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rxraa retinoid X receptor, alpha a [ Danio rerio (zebrafish) ]

Gene ID: 555578, updated on 21-Apr-2024

Summary

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Official Symbol
rxraaprovided by ZNC
Official Full Name
retinoid X receptor, alpha aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-070314-2
See related
Ensembl:ENSDARG00000057737 AllianceGenome:ZFIN:ZDB-GENE-070314-2
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
RXRalpha-B
Summary
Predicted to enable nuclear receptor activity and retinoic acid-responsive element binding activity. Predicted to be involved in several processes, including regulation of transcription by RNA polymerase II; response to retinoic acid; and retinoic acid receptor signaling pathway. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including digestive system; nervous system; neural crest; optic vesicle; and segmental plate. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human RXRA (retinoid X receptor alpha). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

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Location:
chromosome: 21
Exon count:
11
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (17767991..17947564)
105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (17731459..17910928)

Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene BarH-like homeobox 1b Neighboring gene stomatin Neighboring gene gelsolin a Neighboring gene uncharacterized LOC110438227 Neighboring gene dynein, axonemal, intermediate chain 1, paralog 2 Neighboring gene syntaxin 2a

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. Linking chemical exposure to lipid homeostasis: A municipal waste water treatment plant influent is obesogenic for zebrafish larvae. Barbosa MAG, et al. Ecotoxicol Environ Saf, 2019 Oct 30. PMID 31288122
  2. Chronic effects of clofibric acid in zebrafish (Danio rerio): a multigenerational study. Coimbra AM, et al. Aquat Toxicol, 2015 Mar. PMID 25621398
  3. Identification and characterization of a novel retinoic acid response element in zebrafish cyp26a1 promoter. Li J, et al. Anat Rec (Hoboken), 2012 Feb. PMID 22190473
  4. A modifier screen identifies DNAJB6 as a cardiomyopathy susceptibility gene. Ding Y, et al. JCI Insight, 2016 Sep 8. PMID 27642634, Free PMC Article
  5. Environmental relevant concentrations of benzophenone-3 induced developmental neurotoxicity in zebrafish. Tao J, et al. Sci Total Environ, 2020 Jun 15. PMID 32169642

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclear receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nuclear steroid receptor activity IEA
Inferred from Electronic Annotation
more info
  
enables retinoic acid-responsive element binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in response to retinoic acid IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinoic acid receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of RNA polymerase II transcription regulator complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
retinoic acid receptor RXR-alpha-A
Names
NR2B1-B
nuclear receptor subfamily 2 group B member 1-A
retinoid X receptor alpha-A

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_001161551.1 → NP_001155023.1  retinoic acid receptor RXR-alpha-A

    Status: PROVISIONAL

    Source sequence(s)
    CU062650
    UniProtKB/Swiss-Prot
    A2T929, Q1L677
    UniProtKB/TrEMBL
    A0A8M1NUK0, F1Q4V9
    Related
    ENSDARP00000074930.5, ENSDART00000080481.6
    Conserved Domains (3) summary
    cd06943
    Location:225 → 436
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:129 → 205
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:26 → 122
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

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_007132.7 Reference GRCz11 Primary Assembly

    Range
    17767991..17947564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005161183.4 → XP_005161240.1  retinoic acid receptor RXR-alpha-A isoform X1

    UniProtKB/Swiss-Prot
    A2T929, Q1L677
    UniProtKB/TrEMBL
    A0A8M2B8E9
    Conserved Domains (3) summary
    cd06943
    Location:267 → 478
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:166 → 247
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:63 → 159
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

  2. XM_005161184.4 → XP_005161241.1  retinoic acid receptor RXR-alpha-A isoform X2

    UniProtKB/Swiss-Prot
    A2T929, Q1L677
    UniProtKB/TrEMBL
    A0A8M2B855
    Conserved Domains (3) summary
    cd06943
    Location:262 → 473
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:166 → 242
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:63 → 159
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A2T929.2 GenPept UniProtKB/Swiss-Prot:A2T929

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