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

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, Nov 2024]
Expression: Ubiquitous expression in thymus adult (RPKM 39.8), limb E14.5 (RPKM 30.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.
Title: H3K4me3 regulates RNA polymerase II promoter-proximal pause-release.
POLR2A blocks osteoclastic bone resorption and protects against osteoporosis by interacting with CREB1.
Title: POLR2A blocks osteoclastic bone resorption and protects against osteoporosis by interacting with CREB1.
Enhancers predominantly regulate gene expression during differentiation via transcription initiation.
Title: Enhancers predominantly regulate gene expression during differentiation via transcription initiation.
Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements.
Title: Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements.
Dysregulated RPB1 is a central oncogenic hub that drives overgrowth by hijacking an array of oncogenic and anti-apoptosis factors.
Title: Aberrant activation of RPB1 is critical for cell overgrowth in acute myeloid leukemia.
Crosstalk between RNA Pol II C-terminal domain acetylation and phosphorylation via RPRD1B protein and its isoforms has been reported.
Title: Crosstalk between RNA Pol II C-Terminal Domain Acetylation and Phosphorylation via RPRD Proteins.
TBP promotes the association of RNA Polymerase II with mitotic chromosomes, and facilitates transcriptional reactivation following mitosis.
Title: A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes.
significantly higher binding of POLR2A to the Tmem132d promoter region of high anxiety behavior mice than in low anxiety behavior mice
Title: Polymorphism in Tmem132d regulates expression and anxiety-related behavior through binding of RNA polymerase II complex.
Skill learning modulates RNA Pol II poising at immediate early genes in the adult striatum. These experiments demonstrate a novel phenomenon of learning induced transcriptional modulation in adult brain.
Title: Skill Learning Modulates RNA Pol II Poising at Immediate Early Genes in the Adult Striatum.
An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation.
Title: An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Variation

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Alleles

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

Endonuclease-mediated (3)
Targeted (5) 1 citation
Transposon induced (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC56944P1 (e-PCR)
- UniSTS:273359

Polr2a (e-PCR), detects polymorphism
- UniSTS:516596

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
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	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 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 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 II	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity 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

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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

EC 2.7.7.48

EC 2.7.7.6

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)

NM_001291068.1 → NP_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:1058 → 1476

RNAP_II_Rpb1_C; Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain

smart01104
Location:1491 → 1610

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

cd02733
Location:19 → 876

RNAP_II_RPB1_N; Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain

pfam04992
Location:896 → 1079

RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6

cl25496
Location:1857 → 1961

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

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

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.