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; AllianceGenome:HGNC:8634
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
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including eye development; nervous system development; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including adult locomotory behavior; dorsal spinal cord development; and regulation of respiratory gaseous exchange by nervous system process. Predicted to be located in chromatin. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Biomarker of esophagus squamous cell carcinoma. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in adrenal (RPKM 28.9), ovary (RPKM 26.1) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 9q33.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (125747373..125967377)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (137947324..138172756)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (128509652..128729656)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
Title: Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
Title: Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
Title: PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
Title: LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
Title: USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
Title: Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
Circular RNA circ_0032962 promotes trophoblast cell progression as ceRNA to target PBX3 via sponging miR-326 in preeclampsia.
Title: Circular RNA circ_0032962 promotes trophoblast cell progression as ceRNA to target PBX3 via sponging miR-326 in preeclampsia.
The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
Title: The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
Title: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.
Title: MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info

Process	Evidence Code	Pubs
involved_in adult locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in animal organ morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior compartment pattern formation	TAS Traceable Author Statement more info	PubMed
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in dorsal spinal cord development	IEA Inferred from Electronic Annotation more info
involved_in embryonic organ development	IBA Inferred from Biological aspect of Ancestor more info
involved_in eye development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in posterior compartment specification	TAS Traceable Author Statement more info	PubMed
involved_in regulation of respiratory gaseous exchange by nervous system process	IEA Inferred from Electronic Annotation more info
involved_in respiratory gaseous exchange by respiratory system	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
part_of transcription regulator complex	IEA Inferred from Electronic Annotation more info

General protein information

Go to the top of the page Help

Preferred Names: pre-B-cell leukemia transcription factor 3

Names: homeobox protein PBX3; pre-B-cell leukemia homeobox 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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/TrEMBL

Q96AL5

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_001411009.1 → NP_001397938.1 pre-B-cell leukemia transcription factor 3 isoform 4

Status: VALIDATED

Source sequence(s)

AL358074, AL445186

Consensus CDS

CCDS94482.1

UniProtKB/TrEMBL

B7Z4A9, Q5JS98

Related

ENSP00000362586.4, ENST00000373487.8
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

E9PB27, P40426, Q5JSA0, Q5JSA1, Q5VXL3, Q96PF9, Q96PG0

UniProtKB/TrEMBL

B7Z4A9

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: 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_000009.12 Reference GRCh38.p14 Primary Assembly

Range

125747373..125967377

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423441.1 → XP_047279397.1 pre-B-cell leukemia transcription factor 3 isoform X2
XM_047423443.1 → XP_047279399.1 pre-B-cell leukemia transcription factor 3 isoform X4
XM_011518755.3 → XP_011517057.1 pre-B-cell leukemia transcription factor 3 isoform X1

UniProtKB/TrEMBL

Q96AL5

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
XM_047423445.1 → XP_047279401.1 pre-B-cell leukemia transcription factor 3 isoform X6
XM_047423442.1 → XP_047279398.1 pre-B-cell leukemia transcription factor 3 isoform X3

UniProtKB/TrEMBL

Q96AL5
XM_047423444.1 → XP_047279400.1 pre-B-cell leukemia transcription factor 3 isoform X5

UniProtKB/TrEMBL

Q96AL5

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

137947324..138172756

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363048.1 → XP_054219023.1 pre-B-cell leukemia transcription factor 3 isoform X2
XM_054363047.1 → XP_054219022.1 pre-B-cell leukemia transcription factor 3 isoform X1

UniProtKB/TrEMBL

Q96AL5
XM_054363050.1 → XP_054219025.1 pre-B-cell leukemia transcription factor 3 isoform X6
XM_054363049.1 → XP_054219024.1 pre-B-cell leukemia transcription factor 3 isoform X3

UniProtKB/TrEMBL

Q96AL5