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Aliases for HOXC9 Gene

Aliases for HOXC9 Gene

  • Homeobox C9 2 3 5
  • Homeobox Protein Hox-3B 3 4
  • Homeo Box C9 2 3
  • HOX3B 3 4
  • Homeobox Protein Hox-C9 3
  • HOX3 3

External Ids for HOXC9 Gene

Previous HGNC Symbols for HOXC9 Gene

  • HOX3
  • HOX3B

Previous GeneCards Identifiers for HOXC9 Gene

  • GC12M054413
  • GC12P054506
  • GC12P054110
  • GC12P052680
  • GC12P054393
  • GC12P054388
  • GC12P051432
  • GC12P053995
  • GC12P053998
  • GC12P054013
  • GC12P054042
  • GC12P054053
  • GC12P054062

Summaries for HOXC9 Gene

Entrez Gene Summary for HOXC9 Gene

  • This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXC9 Gene

HOXC9 (Homeobox C9) is a Protein Coding gene. Among its related pathways are Differentiation of white and brown adipocyte. GO annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXD9.

UniProtKB/Swiss-Prot for HOXC9 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.

Gene Wiki entry for HOXC9 Gene

Additional gene information for HOXC9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXC9 Gene

Genomics for HOXC9 Gene

Regulatory Elements for HOXC9 Gene

Enhancers for HOXC9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12H054323 1.4 Ensembl ENCODE 19 +333.0 332993 8.3 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ATF7 HOXC8 HOXC9 ENSG00000258086 HOXC5 GPR84 SP1 HOXC6 HOXC4 PCBP2
GH12H054354 2.1 FANTOM5 Ensembl ENCODE dbSUPER 10.2 +363.1 363107 6.6 FEZF1 YBX1 YY1 ZNF143 SP3 MCM3 NFYC MEF2D ZNF610 GLIS1 SP1 PCBP2 ENSG00000258344 CBX5 GPR84 ZNF385A MAP3K12 ATF7 LOC100652999 HNRNPA1
GH12H054195 1.5 FANTOM5 Ensembl ENCODE 12.6 +201.8 201781 3.1 HDGF PKNOX1 TBL1XR1 KLF17 ZNF121 GLIS2 ZNF366 SMARCC2 FOS KLF7 HOXC8 HOXC-AS1 HOXC-AS2 HOXC9 HOXC6 MIR196A2 MIR615 HOXC4 HOXC5 LOC102724030
GH12H054215 1.6 FANTOM5 Ensembl ENCODE 11.7 +222.2 222206 2.6 HDGF PKNOX1 ATF1 ARNT SIN3A ZNF2 ETS1 ZNF121 GLIS2 ZNF143 GPR84 HOXC8 HOXC-AS1 HOXC6 HOXC-AS2 HOXC9 HOXC4 HOXC5 ENSG00000257534 FLJ12825
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXC9 on UCSC Golden Path with GeneCards custom track

Promoters for HOXC9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000052274 1105 401 PKNOX1 ATF1 FEZF1 GLI4 ZNF2 ZNF121 KLF7 REST ZNF488 SMARCB1

Genomic Locations for HOXC9 Gene

Genomic Locations for HOXC9 Gene
8,443 bases
Plus strand

Genomic View for HOXC9 Gene

Genes around HOXC9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXC9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXC9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXC9 Gene

Proteins for HOXC9 Gene

  • Protein details for HOXC9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-C9
    Protein Accession:
    Secondary Accessions:
    • B2RCN7
    • Q9H1I0

    Protein attributes for HOXC9 Gene

    260 amino acids
    Molecular mass:
    29248 Da
    Quaternary structure:
    • Interacts with Geminin/GMNN, which inhibits transcriptional activity.

    Three dimensional structures from OCA and Proteopedia for HOXC9 Gene

neXtProt entry for HOXC9 Gene

Post-translational modifications for HOXC9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXC9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXC9 Gene

Domains & Families for HOXC9 Gene

Gene Families for HOXC9 Gene

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

Suggested Antigen Peptide Sequences for HOXC9 Gene

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 HOXC9: view

Function for HOXC9 Gene

Molecular function for HOXC9 Gene

GENATLAS Biochemistry:
homeo box C9(3B),homologous to mouse Hox-3.2,Drosophila abd-B,involved in mouse posterior limb patterning,expressed in posterior limb
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.

Phenotypes From GWAS Catalog for HOXC9 Gene

Gene Ontology (GO) - Molecular Function for HOXC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXC9: view
genes like me logo Genes that share phenotypes with HOXC9: view

Animal Models for HOXC9 Gene

MGI Knock Outs for HOXC9:

miRNA for HOXC9 Gene

miRTarBase miRNAs that target HOXC9
Targeted motifs for HOXC9 Gene
HOMER Transcription Factor Regulatory Elements motif HOXC9
  • Consensus sequence: GGCCATAAATCA Submotif: canonical Cell Type: Ainv15 GEO ID: GSE21812

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for HOXC9 Gene

Localization for HOXC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXC9 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 HOXC9 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA --
GO:0016235 aggresome IDA --
genes like me logo Genes that share ontologies with HOXC9: view

Pathways & Interactions for HOXC9 Gene

genes like me logo Genes that share pathways with HOXC9: view

Pathways by source for HOXC9 Gene

1 BioSystems pathway for HOXC9 Gene

Gene Ontology (GO) - Biological Process for HOXC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0009952 anterior/posterior pattern specification IEA --
GO:0048704 embryonic skeletal system morphogenesis IEA --
genes like me logo Genes that share ontologies with HOXC9: view

No data available for SIGNOR curated interactions for HOXC9 Gene

Drugs & Compounds for HOXC9 Gene

No Compound Related Data Available

Transcripts for HOXC9 Gene

mRNA/cDNA for HOXC9 Gene

Unigene Clusters for HOXC9 Gene

Homeobox C9:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXC9 Gene

No ASD Table

Relevant External Links for HOXC9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXC9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXC9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXC9 Gene

This gene is overexpressed in Muscle - Skeletal (x9.9), Adipose - Subcutaneous (x4.5), and Fallopian Tube (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HOXC9 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXC9 Gene:


SOURCE GeneReport for Unigene cluster for HOXC9 Gene:


Evidence on tissue expression from TISSUES for HOXC9 Gene

  • Eye(4)
genes like me logo Genes that share expression patterns with HOXC9: view

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXC9 Gene

Orthologs for HOXC9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXC9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXC9 33 34
  • 99.87 (n)
(Bos Taurus)
Mammalia HOXC9 33 34
  • 97.69 (n)
(Mus musculus)
Mammalia Hoxc9 33 16 34
  • 96.03 (n)
(Rattus norvegicus)
Mammalia Hoxc9 33
  • 95.64 (n)
(Canis familiaris)
Mammalia -- 34
  • 42 (a)
(Gallus gallus)
Aves HOXC9 33 34
  • 75.93 (n)
(Anolis carolinensis)
Reptilia HOXC9 34
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733557 33
  • 74.9 (n)
(Danio rerio)
Actinopterygii hoxc9a 33 34
  • 67.05 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 19 (a)
Species where no ortholog for HOXC9 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for HOXC9 Gene

Gene Tree for HOXC9 (if available)
Gene Tree for HOXC9 (if available)

Paralogs for HOXC9 Gene

(9) SIMAP similar genes for HOXC9 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with HOXC9: view

Variants for HOXC9 Gene

Sequence variations from dbSNP and Humsavar for HOXC9 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
VAR_036267 A colorectal cancer sample
rs1000377526 -- 54,000,843(+) CGAGG(A/G)GGCGA intron-variant, upstream-variant-2KB
rs1000467328 -- 54,002,349(+) AGCCT(A/G)GCTAA intron-variant
rs1001251239 -- 53,999,595(+) ACGCA(C/T)TTTTA intron-variant, upstream-variant-2KB
rs1001286191 -- 53,999,315(+) TAAAG(G/T)CGCCT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for HOXC9 Gene

Variant ID Type Subtype PubMed ID
esv2759900 CNV gain+loss 17122850
nsv428282 CNV gain 18775914
nsv826379 CNV gain 20364138

Variation tolerance for HOXC9 Gene

Residual Variation Intolerance Score: 43.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.87; 48.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HOXC9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXC9 Gene

Disorders for HOXC9 Gene

Relevant External Links for HOXC9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for HOXC9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for HOXC9 Gene

Publications for HOXC9 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  3. Complete mutation analysis panel of the 39 human HOX genes. (PMID: 11857506) Kosaki K … Matsuo N (Teratology 2002) 3 4 60
  4. Nomenclature for human homeobox genes. (PMID: 1973146) McAlpine PJ … Shows TB (Genomics 1990) 2 3 60
  5. Organization of human class I homeobox genes. (PMID: 2576652) Boncinelli E … Simeone A (Genome 1989) 3 4 60

Products for HOXC9 Gene

Sources for HOXC9 Gene

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