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    PBX1 PBX homeobox 1 [ Homo sapiens (human) ]

    Gene ID: 5087, updated on 12-Feb-2024

    Summary

    Official Symbol
    PBX1provided by HGNC
    Official Full Name
    PBX homeobox 1provided by HGNC
    Primary source
    HGNC:HGNC:8632
    See related
    Ensembl:ENSG00000185630 MIM:176310; AllianceGenome:HGNC:8632
    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
    Also known as
    CAKUHED
    Summary
    This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]
    Expression
    Ubiquitous expression in endometrium (RPKM 55.3), gall bladder (RPKM 19.2) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PBX1 in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (164559184..164886047)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (163905317..164232389)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (164528421..164855284)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene high mobility group box 3 pseudogene 6 Neighboring gene uncharacterized LOC124904759 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:164528003-164528502 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164559870-164560837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164561919-164562862 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164571452-164572217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164572218-164572982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164578838-164579391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164579392-164579944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164580135-164580676 Neighboring gene hESC enhancers GRCh37_chr1:164581219-164581760 and GRCh37_chr1:164581219-164581760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164581761-164582300 Neighboring gene VISTA enhancer hs1202 Neighboring gene VISTA enhancer hs1235 Neighboring gene RNA, U6 small nuclear 171, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164660437-164660937 Neighboring gene VISTA enhancer hs1144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1496 Neighboring gene Sharpr-MPRA regulatory region 1770 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:164704495-164705047 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:164717166-164718365 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164728525-164729026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164729027-164729526 Neighboring gene PBX1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164769015-164769515 Neighboring gene VISTA enhancer hs1191 Neighboring gene NANOG hESC enhancer GRCh37_chr1:164807885-164808386 Neighboring gene uncharacterized LOC107985451 Neighboring gene Sharpr-MPRA regulatory region 7579 Neighboring gene ribosomal protein L35a pseudogene 7

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2019-09-05)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2019-09-05)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Genome-wide association study of anthropometric traits and evidence of interactions with age and study year in Filipino women.
    EBI GWAS Catalog
    Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
    EBI GWAS Catalog
    Identification of inherited genetic variations influencing prognosis in early-onset breast cancer.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ36189, MGC126627, DKFZp686B09108

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    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 ISA
    Inferred from Sequence Alignment
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA-binding transcription factor binding 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
     
    contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription coregulator binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G2/M transition of mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in adrenal gland development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in animal organ morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in branching involved in ureteric bud morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic hemopoiesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic organ development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic skeletal system development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in eye development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in natural killer cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of G2/M transition of mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in proximal/distal pattern formation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of ossification 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
     
    involved_in sex differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in spleen development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in steroid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thymus development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in urogenital system development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    pre-B-cell leukemia transcription factor 1
    Names
    homeobox protein PBX1
    homeobox protein PRL
    pre-B-cell leukemia homeobox 1

    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.

    Genomic

    1. NG_028246.2 RefSeqGene

      Range
      4825..297472
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001204961.2NP_001191890.1  pre-B-cell leukemia transcription factor 1 isoform 2

      See identical proteins and their annotated locations for NP_001191890.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is missing an internal coding exon compared to variant 1. This results in a frame-shift and a shorter isoform (2, also known as isoform PBX1b) with a distinct C-terminus compared to isoform 1. Variants 2 and 5 encode the same isoform.
      Source sequence(s)
      AK022962, AK291415, AL049381, AL359255, AL390119, BC143451, BX647313, DA483403, DA760179, DB270853
      Consensus CDS
      CCDS55654.1
      UniProtKB/TrEMBL
      Q53YC7
      Related
      ENSP00000356872.1, ENST00000367897.5
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain
    2. NM_001204963.2NP_001191892.1  pre-B-cell leukemia transcription factor 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 3' terminal exon compared to variant 1. This results in a frame-shift and a shorter isoform (3) with a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK299673, AL049381, AL359255, AL390119, BC101578, DA760179, DB270853
      Consensus CDS
      CCDS55653.1
      UniProtKB/TrEMBL
      A8K5V0
      Related
      ENSP00000485692.1, ENST00000627490.2
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain
    3. NM_001353130.1NP_001340059.1  pre-B-cell leukemia transcription factor 1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the 5' coding region and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK291415, AL359255, AL390119, BC143435
      UniProtKB/TrEMBL
      B7Z774
      Related
      ENSP00000514644.1, ENST00000699846.1
      Conserved Domains (2) summary
      cd00086
      Location:151211
      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:6149
      PBC; PBC domain
    4. NM_001353131.2NP_001340060.1  pre-B-cell leukemia transcription factor 1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate 3' terminal exon and lacks an exon in the 3' coding region, compared to variant 1. This results in a frame-shift and a shorter isoform (2, also known as isoform PBX1b) with a distinct C-terminus compared to isoform 1. Variants 2 and 5 encode the same isoform.
      Source sequence(s)
      AL357568, AL359255, AL390119
      Consensus CDS
      CCDS55654.1
      UniProtKB/TrEMBL
      Q53YC7
      Related
      ENSP00000514643.1, ENST00000699845.1
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain
    5. NM_002585.4NP_002576.1  pre-B-cell leukemia transcription factor 1 isoform 1

      See identical proteins and their annotated locations for NP_002576.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (1, also known as isoform PBX1a).
      Source sequence(s)
      AK022962, AK291415, AL049381, AL359255, AL390119, BC101578, BX647313, DA483403, DA760179, DB270853
      Consensus CDS
      CCDS1246.1
      UniProtKB/Swiss-Prot
      B4DSC1, F5H4U9, P40424, Q5T488
      UniProtKB/TrEMBL
      A8K5V0
      Related
      ENSP00000405890.2, ENST00000420696.7
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      164559184..164886047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509590.3XP_011507892.1  pre-B-cell leukemia transcription factor 1 isoform X2

      See identical proteins and their annotated locations for XP_011507892.1

      UniProtKB/TrEMBL
      A8K5V0
      Conserved Domains (2) summary
      cd00086
      Location:290350
      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:40288
      PBC; PBC domain
    2. XM_011509592.3XP_011507894.1  pre-B-cell leukemia transcription factor 1 isoform X5

      See identical proteins and their annotated locations for XP_011507894.1

      Conserved Domains (2) summary
      cd00086
      Location:290350
      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:40288
      PBC; PBC domain
    3. XM_017001395.3XP_016856884.1  pre-B-cell leukemia transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      A8K5V0
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain
    4. XM_047421784.1XP_047277740.1  pre-B-cell leukemia transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      Q53YC7
    5. XM_047421783.1XP_047277739.1  pre-B-cell leukemia transcription factor 1 isoform X1

      UniProtKB/TrEMBL
      A8K5V0
    6. XM_005245229.4XP_005245286.1  pre-B-cell leukemia transcription factor 1 isoform X3

      See identical proteins and their annotated locations for XP_005245286.1

      UniProtKB/Swiss-Prot
      B4DSC1, F5H4U9, P40424, Q5T488
      UniProtKB/TrEMBL
      A8K5V0
      Conserved Domains (2) summary
      cd00086
      Location:234294
      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:40232
      PBC; PBC domain
    7. XM_047421787.1XP_047277743.1  pre-B-cell leukemia transcription factor 1 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      163905317..164232389
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336836.1XP_054192811.1  pre-B-cell leukemia transcription factor 1 isoform X3

      UniProtKB/Swiss-Prot
      B4DSC1, F5H4U9, P40424, Q5T488
      UniProtKB/TrEMBL
      A8K5V0
    2. XM_054336834.1XP_054192809.1  pre-B-cell leukemia transcription factor 1 isoform X1

      UniProtKB/TrEMBL
      A8K5V0
    3. XM_054336839.1XP_054192814.1  pre-B-cell leukemia transcription factor 1 isoform X6

      UniProtKB/TrEMBL
      Q53YC7
    4. XM_054336835.1XP_054192810.1  pre-B-cell leukemia transcription factor 1 isoform X2

      UniProtKB/TrEMBL
      A8K5V0
    5. XM_054336838.1XP_054192813.1  pre-B-cell leukemia transcription factor 1 isoform X5

    6. XM_054336837.1XP_054192812.1  pre-B-cell leukemia transcription factor 1 isoform X4

      UniProtKB/TrEMBL
      A8K5V0