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PBX3 PBX homeobox 3 [ Homo sapiens (human) ]

Gene ID: 5090, updated on 1-Aug-2020

Summary

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Official Symbol
PBX3provided by HGNC
Official Full Name
PBX homeobox 3provided by HGNC
Primary source
HGNC:HGNC:8634
See related
Ensembl:ENSG00000167081 MIM:176312
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Expression
Ubiquitous expression in adrenal (RPKM 28.9), ovary (RPKM 26.1) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See PBX3 in Genome Data Viewer
Location:
9q33.3
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (125747372..125967377)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128509617..128729656)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MAPK associated protein 1 Neighboring gene Sharpr-MPRA regulatory region 13831 Neighboring gene VISTA enhancer hs1030 Neighboring gene VISTA enhancer hs818 Neighboring gene VISTA enhancer hs1102 Neighboring gene uncharacterized LOC51145 Neighboring gene uncharacterized LOC107984127 Neighboring gene VISTA enhancer hs1017 Neighboring gene uncharacterized LOC105376273 Neighboring gene VISTA enhancer hs987

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. PBX3 Is Part of an EMT Regulatory Network and Indicates Poor Outcome in Colorectal Cancer. Lamprecht S, et al. Clin Cancer Res, 2018 Apr 15. PMID 29391352
  2. Silencing Pre-B-cell leukemia homeobox 3 decreases the proliferation of human glioma cells in vitro and in vivo. Xu X, et al. J Neurooncol, 2017 Dec. PMID 28856521
  3. PBX3 is essential for leukemia stem cell maintenance in MLL-rearranged leukemia. Guo H, et al. Int J Cancer, 2017 Jul 15. PMID 28411381
  4. PBX3 is a putative biomarker of aggressive prostate cancer. Ramberg H, et al. Int J Cancer, 2016 Oct 15. PMID 27273830
  5. PBX3 is overexpressed in gastric cancer and regulates cell proliferation. Li Y, et al. Tumour Biol, 2014 May. PMID 24375258

See all (59) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Compared with negative methylation (Nm), DLEC1-positive methylation (Pm) was associated with increased GC risk in PS (OR 2.083, 95% CI 1.220-3.558, P = 0.007), but PBX3 Pm was not associated with GC risk.
    Title: Relationship between DLEC1 and PBX3 promoter methylation and the risk and prognosis of gastric cancer in peripheral blood leukocytes.
  2. EWSR1-PBX3 fusions occur in most (and possibly all) cases of cutaneous syncytial myoepithelioma.
    Title: Cutaneous Syncytial Myoepithelioma Is Characterized by Recurrent EWSR1-PBX3 Fusions.
  3. These results indicated that miR-129-5p suppressed cell proliferation and migration in pancreatic cancer cells by targeting PBX3.
    Title: miR-129-5p suppresses proliferation, migration, and induces apoptosis in pancreatic cancer cells by targeting PBX3.
  4. PBX3 is a novel indicator of EMT in colorectal cancer, part of an EMT regulatory network, and a promising prognostic predictor that may aid in therapeutic decision making for patients with colorectal cancer.
    Title: PBX3 Is Part of an EMT Regulatory Network and Indicates Poor Outcome in Colorectal Cancer.
  5. In response to treatment with si-lncRNA HOST2, si-PBX3, and let-7b mimic, glioma cell lines exhibited decreased cell viability, suppressed cell migration, invasion, and reduced colony formation of glioma cells. This was accompanied by an attenuated tumor formation with smaller volume and weight in nude mice, suggesting that down-regulated HOST2 could inhibit the tumorigenicity of glioma cells
    Title: An in vitro and in vivo study of the role of long non-coding RNA-HOST2 in the proliferation, migration, and invasion of human glioma cells.
  6. miR-526b was decreased in CC cells and CC clinical specimens, especially in CC specimens with stromal invasion, pelvic lymph node metastasis and deficiency vaginal involvement. Moreover, it was proved that the character of miR-526b in CC was dependent on controlling the PBX3-mediated EMT process.
    Title: By downregulating PBX3, miR-526b suppresses the epithelial-mesenchymal transition process in cervical cancer cells.
  7. These data indicate that NPMc+ leukemic cell survival requires upregulation of PBX3 and HOXA9.
    Title: Inactivation of PBX3 and HOXA9 by down-regulating H3K79 methylation represses NPM1-mutated leukemic cell survival.
  8. the present study indicates that PBX 3'UTR may induce inflammatory responses and sepsis via acting as a competing endogenous RNA for HMGB1.
    Title: Pre-B cell leukemia transcription factor 3 induces inflammatory responses in human umbilical vein endothelial cells and murine sepsis via acting a competing endogenous RNA for high mobility group box 1 protein.
  9. Results show that PBX3 expression is increased in both human glioma tissues and cell lines. Furthermore, silencing of PBX3 remarkably reduced glioma cell proliferation and induced apoptosis, while PBX3 overexpression dramatically increased glioma cell proliferation. Finally, PBX3 promoted glioma cell proliferation by modulating cell cycle progression.
    Title: Silencing Pre-B-cell leukemia homeobox 3 decreases the proliferation of human glioma cells in vitro and in vivo.
  10. Silencing PBX3 inhibited the migratory and invasive capacities of glioma cells.
    Title: MicroRNA-98 Attenuates Cell Migration and Invasion in Glioma by Directly Targeting Pre-B Cell Leukemia Homeobox 3.
Submit: New GeneRIF Correction See all GeneRIFs (30)

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

NHGRI GWAS Catalog

Description
Genome-wide association study for biomarker identification of Rapamycin and Everolimus using a lymphoblastoid cell line system.
NHGRI GWA Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
 PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
adult locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
animal organ morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
anterior compartment pattern formation TAS
Traceable Author Statement
more info
 PubMed 
brain development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
dorsal spinal cord development IEA
Inferred from Electronic Annotation
more info
  
embryonic organ development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
eye development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
neuron development IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
posterior compartment specification TAS
Traceable Author Statement
more info
 PubMed 
regulation of respiratory gaseous exchange by neurological system process IEA
Inferred from Electronic Annotation
more info
  
respiratory gaseous exchange IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
  
transcription factor complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
pre-B-cell leukemia transcription factor 3
Names
homeobox protein PBX3
pre-B-cell leukemia homeobox 3

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.

mRNA and Protein(s)

  1. NM_001134778.2 → NP_001128250.1  pre-B-cell leukemia transcription factor 3 isoform 2

    See identical proteins and their annotated locations for NP_001128250.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) utilizes an alternate first exon and 5'UTR; thus, the first likely translation initiation site corresponds to an internal methionine in variant 1. The predicted protein (isoform 2) is N-terminally truncated compared to isoform 1 and is not predicted to have a signal peptide.
    Source sequence(s)
    AK309713, AL358074, BC094883, CD675622, CN372830, CN372832
    Consensus CDS
    CCDS48021.1
    UniProtKB/Swiss-Prot
    P40426
    Related
    ENSP00000387456.2, ENST00000447726.6
    Conserved Domains (2) summary
    cd00086
    Location:161 → 221
    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:1 → 159
    PBC; PBC domain

  2. NM_001330782.2 → NP_001317711.1  pre-B-cell leukemia transcription factor 3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL358074, AL445186, BC094883, BP340711, DA692140
    Consensus CDS
    CCDS83416.1
    UniProtKB/Swiss-Prot
    P40426
    Related
    ENSP00000341990.5, ENST00000342287.9
    Conserved Domains (2) summary
    cd00086
    Location:236 → 296
    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:43 → 234
    PBC; PBC domain

  3. NM_006195.6 → NP_006186.1  pre-B-cell leukemia transcription factor 3 isoform 1

    See identical proteins and their annotated locations for NP_006186.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) utilizes an alternate first exon containing a predicted translation initiation site with a strong Kozak signal; the resulting protein isoform (1) is predicted to have a signal peptide.
    Source sequence(s)
    BC016977, BC094883, X59841
    Consensus CDS
    CCDS6865.1
    UniProtKB/Swiss-Prot
    P40426
    UniProtKB/TrEMBL
    Q96AL5
    Related
    ENSP00000362588.5, ENST00000373489.10
    Conserved Domains (2) summary
    cd00086
    Location:236 → 296
    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:43 → 234
    PBC; PBC domain

RNA

  1. NR_024122.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) omits a coding exon resulting in a frameshift and truncated open reading frame. The transcript is predicted to be a candidate for nonsense-mediated decay and likely does not encode a protein.
    Source sequence(s)
    AF355141, AI479638, BC094883, CD675622, CN372830, CN372832, X59841

  2. NR_024123.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) omits two coding exons resulting in a frameshift and truncated open reading frame. The transcript is predicted to be a candidate for nonsense-mediated decay and likely does not encode a protein.
    Source sequence(s)
    AF355142, AI479638, BC094883, CD675622, CN372830, CN372832, X59841

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    125747372..125967377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006717130.1 → XP_006717193.1  pre-B-cell leukemia transcription factor 3 isoform X1

    UniProtKB/TrEMBL
    Q5JS98
    Related
    ENSP00000362586.4, ENST00000373487.8
    Conserved Domains (2) summary
    cd00086
    Location:236 → 317
    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:43 → 234
    PBC; PBC domain

  2. XM_006717131.1 → XP_006717194.1  pre-B-cell leukemia transcription factor 3 isoform X3

    Conserved Domains (2) summary
    cd00086
    Location:236 → 317
    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:43 → 234
    PBC; PBC domain

  3. XM_006717133.2 → XP_006717196.1  pre-B-cell leukemia transcription factor 3 isoform X5

    See identical proteins and their annotated locations for XP_006717196.1

    Conserved Domains (2) summary
    cd00086
    Location:55 → 136
    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:1 → 53
    PBC; PBC domain

  4. XM_017014786.1 → XP_016870275.1  pre-B-cell leukemia transcription factor 3 isoform X4

    Conserved Domains (2) summary
    cd00086
    Location:161 → 221
    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:1 → 159
    PBC; PBC domain

  5. XM_011518755.2 → XP_011517057.1  pre-B-cell leukemia transcription factor 3 isoform X2

    Related
    ENST00000672674.1
    Conserved Domains (2) summary
    cd00086
    Location:161 → 242
    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:1 → 159
    PBC; PBC domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P40426.1 GenPept UniProtKB/Swiss-Prot:P40426

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