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    rxrab retinoid x receptor, alpha b [ Danio rerio (zebrafish) ]

    Gene ID: 793011, updated on 21-Apr-2024

    Summary

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    Official Symbol
    rxrabprovided by ZNC
    Official Full Name
    retinoid x receptor, alpha bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-990415-243
    See related
    Ensembl:ENSDARG00000035127 AllianceGenome:ZFIN:ZDB-GENE-990415-243
    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; rxra; rxrg; etID309731.5
    Summary
    Enables nuclear receptor 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 cardiovascular system; retina; segmental plate; swim bladder bud; and tail bud. 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: 5
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (64475937..64594159, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (63794879..63912968, complement)

    Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene endothelial differentiation-related factor 1 Neighboring gene bromodomain containing 3b Neighboring gene prostate stem cell antigen-like Neighboring gene olfactomedin 1a

    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. New retinoid X receptor subtypes in zebra fish (Danio rerio) differentially modulate transcription and do not bind 9-cis retinoic acid. Jones BB, et al. Mol Cell Biol, 1995 Oct. PMID 7565671, Free PMC Article
    2. Ultrastructural analysis of the glutamatergic system in the outer plexiform layer of zebrafish retina. Klooster J, et al. J Chem Neuroanat, 2009 Jul. PMID 19481010
    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. Heartbeat regulates cardiogenesis by suppressing retinoic acid signaling via expression of miR-143. Miyasaka KY, et al. Mech Dev, 2011 Jan-Feb. PMID 20869435

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity ISS
    Inferred from Sequence or Structural Similarity
    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 receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nuclear receptor activity ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    acts_upstream_of_or_within intracellular receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    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
    		 PubMed 
    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-B
    Names
    NR2B1-A
    RXRalpha-A
    nuclear receptor subfamily 2 group B member 1-B
    retinoid X receptor alpha-B
    retinoid x receptor, gamma

    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_131153.1 → NP_571228.1  retinoic acid receptor RXR-alpha-B

      See identical proteins and their annotated locations for NP_571228.1

      Status: PROVISIONAL

      Source sequence(s)
      U29894
      UniProtKB/Swiss-Prot
      A2T929, Q1L677, Q90415
      Related
      ENSDARP00000004918.5, ENSDART00000016321.6
      Conserved Domains (3) summary
      cd06943
      Location:146 → 357
      NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
      cd06956
      Location:52 → 128
      NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
      pfam11825
      Location:11 → 44
      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_007116.7 Reference GRCz11 Primary Assembly

      Range
      64475937..64594159 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009301955.3 → XP_009300230.1  retinoic acid receptor RXR-alpha-B isoform X1

      UniProtKB/TrEMBL
      A0A8M3ASV4
      Conserved Domains (3) summary
      cd06943
      Location:261 → 472
      NR_LBD_RXR_like; The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily
      cd06956
      Location:167 → 243
      NR_DBD_RXR; DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers
      pfam11825
      Location:57 → 159
      Nuc_recep-AF1; Nuclear/hormone receptor activator site AF-1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q90415.1 GenPept UniProtKB/Swiss-Prot:Q90415

    Gene LinkOut

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