polr2a RNA polymerase II subunit A [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: polr2aprovided by ZNC
Official Full Name: RNA polymerase II subunit Aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-041008-78
See related: Ensembl:ENSDARG00000099966 AllianceGenome:ZFIN:ZDB-GENE-041008-78
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: im:7136071
Summary: Predicted to enable nucleic acid binding activity. Predicted to contribute to DNA-directed RNA polymerase activity. Predicted to be involved in mRNA transcription by RNA polymerase II. Predicted to be located in chromosome; cytoplasm; and nucleoplasm. Predicted to be part of RNA polymerase II, core complex. Is expressed in blastomere. Orthologous to human POLR2A (RNA polymerase II subunit A). [provided by Alliance of Genome Resources, Jul 2025]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 12

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2025_04	current	GRCz12tu (GCF_049306965.1)	12	NC_133187.1 (24299045..24312211)
RS_2024_08	previous assembly	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (22560131..22573297)

Chromosome 12 - NC_133187.1 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Pathways from PubChem

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General gene information

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Markers

fc44a12.y1 (e-PCR)
- UniSTS:193873

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to DNA-directed RNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-directed RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in mRNA transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of DNA-directed RNA polymerase complex	IEA Inferred from Electronic Annotation more info
part_of RNA polymerase II, core complex	IBA Inferred from Biological aspect of Ancestor more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA-directed RNA polymerase II subunit RPB1

Names: polymerase (RNA) II (DNA directed) polypeptide A

XP_005156282.1

EC 2.7.7.6

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_049306965.1-RS_2025_04

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

Reference GRCz12tu Primary Assembly

Genomic

NC_133187.1 Reference GRCz12tu Primary Assembly

Range

24299045..24312211

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005156225.5 → XP_005156282.1 DNA-directed RNA polymerase II subunit RPB1

UniProtKB/TrEMBL

A0A0R4IMS9, A0A8M2B2W1

Related

ENSDARP00000135038.1, ENSDART00000172066.2

Conserved Domains (8) summary

cd02584
Location:1055 → 1473

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

smart01104
Location:1506 → 1611

CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

PRK08566
Location:16 → 892

PRK08566; DNA-directed RNA polymerase subunit A'; Validated

cd02733
Location:17 → 873

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

pfam04992
Location:893 → 1076

RNA_pol_Rpb1_6; RNA polymerase Rpb1, domain 6

pfam04998
Location:827 → 1425

RNA_pol_Rpb1_5; RNA polymerase Rpb1, domain 5

pfam11786
Location:1494 → 1571

Aft1_HRA; Aft1 HRA domain

cl23782
Location:1869 → 1948

RCR; Chitin synthesis regulation, resistance to Congo red