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Aliases for PBX3 Gene

Aliases for PBX3 Gene

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

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 Childhood Pilocytic Astrocytoma and Pilocytic Astrocytoma. 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 for PBX3 Gene

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

Gene Wiki entry for PBX3 Gene

Additional gene information for PBX3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PBX3 Gene

Genomics for PBX3 Gene

GeneHancer (GH) Regulatory Elements for PBX3 Gene

Promoters and enhancers for PBX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09I125744 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 565.4 -0.2 -166 4.9 HDGF PKNOX1 CLOCK MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B PBX3 LOC51145 GOLGA1 GAPVD1 PRPS1P2 PPP6C
GH09I125829 Enhancer 1.6 UCNEbase FANTOM5 Ensembl ENCODE 24.5 +82.7 82672 1.4 MEIS2 PKNOX1 BATF IRF4 RAD21 YY1 POLR2A NFATC1 ATF7 ETV6 PBX3 LOC51145 GC09P125856 GC09P125762
GH09I125760 Enhancer 1.9 VISTA UCNEbase Ensembl ENCODE 15 +15.4 15428 4.3 PKNOX1 ARNT KLF17 MZF1 ZNF76 FEZF1 ZNF2 ZEB1 ZNF366 ZSCAN5C GC09P125762 PBX3 GC09P125856
GH09I125758 Enhancer 1.8 VISTA UCNEbase Ensembl ENCODE 15.3 +12.2 12182 2 PKNOX1 FOXA2 ARID4B FEZF1 RAD21 ZSCAN9 RARA YY1 CREM IKZF2 GC09P125757 PBX3 GC09P125762
GH09I125548 Enhancer 1.6 UCNEbase Ensembl ENCODE dbSUPER 15.7 -196.9 -196926 3.2 SOX13 ESRRA FOXA2 NFIB ARID4B ZNF384 FEZF1 RFX5 YY1 CTBP1 PBX3 LOC51145 LOC102723468 LOC105376272 MAPKAP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PBX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PBX3 gene promoter:

Genomic Locations for PBX3 Gene

Genomic Locations for PBX3 Gene
220,040 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

No Post-translational modifications

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

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

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
UniProtKB/Swiss-Prot Function:
Transcriptional activator that binds the sequence 5-ATCAATCAA-3.

Phenotypes From GWAS Catalog for PBX3 Gene

Gene Ontology (GO) - Molecular Function for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IEA --
GO:0001205 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI --
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:

Animal Model Products

CRISPR Products

Targeted motifs for PBX3 Gene
HOMER Transcription Factor Regulatory Elements motif PBX3
  • Consensus sequence: CCTGTCAATCAN Submotif: canonical Cell Type: GM12878 GEO ID: GSE32465

Inhibitory RNA Products

Clone Products

  • Addgene plasmids 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 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

Gene Ontology (GO) - Biological Process for PBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002087 regulation of respiratory gaseous exchange by neurological system process IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007387 anterior compartment pattern formation TAS 1682799
genes like me logo Genes that share ontologies with PBX3: view

No data available for SIGNOR curated interactions for PBX3 Gene

Drugs & Compounds for PBX3 Gene

No Compound Related Data Available

Transcripts for PBX3 Gene

Unigene Clusters for PBX3 Gene

Pre-B-cell leukemia homeobox 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids 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
ECgene alternative splicing isoforms for

Expression for PBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for PBX3 Gene

Protein tissue co-expression partners for PBX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PBX3 Gene:


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(4.3)
  • Blood(4.3)
  • Nervous system(2.8)
genes like me logo Genes that share expression patterns with PBX3: view

Primer Products

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
(Bos Taurus)
Mammalia PBX3 34
  • 100 (a)
(Monodelphis domestica)
Mammalia PBX3 34
  • 100 (a)
(Ornithorhynchus anatinus)
Mammalia PBX3 34
  • 99 (a)
(Canis familiaris)
Mammalia PBX3 33 34
  • 97.2 (n)
(Mus musculus)
Mammalia Pbx3 33 16 34
  • 96.01 (n)
(Pan troglodytes)
Mammalia PBX3 33 34
  • 96.01 (n)
(Rattus norvegicus)
Mammalia Pbx3 33
  • 95.31 (n)
(Gallus gallus)
Aves PBX3 33 34
  • 91.53 (n)
(Anolis carolinensis)
Reptilia PBX3 34
  • 99 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pbx3 33
  • 83.37 (n)
Str.11416 33
(Danio rerio)
Actinopterygii pbx3a 33 34
  • 74.03 (n)
pbx3b 33
fruit fly
(Drosophila melanogaster)
Insecta exd 35 34
  • 78 (a)
(Caenorhabditis elegans)
Secernentea ceh-20 35 34
  • 65 (a)
ceh-40 35 34
  • 40 (a)
ceh-60 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8721 34
  • 60 (a)
Species where no ortholog for PBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for PBX3 Gene

Paralogs for PBX3 Gene

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

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

Variants for PBX3 Gene

Sequence variations from dbSNP and Humsavar for PBX3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000027756 -- 125,947,899(+) A/G intron_variant
rs1000035835 -- 125,848,270(+) G/A/T intron_variant
rs1000044934 -- 125,807,463(+) G/A intron_variant
rs1000049935 -- 125,937,009(+) C/T intron_variant
rs1000076937 -- 125,851,852(+) T/G intron_variant

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

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

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

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

Disorders for PBX3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PBX3 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
childhood pilocytic astrocytoma
  • pediatric pilocytic astrocytoma
pilocytic astrocytoma
  • grade i astrocytic tumor
leukemia, acute myeloid
  • aml
- 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
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 58
  2. 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 44 58
  3. 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 44 58
  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 44 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58

Products for PBX3 Gene

  • Addgene plasmids for PBX3

Sources for PBX3 Gene

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