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    rarab retinoic acid receptor, alpha b [ Danio rerio (zebrafish) ]

    Gene ID: 555364, updated on 4-Jan-2025

    Summary

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    Official Symbol
    rarabprovided by ZNC
    Official Full Name
    retinoic acid receptor, alpha bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-980526-72
    See related
    Ensembl:ENSDARG00000034893 AllianceGenome:ZFIN:ZDB-GENE-980526-72
    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
    rara2b; fj66e06; wu:fj66e06
    Summary
    Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II and pectoral fin development. Acts upstream of or within liver development; midbrain-hindbrain boundary development; and secondary heart field specification. Predicted to be active in nucleus. Is expressed in several structures, including endoderm; hindbrain neural keel; mesoderm; nervous system; and neural plate. Human ortholog(s) of this gene implicated in acute promyelocytic leukemia. Orthologous to human RARA (retinoic acid receptor alpha). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See rarab in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (33064437..33277633, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (32933888..33145899, complement)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene low affinity immunoglobulin gamma Fc region receptor II-b-like Neighboring gene uncharacterized LOC137490654 Neighboring gene heat shock protein, alpha-crystallin-related, 9 Neighboring gene peptide YYa

    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. Retinoic acid-mediated gene expression in transgenic reporter zebrafish. Perz-Edwards A, et al. Dev Biol, 2001 Jan 1. PMID 11133156
    2. Retinoic acid signaling is required for a critical early step in zebrafish pancreatic development. Stafford D, et al. Curr Biol, 2002 Jul 23. PMID 12176331
    3. Evolution of nuclear retinoic acid receptor alpha (RARα) phosphorylation sites. Serine gain provides fine-tuned regulation. Samarut E, et al. Mol Biol Evol, 2011 Jul. PMID 21297158
    4. Transgenic retinoic acid sensor lines in zebrafish indicate regions of available embryonic retinoic acid. Mandal A, et al. Dev Dyn, 2013 Aug. PMID 23703807, Free PMC Article
    5. High-throughput custom capture sequencing identifies novel mutations in coloboma-associated genes: Mutation in DNA-binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma. Kalaskar VK, et al. Hum Mutat, 2020 Mar. PMID 31816153, Free PMC Article

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The RA receptors RXR gamma and RAR alpha-b are expressed in patterns consistent with mediating the effects of RA on photoreceptors.
      Title: Plasticity of photoreceptor-generating retinal progenitors revealed by prolonged retinoic acid exposure.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Clone Names

    • MGC55278

    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 repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    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
    		  
    acts_upstream_of_or_within heart development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within liver development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within midbrain-hindbrain boundary development IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in pectoral fin development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within pectoral fin development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 retinoic acid receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within retinoic acid receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within secondary heart field specification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus 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 alpha-B
    Names
    NR1B1-B
    RAR-alpha-2.B
    RAR-alpha-B
    RARalpha-B
    nr1b1b
    nuclear receptor subfamily 1 group B member 1-B
    retinoic acid receptor alpha b1
    retinoic acid receptor alpha-2.B
    retinoic acid receptor, alpha 2b
    zRAR-alpha-2.B

    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_131399.1 → NP_571474.1  retinoic acid receptor alpha-B

      See identical proteins and their annotated locations for NP_571474.1

      Status: PROVISIONAL

      Source sequence(s)
      BC049301
      UniProtKB/Swiss-Prot
      Q7ZTI3, Q90272
      Related
      ENSDARP00000044676.6, ENSDART00000044677.7
      Conserved Domains (2) summary
      cd06937
      Location:182 → 411
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:78 → 153
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

    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_007114.7 Reference GRCz11 Primary Assembly

      Range
      33064437..33277633 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068217050.1 → XP_068073151.1  retinoic acid receptor alpha-B isoform X1

      UniProtKB/TrEMBL
      E7EZ95, U5N4H3
      Related
      ENSDARP00000111644.1, ENSDART00000126022.3

    2. XM_005164029.5 → XP_005164086.1  retinoic acid receptor alpha-B isoform X1

      See identical proteins and their annotated locations for XP_005164086.1

      UniProtKB/TrEMBL
      E7EZ95, U5N4H3
      Conserved Domains (2) summary
      cd06937
      Location:184 → 413
      NR_LBD_RAR; The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily
      cd06964
      Location:80 → 155
      NR_DBD_RAR; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

    Reference GRCz11 ALT_DRER_TU_2

    Genomic

    1. NW_018395227.1 Reference GRCz11 ALT_DRER_TU_2

      Range
      406464..455848 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7ZTI3.1 GenPept UniProtKB/Swiss-Prot:Q7ZTI3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.