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    hoxb3a homeobox B3a [ Danio rerio (zebrafish) ]

    Gene ID: 30339, updated on 9-Dec-2024

    Summary

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    Official Symbol
    hoxb3aprovided by ZNC
    Official Full Name
    homeobox B3aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-990415-104
    See related
    Ensembl:ENSDARG00000029263 AllianceGenome:ZFIN:ZDB-GENE-990415-104
    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
    Z-92; hoxb3; id:ibd3053; wu:fc33f11; zgc:111819
    Summary
    Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Predicted to be active in nucleus. Is expressed in several structures, including ectoderm; hindbrain neural keel; nervous system; neural crest; and pharyngeal arch. Orthologous to human HOXB3 (homeobox B3). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See hoxb3a in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (23698029..23749406)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (23567486..23618858)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103910246 Neighboring gene homeobox B8a Neighboring gene homeobox B7a Neighboring gene homeobox B6a Neighboring gene homeobox B5a Neighboring gene microRNA 10c Neighboring gene homeobox B4a Neighboring gene homeobox B2a Neighboring gene homeobox B1a

    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. A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates. Parker HJ, et al. Nature, 2014 Oct 23. PMID 25219855, Free PMC Article
    2. Conserved co-regulation and promoter sharing of hoxb3a and hoxb4a in zebrafish. Hadrys T, et al. Dev Biol, 2006 Sep 1. PMID 16860306
    3. The retinoic acid metabolising gene, CYP26B1, patterns the cartilaginous cranial neural crest in zebrafish. Reijntjes S, et al. Int J Dev Biol, 2007. PMID 17616924
    4. Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. Scemama JL, et al. J Exp Zool, 2002 Oct 15. PMID 12362434
    5. Development of oculomotor circuitry independent of hox3 genes. Ma LH, et al. Nat Commun, 2014 Jun 25. PMID 24964400, Free PMC Article

    See all (57) 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, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic skeletal system morphogenesis 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 regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    homeobox protein Hox-B3a
    Names
    homeo box B3a
    homeobox gene B-3
    hox-B3

    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_131117.3 → NP_571192.2  homeobox protein Hox-B3a

      See identical proteins and their annotated locations for NP_571192.2

      Status: PROVISIONAL

      Source sequence(s)
      BC095559
      UniProtKB/Swiss-Prot
      O42368
      Related
      ENSDARP00000072928.4, ENSDART00000078466.6
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    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
      23698029..23749406
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068215741.1 → XP_068071842.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Related
      ENSDARP00000155326.1, ENSDART00000184299.1

    2. XM_005171554.4 → XP_005171611.1  homeobox protein Hox-B3a isoform X1

      See identical proteins and their annotated locations for XP_005171611.1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Related
      ENSDARP00000144466.1, ENSDART00000174580.2
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    3. XM_017353138.3 → XP_017208627.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    4. XM_017353141.3 → XP_017208630.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    5. XM_021469305.2 → XP_021324980.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    6. XM_021469306.2 → XP_021324981.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    7. XM_068215740.1 → XP_068071841.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483

    8. XM_017353143.3 → XP_017208632.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Related
      ENSDARP00000156821.1, ENSDART00000182247.1
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    9. XM_017353140.3 → XP_017208629.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    10. XM_021469307.2 → XP_021324982.1  homeobox protein Hox-B3a isoform X1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)

    11. XM_005171562.5 → XP_005171619.1  homeobox protein Hox-B3a isoform X1

      See identical proteins and their annotated locations for XP_005171619.1

      UniProtKB/Swiss-Prot
      O42368, Q4VBK5, Q8AWY5
      UniProtKB/TrEMBL
      A0A8M9P483
      Related
      ENSDARP00000128207.1, ENSDART00000153512.2
      Conserved Domains (2) summary
      pfam00046
      Location:184 → 236
      Homeobox; Homeobox domain
      pfam13293
      Location:353 → 415
      DUF4074; Domain of unknown function (DUF4074)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O42368.3 GenPept UniProtKB/Swiss-Prot:O42368

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