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    hoxb1b homeobox B1b [ Danio rerio (zebrafish) ]

    Gene ID: 30374, updated on 9-Dec-2024

    Summary

    Official Symbol
    hoxb1bprovided by ZNC
    Official Full Name
    homeobox B1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-980526-290
    See related
    AllianceGenome:ZFIN:ZDB-GENE-980526-290
    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
    cb249; hoxa1; Hoxa-1; id:ibd5001
    Summary
    Enables sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including establishment of mitotic spindle orientation; hindbrain development; and neural keel formation. Located in nucleus. Is expressed in several structures, including germ ring; mesoderm; neural keel; neural plate; and presumptive neural plate. Orthologous to human HOXB1 (homeobox B1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
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    Genomic context

    See hoxb1b in Genome Data Viewer
    Location:
    chromosome: 12
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (27141140..27142834)
    105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (27032911..27051475)

    Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene si:busm1-227h09.4, pseudogene Neighboring gene uncharacterized LOC100535964 Neighboring gene homeobox B5b Neighboring gene microRNA 10a Neighboring gene src kinase associated phosphoprotein 1 Neighboring gene proteasome activator subunit 3 Neighboring gene NBR1 autophagy cargo receptor a

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    General gene information

    Markers

    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
     
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within establishment of mitotic spindle orientation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within fourth ventricle development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in hindbrain development IGI
    Inferred from Genetic Interaction
    more info
     
    acts_upstream_of_or_within hindbrain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within hindbrain morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neural keel formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within nucleosome organization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within otic vesicle development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IGI
    Inferred from Genetic Interaction
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    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
     
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within rhombomere 4 development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within rhombomere 4 formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within rhombomere morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ventriculo bulbo valve morphogenesis 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 IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    homeobox protein Hox-B1b
    Names
    homeo box B1b
    homeobox gene A-1
    homeobox protein Hox-A1
    hox-A1

    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_131142.2NP_571217.2  homeobox protein Hox-B1b

      See identical proteins and their annotated locations for NP_571217.2

      Status: PROVISIONAL

      Source sequence(s)
      BC133876
      UniProtKB/Swiss-Prot
      Q4PR97, Q8JH52, Q90423, Q98SH8
      UniProtKB/TrEMBL
      A3KNJ6
      Conserved Domains (1) summary
      pfam00046
      Location:212265
      Homeobox; Homeobox domain

    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_007123.7 Reference GRCz11 Primary Assembly

      Range
      27141140..27142834
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394847.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      45256..46950
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)