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    PBX4 PBX homeobox 4 [ Homo sapiens (human) ]

    Gene ID: 80714, updated on 27-Nov-2024

    Summary

    Official Symbol
    PBX4provided by HGNC
    Official Full Name
    PBX homeobox 4provided by HGNC
    Primary source
    HGNC:HGNC:13403
    See related
    Ensembl:ENSG00000105717 MIM:608127; AllianceGenome:HGNC:13403
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a member of the pre-B cell leukemia transcription factor family. These proteins are homeobox proteins that play critical roles in embryonic development and cellular differentiation both as Hox cofactors and through Hox-independent pathways. The encoded protein contains a homeobox DNA-binding domain, but specific functions of the protein have not been determined. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2011]
    Expression
    Broad expression in thyroid (RPKM 3.9), testis (RPKM 2.5) and 18 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PBX4 in Genome Data Viewer
    Location:
    19p13.11
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (19561713..19618687, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19699203..19756196, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19672522..19729496, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19640455-19641386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10447 Neighboring gene YjeF N-terminal domain containing 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19650412-19651074 Neighboring gene Sharpr-MPRA regulatory region 4095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19656191-19656874 Neighboring gene cartilage intermediate layer protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19662820-19663379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19671101-19671600 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686115-19686616 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:19686617-19687116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19690665-19691164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19703425-19704049 Neighboring gene PHF5A pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19722648-19723212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10450 Neighboring gene Sharpr-MPRA regulatory region 12805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10451 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19739417-19740339 Neighboring gene lysophosphatidic acid receptor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19753343-19754298 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10453 Neighboring gene GEM interacting protein

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    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
     
    involved_in positive regulation of DNA-templated transcription IC
    Inferred by Curator
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in XY body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in nucleus IC
    Inferred by Curator
    more info
    PubMed 

    General protein information

    Preferred Names
    pre-B-cell leukemia transcription factor 4
    Names
    homeobox protein PBX4
    pre-B-cell leukemia homeobox 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_025245.3NP_079521.1  pre-B-cell leukemia transcription factor 4

      See identical proteins and their annotated locations for NP_079521.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and is protein-coding.
      Source sequence(s)
      BC141859
      Consensus CDS
      CCDS12406.1
      UniProtKB/Swiss-Prot
      A5D8Y0, B3KUK9, Q9BYU1
      Related
      ENSP00000251203.5, ENST00000251203.14
      Conserved Domains (2) summary
      cd00086
      Location:211272
      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:18209
      PBC; PBC domain

    RNA

    1. NR_038198.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK097427, BC143588, CK300861
      Related
      ENST00000557978.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      19561713..19618687 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439471.1XP_047295427.1  pre-B-cell leukemia transcription factor 4 isoform X2

    2. XM_006722911.4XP_006722974.1  pre-B-cell leukemia transcription factor 4 isoform X2

      See identical proteins and their annotated locations for XP_006722974.1

      Conserved Domains (2) summary
      cd00086
      Location:125186
      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:1123
      PBC; PBC domain
    3. XM_011528320.4XP_011526622.1  pre-B-cell leukemia transcription factor 4 isoform X1

      Conserved Domains (2) summary
      cd00086
      Location:228289
      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:18226
      PBC; PBC domain
    4. XM_011528322.2XP_011526624.1  pre-B-cell leukemia transcription factor 4 isoform X2

      See identical proteins and their annotated locations for XP_011526624.1

      Conserved Domains (2) summary
      cd00086
      Location:125186
      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:1123
      PBC; PBC domain
    5. XM_017027329.3XP_016882818.1  pre-B-cell leukemia transcription factor 4 isoform X4

    6. XM_047439472.1XP_047295428.1  pre-B-cell leukemia transcription factor 4 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      19699203..19756196 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322237.1XP_054178212.1  pre-B-cell leukemia transcription factor 4 isoform X2

    2. XM_054322236.1XP_054178211.1  pre-B-cell leukemia transcription factor 4 isoform X2

    3. XM_054322234.1XP_054178209.1  pre-B-cell leukemia transcription factor 4 isoform X1

    4. XM_054322235.1XP_054178210.1  pre-B-cell leukemia transcription factor 4 isoform X2

    5. XM_054322239.1XP_054178214.1  pre-B-cell leukemia transcription factor 4 isoform X4

    6. XM_054322238.1XP_054178213.1  pre-B-cell leukemia transcription factor 4 isoform X3