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

Gene ID: 363633, updated on 13-Jul-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
EnsemblRapid: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
    Related
    ENSRNOP00000061492.1, ENSRNOT00000068013.5

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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