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PBX1 PBX homeobox 1 [ Homo sapiens (human) ]

Gene ID: 5087, updated on 10-Oct-2019

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
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

Genomic context

See PBX1 in Genome Data Viewer
Location:
1q23.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (164559184..164886047)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (164528597..164821067)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U5F small nuclear 6, pseudogene Neighboring gene high mobility group box 3 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 14887 Neighboring gene VISTA enhancer hs1202 Neighboring gene VISTA enhancer hs1235 Neighboring gene RNA, U6 small nuclear 171, pseudogene Neighboring gene VISTA enhancer hs1144 Neighboring gene PBX1 intron CAGE-defined high expression enhancer Neighboring gene PBX1 antisense RNA 1 Neighboring gene VISTA enhancer hs1191 Neighboring gene uncharacterized LOC107985451 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

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ36189, MGC126627, DKFZp686B09108

Gene Ontology Provided by GOA

Process Evidence Code Pubs
adrenal gland development IEA
Inferred from Electronic Annotation
more info
 
anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
 
branching involved in ureteric bud morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic hemopoiesis IEA
Inferred from Electronic Annotation
more info
 
embryonic limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of G2/M transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription of Notch receptor target TAS
Traceable Author Statement
more info
 
proximal/distal pattern formation IEA
Inferred from Electronic Annotation
more info
 
regulation of ossification IEA
Inferred from Electronic Annotation
more info
 
sex differentiation IEA
Inferred from Electronic Annotation
more info
 
somatic stem cell population maintenance TAS
Traceable Author Statement
more info
 
spleen development IEA
Inferred from Electronic Annotation
more info
 
steroid biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
thymus development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
RNA polymerase II transcription factor complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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)

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
    5001..297471
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001204961.1NP_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
    A8K5V0, Q53YC7
    Related
    ENSP00000356872.1, ENST00000367897.5
    Conserved Domains (2) summary
    pfam03792
    Location:40232
    PBC; PBC domain
    pfam05920
    Location:252290
    Homeobox_KN; Homeobox KN domain
  2. NM_001204963.1NP_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/Swiss-Prot
    P40424
    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
    Related
    ENSP00000439943.2, ENST00000540236.3
    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_001353131.1NP_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
    Conserved Domains (2) summary
    pfam03792
    Location:40232
    PBC; PBC domain
    pfam05920
    Location:252290
    Homeobox_KN; Homeobox KN 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
    P40424
    UniProtKB/TrEMBL
    A0A024R919, A8K5V0
    Related
    ENSP00000405890.1, ENST00000420696.6
    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: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011509590.2XP_011507892.1  pre-B-cell leukemia transcription factor 1 isoform X2

    See identical proteins and their annotated locations for XP_011507892.1

    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
  2. XM_011509592.2XP_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_017001395.2XP_016856884.1  pre-B-cell leukemia transcription factor 1 isoform X4

    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_005245228.3XP_005245285.1  pre-B-cell leukemia transcription factor 1 isoform X1

    See identical proteins and their annotated locations for XP_005245285.1

    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
  5. XM_011509591.2XP_011507893.1  pre-B-cell leukemia transcription factor 1 isoform X5

    See identical proteins and their annotated locations for XP_011507893.1

    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
  6. XM_005245229.3XP_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
    P40424
    UniProtKB/TrEMBL
    A0A024R919
    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
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