Aliases for PBX3 Gene

Aliases for PBX3 Gene

  • PBX Homeobox 3 2 3 5
  • Pre-B-Cell Leukemia Transcription Factor 3 2 3 4
  • Pre-B-Cell Leukemia Homeobox 3 2 3
  • Homeobox Protein PBX3 3 4
  • PBX3 5

External Ids for PBX3 Gene

Previous GeneCards Identifiers for PBX3 Gene

  • GC09P119624
  • GC09P120156
  • GC09P121963
  • GC09P123885
  • GC09P125589
  • GC09P127549
  • GC09P128508
  • GC09P098122
  • GC09P128511
  • GC09P128513

Summaries for PBX3 Gene

GeneCards Summary for PBX3 Gene

PBX3 (PBX Homeobox 3) is a Protein Coding gene. Diseases associated with PBX3 include Myoepithelioma and Bone Epithelioid Hemangioma. Among its related pathways are Mesodermal Commitment Pathway and Transcriptional misregulation in cancer. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is PBX1.

UniProtKB/Swiss-Prot Summary for PBX3 Gene

  • Transcriptional activator that binds the sequence 5'-ATCAATCAA-3'.

Gene Wiki entry for PBX3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PBX3 Gene

Genomics for PBX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PBX3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PBX3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PBX3

Top Transcription factor binding sites by QIAGEN in the PBX3 gene promoter:
  • AREB6
  • Hlf
  • HSF2
  • MZF-1
  • POU3F2
  • RFX1

Genomic Locations for PBX3 Gene

Latest Assembly
220,033 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
220,005 bases
Plus strand

(GRCh37/hg19 by Ensembl)
220,033 bases
Plus strand

Genomic View for PBX3 Gene

Genes around PBX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PBX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PBX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PBX3 Gene

Proteins for PBX3 Gene

  • Protein details for PBX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pre-B-cell leukemia transcription factor 3
    Protein Accession:
    Secondary Accessions:
    • E9PB27
    • Q5JSA0
    • Q5JSA1
    • Q5VXL3
    • Q96PF9
    • Q96PG0

    Protein attributes for PBX3 Gene

    434 amino acids
    Molecular mass:
    47190 Da
    Quaternary structure:
    • Interacts with PBXIP1.

    Alternative splice isoforms for PBX3 Gene


neXtProt entry for PBX3 Gene

Post-translational modifications for PBX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PBX3 Gene

Domains & Families for PBX3 Gene

Gene Families for PBX3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PBX3 Gene

  • PBX domain

Suggested Antigen Peptide Sequences for PBX3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55160, highly similar to Pre-B-cell leukemia transcription factor 3 (B7Z5Q0_HUMAN)
  • Homeobox protein PBX3 (PBX3_HUMAN)
  • Pre-B-cell leukemia homeobox 3 (Q5JS99_HUMAN)
  • PBX3 protein (Q96AL5_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the TALE/PBX homeobox family.
  • Belongs to the TALE/PBX homeobox family.
genes like me logo Genes that share domains with PBX3: view

Function for PBX3 Gene

Molecular function for PBX3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional activator that binds the sequence 5'-ATCAATCAA-3'.
GENATLAS Biochemistry:
transcription factor,with an atypical homeo domain,homologous to PBX1,expressed in most tissues,fetal and adult,binding DNA cooperatively with the heterodimer E2A/myogenic transcription factors

Phenotypes From GWAS Catalog for PBX3 Gene

Gene Ontology (GO) - Molecular Function for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IEA --
genes like me logo Genes that share ontologies with PBX3: view
genes like me logo Genes that share phenotypes with PBX3: view

Animal Models for PBX3 Gene

MGI Knock Outs for PBX3:
  • Pbx3 Pbx3<tm1Mlc>
  • Pbx3 Pbx3<tm1.1Og>
  • Pbx3 Pbx3<tm1a(EUCOMM)Wtsi>
  • Pbx3 Pbx3<tm1b(EUCOMM)Wtsi>
Targeted motifs for PBX3 Gene
HOMER Transcription Factor Regulatory Elements motif PBX3
  • Consensus sequence: CCTGTCAATCAN Submotif: canonical Cell Type: GM12878 GEO ID: GSE32465

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PBX3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for PBX3 Gene

Localization for PBX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PBX3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PBX3 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin ISA --
GO:0005634 nucleus IEA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with PBX3: view

Pathways & Interactions for PBX3 Gene

genes like me logo Genes that share pathways with PBX3: view

Pathways by source for PBX3 Gene

2 BioSystems pathways for PBX3 Gene
1 KEGG pathway for PBX3 Gene

SIGNOR curated interactions for PBX3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001654 eye development IBA 21873635
GO:0002087 regulation of respiratory gaseous exchange by neurological system process IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0007387 anterior compartment pattern formation TAS 1682799
genes like me logo Genes that share ontologies with PBX3: view

Drugs & Compounds for PBX3 Gene

No Compound Related Data Available

Transcripts for PBX3 Gene

mRNA/cDNA for PBX3 Gene

18 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PBX3

Alternative Splicing Database (ASD) splice patterns (SP) for PBX3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b
SP1: - - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - - - - - - - - - - -
SP5: - - - - - - - - - -
SP6: - -
SP7: - -
SP8: - - - -
SP9: - -
SP10: - - - - - -
SP11: - - - - - - -
SP12: - - - - - -

Relevant External Links for PBX3 Gene

GeneLoc Exon Structure for

Expression for PBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PBX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PBX3 Gene

This gene is overexpressed in Ovary (14.2), Uterus (11.4), Fetal gut (10.9), Fetal ovary (7.6), Islet of Langerhans (6.6), and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PBX3 Gene

Protein tissue co-expression partners for PBX3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PBX3

SOURCE GeneReport for Unigene cluster for PBX3 Gene:


mRNA Expression by UniProt/SwissProt for PBX3 Gene:

Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for PBX3 Gene

  • Adrenal gland(4.4)
  • Blood(4.4)
  • Nervous system(3.2)
  • Muscle(2.3)
  • Heart(2.2)
  • Skin(2.1)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with PBX3: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PBX3 Gene

Orthologs for PBX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PBX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Monodelphis domestica)
Mammalia PBX3 31
  • 100 (a)
(Bos Taurus)
Mammalia PBX3 31
  • 100 (a)
(Ornithorhynchus anatinus)
Mammalia PBX3 31
  • 99 (a)
(Canis familiaris)
Mammalia PBX3 30 31
  • 97.2 (n)
(Mus musculus)
Mammalia Pbx3 30 17 31
  • 96.01 (n)
(Pan troglodytes)
Mammalia PBX3 30 31
  • 96.01 (n)
(Rattus norvegicus)
Mammalia Pbx3 30
  • 95.31 (n)
(Gallus gallus)
Aves PBX3 30 31
  • 91.53 (n)
(Anolis carolinensis)
Reptilia PBX3 31
  • 99 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pbx3 30
  • 83.37 (n)
Str.11416 30
(Danio rerio)
Actinopterygii pbx3a 30 31
  • 74.03 (n)
pbx3b 30
Fruit Fly
(Drosophila melanogaster)
Insecta exd 31 32
  • 71 (a)
(Caenorhabditis elegans)
Secernentea ceh-20 31 32
  • 56 (a)
ceh-40 31 32
  • 34 (a)
ceh-60 31
  • 29 (a)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.8721 31
  • 60 (a)
Species where no ortholog for PBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PBX3 Gene

Gene Tree for PBX3 (if available)
Gene Tree for PBX3 (if available)
Evolutionary constrained regions (ECRs) for PBX3: view image

Paralogs for PBX3 Gene

(6) SIMAP similar genes for PBX3 Gene using alignment to 6 proteins:

  • H0Y5D0_HUMAN
  • Q5JS98_HUMAN
  • Q96AL5_HUMAN
genes like me logo Genes that share paralogs with PBX3: view

Variants for PBX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PBX3 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs1588347162 Likely Benign: not provided 125,963,005(+) C/A

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PBX3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PBX3 Gene

Variant ID Type Subtype PubMed ID
dgv12867n54 CNV gain 21841781
dgv4138n106 CNV deletion 24896259
esv1270380 CNV insertion 17803354
esv26440 CNV loss 19812545
esv2678016 CNV deletion 23128226
esv2739043 CNV deletion 23290073
esv3401032 CNV insertion 20981092
esv3545450 CNV deletion 23714750
esv3576704 CNV gain 25503493
esv3621756 CNV loss 21293372
esv3621757 CNV loss 21293372
esv987876 CNV insertion 20482838
nsv1052626 CNV gain 25217958
nsv1054231 CNV gain 25217958
nsv1110581 CNV duplication 24896259
nsv1137504 CNV deletion 24896259
nsv416676 CNV deletion 16902084
nsv477925 CNV novel sequence insertion 20440878
nsv479202 CNV novel sequence insertion 20440878
nsv480848 CNV novel sequence insertion 20440878
nsv509321 CNV insertion 20534489
nsv615294 CNV loss 21841781
nsv615295 CNV gain 21841781
nsv615300 CNV gain+loss 21841781
nsv615301 CNV loss 21841781
nsv615303 CNV gain 21841781
nsv615306 CNV gain 21841781
nsv615307 CNV gain 21841781
nsv6715 CNV insertion 18451855
nsv825078 CNV gain 20364138
nsv825079 CNV gain 20364138
nsv951761 CNV duplication 24416366

Variation tolerance for PBX3 Gene

Residual Variation Intolerance Score: 18.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.46; 28.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PBX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PBX3 Gene

Disorders for PBX3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PBX3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
  • benign myoepithelioma
bone epithelioid hemangioma
  • bone hemangioma
pilocytic astrocytoma
  • grade i astrocytic tumor
chondrosarcoma, extraskeletal myxoid
  • emc
- elite association - COSMIC cancer census association via MalaCards
Search PBX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PBX3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PBX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PBX3 Gene

Publications for PBX3 Gene

  1. PBX2 and PBX3, new homeobox genes with extensive homology to the human proto-oncogene PBX1. (PMID: 1682799) Monica K … Cleary ML (Molecular and cellular biology 1991) 2 3 4
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  3. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. (PMID: 20583170) Letra A … Vieira AR (American journal of medical genetics. Part A 2010) 3 41
  4. Lack of replication of celiac disease risk variants reported in a Spanish population using an independent Spanish sample. (PMID: 19626039) Dema B … Núñez C (Genes and immunity 2009) 3 41
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4

Products for PBX3 Gene

Sources for PBX3 Gene