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	current	GRCh38.p12 (GCF_000001405.38)	9	NC_000009.12 (125747338..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 FunctionsWhat's a GeneRIF?

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.
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.
miR-33a-3p suppressed the malignant phenotype while also inhibiting PBX3 expression in hepatocellular cancer
Title: MicroRNA-33a-3p suppresses cell migration and invasion by directly targeting PBX3 in human hepatocellular carcinoma.
Results found that PBX3 is epigenetically aberrant in leukemia stem cell maintenance of MLL-rearranged AML and is essential for leukemia development.
Title: PBX3 is essential for leukemia stem cell maintenance in MLL-rearranged leukemia.
results suggest that miR-144-3p suppresses GC progression by inhibiting EMT through targeting PBX3
Title: MicroRNA-144-3p suppresses gastric cancer progression by inhibiting epithelial-to-mesenchymal transition through targeting PBX3.
Patients undergoing radical prostatectomy, with high levels of PBX3 mRNA, had improved prostate cancer specific survival compared to patients expressing low levels.
Title: PBX3 is a putative biomarker of aggressive prostate cancer.
Our findings collectively indicate that miR-320a inhibits cell proliferation and induces apoptosis in MM cells by directly targeting PBX3, supporting its utility as a novel and potential therapeutic agent for miRNA-based MM therapy.
Title: miR-320a regulates cell proliferation and apoptosis in multiple myeloma by targeting pre-B-cell leukemia transcription factor 3.
Studies implicate PBX3/MEIS1 interaction as a driver of cell transformation and leukemogenesis, and that this axis may play a critical role in the regulation of the core transcriptional programs activated in MLL-rearranged and HOX-overexpressing AML.
Title: PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease.
let-7c, miR-200b, miR-222 and miR-424 target PBX3, which is necessary for the acquisition and maintenance of liver tumour-initiating cells properties.
Title: PBX3 is targeted by multiple miRNAs and is essential for liver tumour-initiating cells.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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 NHGRI GWA 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)

Pathways from BioSystems

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Endoderm Differentiation, organism-specific biosystem (from WikiPathways)
Endoderm Differentiation, organism-specific biosystemModel depicting endoderm specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell lin...
Mesodermal Commitment Pathway, organism-specific biosystem (from WikiPathways)
Mesodermal Commitment Pathway, organism-specific biosystemModel depicting mesodermal specification based on the literature and highly enriched gene expression profiles via comparison across dozens of independent induced and embryonic pluripotent stem cell l...
Transcriptional misregulation in cancer, organism-specific biosystem (from KEGG)
Transcriptional misregulation in cancer, organism-specific biosystem
Transcriptional misregulation in cancer
Transcriptional misregulation in cancer, conserved biosystem (from KEGG)
Transcriptional misregulation in cancer, conserved biosystem
Transcriptional misregulation in cancer

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: 229 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	ISA Inferred from Sequence Alignment more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
DNA-binding transcription factor activity, RNA polymerase II-specific	NAS Non-traceable Author Statement more info	PubMed
RNA polymerase II distal enhancer 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
anterior compartment pattern formation	TAS Traceable Author Statement more info	PubMed
dorsal spinal cord development	IEA Inferred from Electronic Annotation more info
neuron development	IEA Inferred from Electronic Annotation more info
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
nucleus	IEA Inferred from Electronic Annotation 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_001134778.1 → 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, 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_001330782.1 → 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, ENST00000373489.9

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

RNA

NR_024122.1 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_024123.1 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

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

Reference GRCh38.p12 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p12 Primary Assembly

Range

125747338..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

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