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    pbx3b pre-B-cell leukemia homeobox 3b [ Danio rerio (zebrafish) ]

    Gene ID: 58140, updated on 19-May-2024

    Summary

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    Official Symbol
    pbx3bprovided by ZNC
    Official Full Name
    pre-B-cell leukemia homeobox 3bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000405-3
    See related
    Ensembl:ENSDARG00000013615 AllianceGenome:ZFIN:ZDB-GENE-000405-3
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    pbx3.1
    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 animal organ development; neuron development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be located in nucleus. Is expressed in brain; eye; and telencephalon. Orthologous to human PBX3 (PBX homeobox 3). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See pbx3b in Genome Data Viewer
    Location:
    chromosome: 8
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (33895773..34052837, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (33920777..34077821, complement)

    Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene multivesicular body subunit 12Bb Neighboring gene uncharacterized LOC101882658 Neighboring gene uncharacterized LOC103911527 Neighboring gene GTPase activating protein and VPS9 domains 1

    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. lazarus is a novel pbx gene that globally mediates hox gene function in zebrafish. Pöpperl H, et al. Mol Cell, 2000 Aug. PMID 10983974
    2. Embryonic ionizing radiation exposure results in expression alterations of genes associated with cardiovascular and neurological development, function, and disease and modified cardiovascular function in zebrafish. Freeman JL, et al. Front Genet, 2014. PMID 25147559, Free PMC Article
    3. A long noncoding RNA cluster-based genomic locus maintains proper development and visual function. Wang F, et al. Nucleic Acids Res, 2019 Jul 9. PMID 31127312, Free PMC Article
    4. Functional testing of a human PBX3 variant in zebrafish reveals a potential modifier role in congenital heart defects. Farr GH 3rd, et al. Dis Model Mech, 2018 Oct 18. PMID 30355621, Free PMC Article
    5. Eliminating zebrafish pbx proteins reveals a hindbrain ground state. Waskiewicz AJ, et al. Dev Cell, 2002 Nov. PMID 12431378

    See all (13) 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 animal organ morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryonic organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in eye development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron development 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
    pre-B-cell leukemia transcription factor 3; pre-B-cell leukemia transcription factor 3b

    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_001098243.3 → NP_001091713.1  pre-B-cell leukemia transcription factor 3b isoform 1

      See identical proteins and their annotated locations for NP_001091713.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      CU861465, FP101862, FQ311919
      UniProtKB/TrEMBL
      A0A0R4IQU1, A0A2R8QHY2, A4UU10, F1RAB0
      Related
      ENSDARP00000136557.1, ENSDART00000105204.5
      Conserved Domains (2) summary
      cd00086
      Location:235 → 305
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 233
      PBC; PBC domain

    2. NM_001328420.1 → NP_001315349.1  pre-B-cell leukemia transcription factor 3b isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      CU861465, FP101862, FQ311919
      UniProtKB/TrEMBL
      A0A0R4IB75, A0A8M1PA01, B0V334, F1R4R6
      Related
      ENSDARP00000130018.2, ENSDART00000048994.7
      Conserved Domains (2) summary
      cd00086
      Location:235 → 295
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 233
      PBC; PBC domain

    3. NM_131616.3 → NP_571691.1  pre-B-cell leukemia transcription factor 3b isoform 2

      See identical proteins and their annotated locations for NP_571691.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      CU861465, FP101862, FQ311919
      UniProtKB/TrEMBL
      A0A0R4IE45, B0V333, F1RCF9, Q9I9B5
      Related
      ENSDARP00000140154.1, ENSDART00000040126.10
      Conserved Domains (2) summary
      cd00086
      Location:235 → 295
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 233
      PBC; PBC domain

    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_007119.7 Reference GRCz11 Primary Assembly

      Range
      33895773..34052837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009304091.3 → XP_009302366.1  pre-B-cell leukemia transcription factor 3 isoform X7

      UniProtKB/TrEMBL
      A0A8M3AVA3
      Conserved Domains (2) summary
      cd00086
      Location:237 → 307
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 235
      PBC; PBC domain

    2. XM_009304083.3 → XP_009302358.1  pre-B-cell leukemia transcription factor 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M3AV99
      Conserved Domains (2) summary
      cd00086
      Location:237 → 307
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 235
      PBC; PBC domain

    3. XM_009304085.3 → XP_009302360.1  pre-B-cell leukemia transcription factor 3 isoform X3

      UniProtKB/TrEMBL
      A0A8M3B234
      Conserved Domains (2) summary
      cd00086
      Location:237 → 297
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 235
      PBC; PBC domain

    4. XM_009304084.3 → XP_009302359.1  pre-B-cell leukemia transcription factor 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M3B506
      Conserved Domains (2) summary
      cd00086
      Location:235 → 305
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 233
      PBC; PBC domain

    5. XM_009304088.3 → XP_009302363.1  pre-B-cell leukemia transcription factor 3 isoform X5

      UniProtKB/TrEMBL
      A0A8M3BBW5
      Conserved Domains (2) summary
      cd00086
      Location:237 → 307
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 235
      PBC; PBC domain

    6. XM_009304086.3 → XP_009302361.1  pre-B-cell leukemia transcription factor 3 isoform X4

      UniProtKB/TrEMBL
      A0A8M3AVA6
      Conserved Domains (2) summary
      cd00086
      Location:235 → 295
      homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
      pfam03792
      Location:42 → 233
      PBC; PBC domain

    7. XM_017357367.2 → XP_017212856.1  pre-B-cell leukemia transcription factor 3 isoform X6

      UniProtKB/TrEMBL
      A0A8M6Z257

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394734.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      68121..216372 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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