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PBX1 PBX homeobox 1 [ Homo sapiens (human) ]

Gene ID: 5087, updated on 3-Dec-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
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Genomic context

See PBX1 in Genome Data Viewer
Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (164559184..164886047)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (163905317..164232389)
RS_2024_09 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

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 DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
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 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 
located_in 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_2024_08

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