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PBX3 PBX homeobox 3 [ Homo sapiens (human) ]

Gene ID: 5090, updated on 11-Apr-2024

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; 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 animal organ development; neuron 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 nucleus. Predicted to be part of chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in adrenal (RPKM 28.9), ovary (RPKM 26.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9q33.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125747373..125967377)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137947324..138172756)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128509652..128729656)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene MAPK associated protein 1 Neighboring gene uncharacterized LOC124902358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128458383-128459122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20278 Neighboring gene Sharpr-MPRA regulatory region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20281 Neighboring gene VISTA enhancer hs1030 Neighboring gene VISTA enhancer hs818 Neighboring gene VISTA enhancer hs1102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128540192-128540692 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:128541469-128542156 Neighboring gene PBX3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29015 Neighboring gene uncharacterized LOC124902271 Neighboring gene Sharpr-MPRA regulatory region 15662 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:128640594-128641187 Neighboring gene VISTA enhancer hs1017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20284 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:128713417-128713932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128750389-128751195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128751196-128752001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128761012-128761512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128761513-128762013 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128786371-128786870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128792624-128793228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128793229-128793833 Neighboring gene uncharacterized LOC105376273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128821617-128822118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128822119-128822618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128830736-128831236 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:128836813-128837313 Neighboring gene VISTA enhancer hs987 Neighboring gene uncharacterized LOC105376274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128908419-128909393

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 Promotes Tumor Growth and Angiogenesis via Activation of AT1R/VEGFR2 Pathway in Papillary Thyroid Carcinoma. Chen Q, et al. Biomed Res Int, 2020. PMID 32047817, Free PMC Article
  2. PBX3 hypermethylation in peripheral blood leukocytes predicts better prognosis in colorectal cancer: A propensity score analysis. Sun H, et al. Cancer Med, 2019 Jul. PMID 31140752, Free PMC Article
  3. 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
  4. 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
  5. PBX3 is essential for leukemia stem cell maintenance in MLL-rearranged leukemia. Guo H, et al. Int J Cancer, 2017 Jul 15. PMID 28411381

See all (80) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
    Title: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
  9. MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.
    Title: MiR-320a inhibits malignant phenotype of melanoma cells via targeting PBX3.
  10. MiR-655-3p inhibits growth and invasiveness of trophoblasts via targeting PBX3 and thus deteriorates preeclampsia.
    Title: MiR-655-3p inhibits growth and invasiveness of trophoblasts via targeting PBX3 and thus deteriorates preeclampsia.
Submit: New GeneRIF Correction See all GeneRIFs (46)

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

EBI GWAS Catalog

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

Pathways from PubChem

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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
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
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 regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in respiratory gaseous exchange by respiratory system IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of transcription regulator 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/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

  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_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
    Q5JS98
    Related
    ENSP00000362586.4, ENST00000373487.8

  4. 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

  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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    125747373..125967377
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423441.1 → XP_047279397.1  pre-B-cell leukemia transcription factor 3 isoform X2

  2. XM_047423443.1 → XP_047279399.1  pre-B-cell leukemia transcription factor 3 isoform X4

  3. 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

  4. XM_047423445.1 → XP_047279401.1  pre-B-cell leukemia transcription factor 3 isoform X6

  5. XM_047423442.1 → XP_047279398.1  pre-B-cell leukemia transcription factor 3 isoform X3

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137947324..138172756
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

  2. XM_054363047.1 → XP_054219022.1  pre-B-cell leukemia transcription factor 3 isoform X1

  3. XM_054363050.1 → XP_054219025.1  pre-B-cell leukemia transcription factor 3 isoform X6

  4. XM_054363049.1 → XP_054219024.1  pre-B-cell leukemia transcription factor 3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P40426.1 GenPept UniProtKB/Swiss-Prot:P40426

Gene LinkOut

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