PBX3 PBX homeobox 3 [Homo sapiens (human)] - Gene

Summary

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

Location:: 9q33.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
109.20200815	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_000009.12 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?

PBL PBX3 hypermethylation is positively associated with better prognosis of CRC, especially for the UICC stage III CRC patients and colon cancer patients.
Title: PBX3 hypermethylation in peripheral blood leukocytes predicts better prognosis in colorectal cancer: A propensity score analysis.
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.
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.
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.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (31)

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
Genome-wide association study for biomarker identification of Rapamycin and Everolimus using a lymphoblastoid cell line system. GeneReviews: Not available

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

RH69772 (e-PCR)
- UniSTS:55555

G32940 (e-PCR)
- UniSTS:117518

G07093 (e-PCR)
- UniSTS:274

SHGC-30429 (e-PCR)
- UniSTS:26658

RH118782 (e-PCR)
- UniSTS:138283

PBX3_2144 (e-PCR)
- UniSTS:280889

SGC30847 (e-PCR)
- UniSTS:36417

A009U31 (e-PCR)
- UniSTS:56130

WI-16961 (e-PCR)
- UniSTS:70983

STS-H74197 (e-PCR)
- UniSTS:46180

A009X15 (e-PCR)
- UniSTS:21873

SHGC-33994 (e-PCR)
- UniSTS:51602

G32849 (e-PCR)
- UniSTS:117428

RH45491 (e-PCR)
- UniSTS:82884

Homology

Homologs of the PBX3 gene: The PBX3 gene is conserved in chimpanzee, Rhesus monkey, dog, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 302 organisms have orthologs with human gene PBX3
Orthologs

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	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor 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
regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
respiratory gaseous exchange	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
nuclear chromatin	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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)

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
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
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

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
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 Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p13 Primary Assembly

Range

125747372..125967377

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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