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    Pbx3 PBX homeobox 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 311876, updated on 9-Dec-2024

    Summary

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    Symbol
    Pbx3provided by RGD
    Full Name
    PBX homeobox 3provided by RGD
    Primary source
    RGD:1307198
    See related
    EnsemblRapid:ENSRNOG00000022162 AllianceGenome:RGD:1307198
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription activator 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 positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including adult locomotory behavior; dorsal spinal cord development; and regulation of respiratory gaseous exchange by nervous system process. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human PBX3 (PBX homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Lung (RPKM 85.8), Brain (RPKM 65.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pbx3 in Genome Data Viewer
    Location:
    3p11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (37886241..38079956, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (17488691..17682412, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (13241031..13436084, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120101526 Neighboring gene uncharacterized LOC108350352 Neighboring gene uncharacterized LOC103691768 Neighboring gene uncharacterized LOC108350353 Neighboring gene MAPK associated protein 1 Neighboring gene ribosomal protein S7, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Downregulation of lncRNA-HEIH curbs esophageal squamous cell carcinoma progression by modulating miR-4458/PBX3. Wang D, et al. Thorac Cancer, 2020 Jul. PMID 32449803, Free PMC Article
    2. Non-synonymous variants in pre-B cell leukemia homeobox (PBX) genes are associated with congenital heart defects. Arrington CB, et al. Eur J Med Genet, 2012 Apr. PMID 22426282, Free PMC Article
    3. In vitro visualization of respiratory neuron activity in the newborn mouse ventral medulla. Onimaru H, et al. Brain Res Dev Brain Res, 2004 Nov 25. PMID 15527896
    4. LncRNA H19 suppresses pyroptosis of cardiomyocytes to attenuate myocardial infarction in a PBX3/CYP1B1-dependent manner. Han Y, et al. Mol Cell Biochem, 2021 Mar. PMID 33389498
    5. Pbx3 is required for normal locomotion and dorsal horn development. Rottkamp CA, et al. Dev Biol, 2008 Feb 1. PMID 18155191

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LncRNA H19 suppresses pyroptosis of cardiomyocytes to attenuate myocardial infarction in a PBX3/CYP1B1-dependent manner.
      Title: LncRNA H19 suppresses pyroptosis of cardiomyocytes to attenuate myocardial infarction in a PBX3/CYP1B1-dependent manner.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    acts_upstream_of_or_within dorsal spinal cord development ISO
    Inferred from Sequence Orthology
    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 neuron development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of respiratory gaseous exchange by nervous system process ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within respiratory gaseous exchange by respiratory system ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    pre-B-cell leukemia transcription factor 3
    Names
    pre-B-cell leukemia homeobox 3
    pre-B-cell leukemia transcription factor 3-like

    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_001107834.1 → NP_001101304.1  pre-B-cell leukemia transcription factor 3

      See identical proteins and their annotated locations for NP_001101304.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474001
      UniProtKB/TrEMBL
      A6JUC0, D4AB31
      Related
      ENSRNOP00000087541.2, ENSRNOT00000096937.2
      Conserved Domains (2) summary
      cd00086
      Location:236 → 296
      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:43 → 234
      PBC; PBC domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      37886241..38079956 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039105260.2 → XP_038961188.1  pre-B-cell leukemia transcription factor 3 isoform X2

      Conserved Domains (2) summary
      cd00086
      Location:55 → 115
      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:1 → 53
      PBC; PBC domain

    2. XM_006233975.4 → XP_006234037.1  pre-B-cell leukemia transcription factor 3 isoform X1

      See identical proteins and their annotated locations for XP_006234037.1

      UniProtKB/TrEMBL
      A0A0G2K9K8, A0A8I6AGR6
      Related
      ENSRNOP00000075035.3, ENSRNOT00000082036.3
      Conserved Domains (2) summary
      cd00086
      Location:236 → 296
      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:43 → 234
      PBC; PBC domain
    Nucleotide Protein Strain
    Heading Accession and Version

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