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

Gene ID: 58140, updated on 2-Nov-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 several processes, including eye development; nervous system development; 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 brain; eye; and telencephalon. Orthologous to human PBX3 (PBX homeobox 3). [provided by Alliance of Genome Resources, Nov 2024]
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:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (33895773..34052413, 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 LOC137496300 Neighboring gene uncharacterized LOC137496366 Neighboring gene uncharacterized LOC101882658 Neighboring gene uncharacterized LOC137490336 Neighboring gene uncharacterized LOC137496367

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 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. In toto imaging of early enteric nervous system development reveals that gut colonization is tied to proliferation downstream of Ret. Baker PA, et al. Development, 2022 Nov 1. PMID 36300492, Free PMC Article
  2. lazarus is a novel pbx gene that globally mediates hox gene function in zebrafish. Pöpperl H, et al. Mol Cell, 2000 Aug. PMID 10983974
  3. 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
  4. 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
  5. 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

See all (15) 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 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: 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_007119.7 Reference GRCz11 Primary Assembly

    Range
    33895773..34052413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009304086.4 → XP_009302361.1  pre-B-cell leukemia transcription factor 3b isoform X2

    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

  2. XM_009304084.4 → XP_009302359.1  pre-B-cell leukemia transcription factor 3b isoform X1

    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

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

Gene LinkOut

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