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

Gene ID: 553347, updated on 9-Mar-2023

Summary

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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 DNA binding activity; metal ion binding activity; and nucleotidyltransferase activity. Predicted to contribute to RNA polymerase II activity. Predicted to act upstream of or within transcription by RNA polymerase II. Predicted to be located in nucleus. 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, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See polr2a in Genome Data Viewer
Location:
chromosome: 12
Exon count:
28
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (22560121..22573297)
105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (22438897..22451986)
103 previous assembly Zv9 (GCF_000002035.4) 12 NC_007123.5 (23915625..23928776)

Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene sex hormone-binding globulin Neighboring gene zinc finger and BTB domain containing 4 Neighboring gene capping protein (actin filament), gelsolin-like b Neighboring gene si:dkey-219e21.2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Brd4 associates with mitotic chromosomes throughout early zebrafish embryogenesis. Toyama R, et al. Dev Dyn, 2008 Jun. PMID 18498094, Free PMC Article
  2. Identification of Spt5 target genes in zebrafish development reveals its dual activity in vivo. Krishnan K, et al. PLoS One, 2008. PMID 18978947, Free PMC Article
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
  5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-directed 5'-3' RNA polymerase activity IEA
Inferred from Electronic Annotation
more info
  
contributes_to RNA polymerase II activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables metal ion 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
  
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
 PubMed 
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

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007123.7 Reference GRCz11 Primary Assembly

    Range
    22560121..22573297
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005156225.4 → 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
Nucleotide Protein Strain
Heading Accession and Version

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