, 2012 Nov. PMID 23026235
    2. Per-unit-living tissue normalization of real-time RT-PCR data in ischemic rat hearts. Ellefsen S, et al. Physiol Genomics, 2012 Jun 15. PMID 22535878
    3. Intermittent hypoxia regulates RNA polymerase II in hippocampus and prefrontal cortex. Ignacak ML, et al. Neuroscience, 2009 Feb 18. PMID 19095046, Free PMC Article
    4. Unique subcellular distribution of RPB1 with a phosphorylated C-terminal domain (CTD) in mouse oocytes during meiotic division and its relationship with chromosome separation. Wei H, et al. J Reprod Dev, 2015. PMID 26346254, Free PMC Article
    5. Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Becanovic K, et al. Hum Mol Genet, 2010 Apr 15. PMID 20089533, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. pVHL specifically binds the hyperphosphorylated Rpb1 in a proline-hydroxylation-dependent manner, targeting it for ubiquitination
      Title: von Hippel-Lindau protein binds hyperphosphorylated large subunit of RNA polymerase II through a proline hydroxylation motif and targets it for ubiquitination.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-directed 5'-3' RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    contributes_to RNA polymerase II activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA-dependent RNA polymerase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables core promoter sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    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 promoter-specific chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 cellular response to oxygen levels IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in positive regulation of RNA splicing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to organic cyclic compound IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of Prp19 complex ISO
    Inferred from Sequence Orthology
    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 euchromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    NOT located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA-directed RNA polymerase II subunit RPB1
    Names
    Polymerase (RNA II (DNA directed), large polypeptide
    polymerase (RNA) II (DNA directed) polypeptide A, 220kDa
    polymerase (RNA) II subunit A
    NP_001413970.1
    XP_038943240.1
    XP_063125589.1

    NCBI Reference Sequences (RefSeq)

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    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_001427041.1 → NP_001413970.1  DNA-directed RNA polymerase II subunit RPB1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8I6ASE2, D4A5A6

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      54951162..54977179 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269519.1 → XP_063125589.1  DNA-directed RNA polymerase II subunit RPB1 isoform X2

    2. XM_039087312.2 → XP_038943240.1  DNA-directed RNA polymerase II subunit RPB1 isoform X1

      Conserved Domains (5) summary
      cd02584
      Location:1025 → 1443
      RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain
      smart01104
      Location:1458 → 1577
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
      cd02733
      Location:1 → 843
      RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain
      pfam05109
      Location:1821 → 1926
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam04992
      Location:863 → 1046
      RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6
    Nucleotide Protein Strain
    Heading Accession and Version

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