PBX1 PBX homeobox 1 [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Whole Exome Sequencing Revealing a Novel PBX1 Gene Variant in a Chinese Family Causing Recurrent Neonatal Death.
Title: Whole Exome Sequencing Revealing a Novel PBX1 Gene Variant in a Chinese Family Causing Recurrent Neonatal Death.
PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications.
Title: PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications.
Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
Title: Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis.
Title: Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis.
Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
Title: Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression.
Title: Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression.
Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
Title: Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-kappaB activation.
Title: Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-κB activation.
Molecular characterization of TCF3::PBX1 chromosomal breakpoints in acute lymphoblastic leukemia and their use for measurable residual disease assessment.
Title: Molecular characterization of TCF3::PBX1 chromosomal breakpoints in acute lymphoblastic leukemia and their use for measurable residual disease assessment.
PBX1-promoted SFRP4 transcription inhibits cell proliferation and epithelial-mesenchymal transition in endometrial carcinoma.
Title: PBX1-promoted SFRP4 transcription inhibits cell proliferation and epithelial-mesenchymal transition in endometrial carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (109)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay MedGen: C4539968 OMIM: 617641 GeneReviews: Not available	Compare labs

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 EBI GWAS CatalogPubMed
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A007I06 (e-PCR)
- UniSTS:62720

D1S1720 (e-PCR)
- UniSTS:150039

RH36292 (e-PCR)
- UniSTS:10523

RH64526 (e-PCR)
- UniSTS:52782

G15916 (e-PCR)
- UniSTS:78899

SHGC-148519 (e-PCR)
- UniSTS:176438

PBX1_2674 (e-PCR)
- UniSTS:280888

1564 (e-PCR)
- UniSTS:17977

D1S2454 (e-PCR)
- UniSTS:47678

D13S1219 (e-PCR)
- UniSTS:154178

RH103544 (e-PCR)
- UniSTS:97869

WI-22552 (e-PCR)
- UniSTS:25167

RH48390 (e-PCR)
- UniSTS:68177

RH92739 (e-PCR)
- UniSTS:90716

A003N37 (e-PCR)
- UniSTS:1376

RH102792 (e-PCR)
- UniSTS:97126

SHGC-79383 (e-PCR)
- UniSTS:103276

SHGC-144759 (e-PCR)
- UniSTS:172399

SHGC-84103 (e-PCR)
- UniSTS:104565

WI-17626 (e-PCR)
- UniSTS:3968

RH26827 (e-PCR)
- UniSTS:13448

SHGC-83793 (e-PCR)
- UniSTS:101778

AL034071 (e-PCR)
- UniSTS:93843

D1S1576 (e-PCR)
- UniSTS:82074

RH36084 (e-PCR)
- UniSTS:33946

D1S1548 (e-PCR)
- UniSTS:13731

RH75790 (e-PCR)
- UniSTS:90797

RH94226 (e-PCR)
- UniSTS:89778

D1S2505E (e-PCR)
- UniSTS:154038

WI-16891 (e-PCR)
- UniSTS:54721

RH119851 (e-PCR)
- UniSTS:133596

SHGC-36037 (e-PCR)
- UniSTS:21478

D1S1716 (e-PCR)
- UniSTS:149995

NoName (e-PCR)
- UniSTS:484332

RH68666 (e-PCR)
- UniSTS:52462

AL033591 (e-PCR)
- UniSTS:93438

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	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 DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
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 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

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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)

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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.

Genomic

NG_028246.2 RefSeqGene

Range

4825..297472

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001204961.2 → NP_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:234 → 294

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:40 → 232

PBC; PBC domain
NM_001204963.2 → NP_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:234 → 294

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:40 → 232

PBC; PBC domain
NM_001353130.1 → NP_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:151 → 211

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:6 → 149

PBC; PBC domain
NM_001353131.2 → NP_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:234 → 294

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:40 → 232

PBC; PBC domain
NM_002585.4 → NP_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:234 → 294

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:40 → 232

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

164559184..164886047

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011509590.3 → XP_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:290 → 350

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:40 → 288

PBC; PBC domain
XM_011509592.3 → XP_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:290 → 350

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:40 → 288

PBC; PBC domain
XM_017001395.3 → XP_016856884.1 pre-B-cell leukemia transcription factor 1 isoform X4

UniProtKB/TrEMBL

A8K5V0

Conserved Domains (2) summary

cd00086
Location:234 → 294

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:40 → 232

PBC; PBC domain
XM_047421784.1 → XP_047277740.1 pre-B-cell leukemia transcription factor 1 isoform X6

UniProtKB/TrEMBL

Q53YC7
XM_047421783.1 → XP_047277739.1 pre-B-cell leukemia transcription factor 1 isoform X1
XM_005245229.4 → XP_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:234 → 294

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:40 → 232

PBC; PBC domain
XM_047421787.1 → XP_047277743.1 pre-B-cell leukemia transcription factor 1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

163905317..164232389

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

B4DSC1, F5H4U9, P40424, Q5T488
XM_054336834.1 → XP_054192809.1 pre-B-cell leukemia transcription factor 1 isoform X1
XM_054336839.1 → XP_054192814.1 pre-B-cell leukemia transcription factor 1 isoform X6

UniProtKB/TrEMBL

Q53YC7
XM_054336835.1 → XP_054192810.1 pre-B-cell leukemia transcription factor 1 isoform X2
XM_054336838.1 → XP_054192813.1 pre-B-cell leukemia transcription factor 1 isoform X5
XM_054336837.1 → XP_054192812.1 pre-B-cell leukemia transcription factor 1 isoform X4