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Aliases for HOXB13 Gene

Aliases for HOXB13 Gene

  • Homeobox B13 2 3 5
  • Homeobox Protein Hox-B13 3
  • Homeo Box B13 2
  • PSGD 3

External Ids for HOXB13 Gene

Previous GeneCards Identifiers for HOXB13 Gene

  • GC17M046514
  • GC17M049284
  • GC17M047145
  • GC17M047278
  • GC17M044158
  • GC17M046802
  • GC17M042171

Summaries for HOXB13 Gene

Entrez Gene Summary for HOXB13 Gene

  • This gene encodes a transcription factor that belongs to the homeobox gene family. Genes of this family are highly conserved among vertebrates and essential for vertebrate embryonic development. This gene has been implicated to play a role in fetal skin development and cutaneous regeneration. In mice, a similar gene was shown to exhibit temporal and spatial colinearity in the main body axis of the embryo, but was not expressed in the secondary axes, which suggests functions in body patterning along the axis. This gene and other HOXB genes form a gene cluster at chromosome the 17q21-22 region. [provided by RefSeq, Jul 2008]

CIViC summary for HOXB13 Gene

GeneCards Summary for HOXB13 Gene

HOXB13 (Homeobox B13) is a Protein Coding gene. Diseases associated with HOXB13 include Prostate Cancer and Spinal Cord Ependymoma. Among its related pathways are Regulation of Androgen receptor activity and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXA13.

UniProtKB/Swiss-Prot for HOXB13 Gene

  • Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds preferentially to methylated DNA (PubMed:28473536).

Gene Wiki entry for HOXB13 Gene

Additional gene information for HOXB13 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXB13 Gene

Genomics for HOXB13 Gene

GeneHancer (GH) Regulatory Elements for HOXB13 Gene

Promoters and enhancers for HOXB13 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
GH17J048728 Promoter/Enhancer 1.7 EPDnew ENCODE dbSUPER 650.7 +0.3 312 0.8 PKNOX1 SIN3A FEZF1 GLI4 ZNF2 GLIS2 ZNF213 KLF7 SP3 REST HOXB13 UBE2Z SP2 ENSG00000264701 CDK5RAP3 SCRN2 ENSG00000266601 CBX1 SUMO2P17 ENSG00000230532
GH17J048994 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 10.6 -270.3 -270270 10.8 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 IGF2BP1 ENSG00000250838 ENSG00000262837 UBE2Z FAM117A FLJ45513 ENSG00000238804 SUMO2P17 KAT7 PRAC1
GH17J048623 Promoter/Enhancer 2 EPDnew FANTOM5 ENCODE dbSUPER 9.5 +102.5 102528 6.4 HDGF PKNOX1 SMAD1 ARNT SIN3A FEZF1 YY1 POLR2B ZNF766 CBX5 HOXB9 ENSG00000264701 ENSG00000230532 SUMO2P17 SP2 CDK5RAP3 PRAC2 PRAC1 HOXB13 LOC105371811
GH17J048840 Promoter/Enhancer 1.3 Ensembl ENCODE 10.4 -112.8 -112761 3.9 HDGF BMI1 BATF IRF4 RAD21 ZNF766 ATF7 ETV6 BCLAF1 IKZF2 ATP5MC1 TTLL6 PRAC1 PRAC2 HOXB13 LOC105371811 CALCOCO2 UBE2Z FAM117A GC17P048882
GH17J048869 Enhancer 1.2 Ensembl ENCODE 10.7 -142.5 -142528 5.1 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 SP5 NFYC MXD4 ATP5MC1 TTLL6 CALCOCO2 UBE2Z ENSG00000230532 HOXB13 PRAC1 PRAC2 SUMO2P17 LOC105371811
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXB13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXB13 gene promoter:
  • p53
  • PPAR-gamma2
  • PPAR-gamma1
  • MEF-2A
  • aMEF-2
  • LUN-1
  • RSRFC4
  • AREB6
  • Evi-1
  • AML1a

Genomic Locations for HOXB13 Gene

Genomic Locations for HOXB13 Gene
4,416 bases
Minus strand
4,416 bases
Minus strand

Genomic View for HOXB13 Gene

Genes around HOXB13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXB13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXB13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXB13 Gene

Proteins for HOXB13 Gene

  • Protein details for HOXB13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-B13
    Protein Accession:
    Secondary Accessions:
    • B2R878
    • Q96QM4
    • Q99810

    Protein attributes for HOXB13 Gene

    284 amino acids
    Molecular mass:
    30676 Da
    Quaternary structure:
    • Heterodimer with MEIS1 (PubMed:28473536). Heterodimer with MEIS2 (Ref.8).

    Three dimensional structures from OCA and Proteopedia for HOXB13 Gene

neXtProt entry for HOXB13 Gene

Post-translational modifications for HOXB13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXB13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXB13 Gene

Domains & Families for HOXB13 Gene

Gene Families for HOXB13 Gene

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

Protein Domains for HOXB13 Gene

Suggested Antigen Peptide Sequences for HOXB13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Abd-B homeobox family.
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXB13: view

Function for HOXB13 Gene

Molecular function for HOXB13 Gene

UniProtKB/Swiss-Prot Function:
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds preferentially to methylated DNA (PubMed:28473536).
GENATLAS Biochemistry:
homeo box B13

Phenotypes From GWAS Catalog for HOXB13 Gene

Gene Ontology (GO) - Molecular Function for HOXB13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IC --
GO:0003677 DNA binding IEA --
GO:0043565 sequence-specific DNA binding IDA 23332764
genes like me logo Genes that share ontologies with HOXB13: view
genes like me logo Genes that share phenotypes with HOXB13: view

Animal Models for HOXB13 Gene

MGI Knock Outs for HOXB13:

Animal Model Products

Targeted motifs for HOXB13 Gene
HOMER Transcription Factor Regulatory Elements motif HOXB13
  • Consensus sequence: TTTTATKRGG Submotif: canonical Cell Type: ProstateTumor GEO ID: GSE56288

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for HOXB13 Gene

Localization for HOXB13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXB13 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 HOXB13 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXB13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with HOXB13: view

Pathways & Interactions for HOXB13 Gene

genes like me logo Genes that share pathways with HOXB13: view

Pathways by source for HOXB13 Gene

1 BioSystems pathway for HOXB13 Gene
1 Cell Signaling Technology pathway for HOXB13 Gene

Gene Ontology (GO) - Biological Process for HOXB13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IDA 15126340
GO:0001525 angiogenesis IEP 17972163
GO:0002009 morphogenesis of an epithelium IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with HOXB13: view

No data available for SIGNOR curated interactions for HOXB13 Gene

Drugs & Compounds for HOXB13 Gene

No Compound Related Data Available

Transcripts for HOXB13 Gene

mRNA/cDNA for HOXB13 Gene

(1) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(118) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXB13 Gene

Homeobox B13:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXB13 Gene

No ASD Table

Relevant External Links for HOXB13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXB13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXB13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXB13 Gene

This gene is overexpressed in Prostate (x39.8).

Protein differential expression in normal tissues from HIPED for HOXB13 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HOXB13 Gene

Protein tissue co-expression partners for HOXB13 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXB13 Gene:


SOURCE GeneReport for Unigene cluster for HOXB13 Gene:


Evidence on tissue expression from TISSUES for HOXB13 Gene

  • Intestine(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXB13 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • reproductive
Head and neck:
  • brain
  • cerebellum
  • head
  • prostate
  • spinal cord
genes like me logo Genes that share expression patterns with HOXB13: view

No data available for mRNA Expression by UniProt/SwissProt for HOXB13 Gene

Orthologs for HOXB13 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXB13 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXB13 34 33
  • 99.53 (n)
(Bos Taurus)
Mammalia HOXB13 34 33
  • 89.55 (n)
(Rattus norvegicus)
Mammalia Hoxb13 33
  • 87.91 (n)
(Mus musculus)
Mammalia Hoxb13 16 34 33
  • 87.56 (n)
(Monodelphis domestica)
Mammalia HOXB13 34
  • 86 (a)
(Canis familiaris)
Mammalia HOXB13 34 33
  • 85.04 (n)
(Ornithorhynchus anatinus)
Mammalia HOXB13 34
  • 80 (a)
(Gallus gallus)
Aves HOXB13 34 33
  • 67.06 (n)
(Anolis carolinensis)
Reptilia HOXB13 34
  • 72 (a)
(Danio rerio)
Actinopterygii hoxb13a 34 33
  • 64.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta Abd-B 34
  • 15 (a)
Species where no ortholog for HOXB13 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOXB13 Gene

Gene Tree for HOXB13 (if available)
Gene Tree for HOXB13 (if available)
Evolutionary constrained regions (ECRs) for HOXB13: view image

Paralogs for HOXB13 Gene

(6) SIMAP similar genes for HOXB13 Gene using alignment to 3 proteins:

  • Q4KR72_HUMAN
genes like me logo Genes that share paralogs with HOXB13: view

Variants for HOXB13 Gene

Sequence variations from dbSNP and Humsavar for HOXB13 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1014715541 uncertain-significance, Hereditary cancer-predisposing syndrome 48,727,035(-) C/A/G/T coding_sequence_variant, missense_variant
rs138213197 pathogenic, risk-factor, likely-pathogenic, Prostate cancer susceptibility, not provided, Hereditary cancer-predisposing syndrome, Prostate cancer (PC) [MIM:176807] 48,728,343(-) C/T coding_sequence_variant, missense_variant
rs138675188 benign, likely-benign, not specified, Hereditary cancer-predisposing syndrome 48,726,910(-) C/T coding_sequence_variant, synonymous_variant
rs139475791 uncertain-significance, Hereditary cancer-predisposing syndrome 48,726,996(-) G/A/C coding_sequence_variant, missense_variant
rs143945091 likely-benign, Hereditary cancer-predisposing syndrome 48,728,027(-) G/A coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXB13 Gene

Variant ID Type Subtype PubMed ID
esv2758694 CNV gain 17122850

Variation tolerance for HOXB13 Gene

Residual Variation Intolerance Score: 25.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.00; 20.65% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXB13 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 HOXB13 Gene

Disorders for HOXB13 Gene

MalaCards: The human disease database

(6) MalaCards diseases for HOXB13 Gene - From: HGMD, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
prostate cancer
  • prostate cancer, susceptibility to
spinal cord ependymoma
  • ependymal neoplasm of the spinal cord
spinal cord glioma
  • glial neoplasm spinal cord
spinal cancer
  • spinal cord cancer
myxopapillary ependymoma
  • ependymoma myxopapillary
- elite association - COSMIC cancer census association via MalaCards


  • Prostate cancer (PC) [MIM:176807]: A malignancy originating in tissues of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. {ECO:0000269 PubMed:22236224, ECO:0000269 PubMed:22714738, ECO:0000269 PubMed:23064873, ECO:0000269 PubMed:23292082, ECO:0000269 PubMed:25629170, ECO:0000269 PubMed:27424772}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for HOXB13

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 HOXB13: view

No data available for Genatlas for HOXB13 Gene

Publications for HOXB13 Gene

  1. Modulation of the human homeobox genes PRX-2 and HOXB13 in scarless fetal wounds. (PMID: 9665387) Stelnicki EJ … Largman C (The Journal of investigative dermatology 1998) 2 3 4 58
  2. Hoxb-13: a new Hox gene in a distant region of the HOXB cluster maintains colinearity. (PMID: 8756292) Zeltser L … Heintz N (Development (Cambridge, England) 1996) 2 3 4 58
  3. Impact of cytosine methylation on DNA binding specificities of human transcription factors. (PMID: 28473536) Yin Y … Taipale J (Science (New York, N.Y.) 2017) 3 4 58
  4. Recurrent HOXB13 mutations in the Dutch population do not associate with increased breast cancer risk. (PMID: 27424772) Liu J … Hollestelle A (Scientific reports 2016) 3 4 58
  5. Imputation of the rare HOXB13 G84E mutation and cancer risk in a large population-based cohort. (PMID: 25629170) Hoffmann TJ … Witte JS (PLoS genetics 2015) 3 4 58

Products for HOXB13 Gene

Sources for HOXB13 Gene

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