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rxrbb retinoid x receptor, beta b [ Danio rerio (zebrafish) ]

Gene ID: 30486, updated on 18-Sep-2024

Summary

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Official Symbol
rxrbbprovided by ZNC
Official Full Name
retinoid x receptor, beta bprovided by ZNC
Primary source
ZFIN:ZDB-GENE-990415-242
See related
Ensembl:ENSDARG00000002006 AllianceGenome:ZFIN:ZDB-GENE-990415-242
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
RXR; rxrd; unp286
Summary
Enables DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in negative 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 blastoderm; ovary; and testis. Orthologous to human RXRB (retinoid X receptor beta). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
all
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Genomic context

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See rxrbb in Genome Data Viewer
Location:
chromosome: 16
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (18535596..18570789)
105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (18730049..18763291)

Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101883025 Neighboring gene uncharacterized LOC137487889 Neighboring gene formin homology 2 domain containing 3b Neighboring gene solute carrier family 6 member 19b

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 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. Linkage of RXRB-like genes to class I and not to class II Mhc genes in the zebrafish. Gongora R, et al. Immunogenetics, 1998 Jul. PMID 9634478
  2. The orphan COUP-TF nuclear receptors are markers for neurogenesis from cnidarians to vertebrates. Gauchat D, et al. Dev Biol, 2004 Nov 1. PMID 15464576
  3. Retinoid requirements in the reproduction of zebrafish. Alsop D, et al. Gen Comp Endocrinol, 2008 Mar 1. PMID 18158153
  4. 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
  5. Thyroid hormone regulates abrupt skin morphogenesis during zebrafish postembryonic development. Aman AJ, et al. Dev Biol, 2021 Sep. PMID 34089732, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

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 DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
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 cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
  
involved_in nervous system development 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
  
acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
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-beta-B
Names
NR2B2-B
nuclear receptor subfamily 2 group B member 2-B
retinoic acid receptor RXR-delta
retinoid X receptor beta-B
retinoid X receptor delta
retinoid receptor-delta
retinoid x receptor, delta

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_131238.1 → NP_571313.1  retinoic acid receptor RXR-beta-B

    See identical proteins and their annotated locations for NP_571313.1

    Status: PROVISIONAL

    Source sequence(s)
    U29941
    UniProtKB/Swiss-Prot
    Q90417
    Related
    ENSDARP00000022973.8, ENSDART00000021596.9
    Conserved Domains (3) summary
    cd06943
    Location:183 → 403
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:89 → 164
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:21 → 77
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007127.7 Reference GRCz11 Primary Assembly

    Range
    18535596..18570789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021466616.2 → XP_021322291.1  retinoic acid receptor RXR-beta-B isoform X1

    UniProtKB/TrEMBL
    B3DG77
    Conserved Domains (3) summary
    cd06943
    Location:183 → 403
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:89 → 164
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:21 → 78
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

  2. XM_021466617.2 → XP_021322292.1  retinoic acid receptor RXR-beta-B isoform X1

    UniProtKB/TrEMBL
    B3DG77
    Related
    ENSDARP00000145278.1, ENSDART00000180168.1
    Conserved Domains (3) summary
    cd06943
    Location:183 → 403
    NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
    cd06956
    Location:89 → 164
    NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
    pfam11825
    Location:21 → 78
    Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394959.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    166151..194337
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q90417.1 GenPept UniProtKB/Swiss-Prot:Q90417

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