Free for academic non-profit institutions. Other users need a Commercial license

Aliases for HOXC12 Gene

Subcategory (RNA class) for HOXC12 Gene


Aliases for HOXC12 Gene

  • Homeobox C12 2 3 5
  • Homeobox Protein Hox-3F 3 4
  • Homeo Box C12 2 3
  • HOC3F 3 4
  • HOX3F 3 4
  • Homeobox Protein Hox-C12 3
  • Homeo Box 3F 3
  • HOX3 3

External Ids for HOXC12 Gene

ORGUL Members for HOXC12 Gene

Previous HGNC Symbols for HOXC12 Gene

  • HOX3
  • HOX3F
  • HOC3F

Previous GeneCards Identifiers for HOXC12 Gene

  • GC12U990037
  • GC12P054461
  • GC12P054065
  • GC12P052634
  • GC12P054349
  • GC12P051386
  • GC12P054354
  • GC12P054358

Summaries for HOXC12 Gene

Entrez Gene Summary for HOXC12 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 HOXC12 Gene

HOXC12 (Homeobox C12) is a Protein Coding gene, and is affiliated with the lncRNA class. Diseases associated with HOXC12 include Clubfoot. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXD12.

UniProtKB/Swiss-Prot for HOXC12 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 HOXC12 Gene

Additional gene information for HOXC12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXC12 Gene

Genomics for HOXC12 Gene

GeneHancer (GH) Regulatory Elements for HOXC12 Gene

Promoters and enhancers for HOXC12 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
GH12I053954 Promoter 0.8 EPDnew 550.8 +0.1 50 0.1 USF1 SUZ12 CTBP2 EZH2 GC12P053956 GC12P053957 HOXC12 LOC105369775
GH12I053971 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.1 +35.4 35409 36.8 FEZF1 DMAP1 IRF4 ZNF213 ZNF416 ZNF143 ZNF548 SP3 NFYC ZNF610 HOXC11 HOXC9 HOXC6 HOXC10 GC12P054010 GC12P054044 MIR196A2 HNRNPA1 ZNF740 ENSG00000258344
GH12I054377 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 6 +424.3 424346 2.4 HDGF PKNOX1 ARNT ARID4B SIN3A ZNF2 ZNF213 ZNF207 ZNF143 KLF13 ENSG00000258086 HOXC5 MIR148B RNU6-950P COPZ1 HOXC8 ITGA5 HOXC9 HOXC12 ZNF385A
GH12I054373 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 5.9 +420.6 420588 4.6 KLF1 PKNOX1 ZSCAN4 KLF17 ZIC2 ZFHX2 ZNF316 GLIS2 PRDM10 MAFK MIR148B RNU6-950P COPZ1 ITGA5 ZNF385A HOXC12 HNRNPA1 GPR84 LOC102724050 ENSG00000258086
GH12I054050 Enhancer 0.6 FANTOM5 1.9 +95.7 95672 0.2 MAZ RNF2 TSHZ1 ZNF843 BCL11B ZBTB7A BCL11A ZNF366 ZSCAN16 PATZ1 ATP5MC2 HOXC11 HOXC12 ATF7 FLJ12825 GC12P054078 PIR31123 HOXC4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HOXC12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXC12 gene promoter:

Genomic Locations for HOXC12 Gene

Genomic Locations for HOXC12 Gene
4,123 bases
Plus strand

Genomic View for HOXC12 Gene

Genes around HOXC12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXC12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXC12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXC12 Gene

Proteins for HOXC12 Gene

  • Protein details for HOXC12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-C12
    Protein Accession:
    Secondary Accessions:
    • Q9BXJ6

    Protein attributes for HOXC12 Gene

    282 amino acids
    Molecular mass:
    30171 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXC12 Gene

Post-translational modifications for HOXC12 Gene

No Post-translational modifications

Other Protein References for HOXC12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXC12 Gene

Domains & Families for HOXC12 Gene

Gene Families for HOXC12 Gene

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

Suggested Antigen Peptide Sequences for HOXC12 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 HOXC12: view

Function for HOXC12 Gene

Molecular function for HOXC12 Gene

GENATLAS Biochemistry:
homeo box C12(3F)
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 HOXC12 Gene

Gene Ontology (GO) - Molecular Function for HOXC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXC12: view
genes like me logo Genes that share phenotypes with HOXC12: view

Animal Models for HOXC12 Gene

MGI Knock Outs for HOXC12:

Animal Model Products

CRISPR Products

miRNA for HOXC12 Gene

miRTarBase miRNAs that target HOXC12

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXC12 Gene

Localization for HOXC12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXC12 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 HOXC12 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXC12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with HOXC12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HOXC12 Gene

Pathways & Interactions for HOXC12 Gene

SuperPathways for HOXC12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HOXC12 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 --
genes like me logo Genes that share ontologies with HOXC12: view

No data available for Pathways by source and SIGNOR curated interactions for HOXC12 Gene

Drugs & Compounds for HOXC12 Gene

No Compound Related Data Available

Transcripts for HOXC12 Gene

mRNA/cDNA for HOXC12 Gene

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

Unigene Clusters for HOXC12 Gene

Homeobox C12:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXC12 Gene

No ASD Table

Relevant External Links for HOXC12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXC12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXC12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXC12 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x18.2), Artery - Tibial (x10.4), Skin - Not Sun Exposed (Suprapubic) (x9.4), and Adipose - Subcutaneous (x7.4).

Protein differential expression in normal tissues from HIPED for HOXC12 Gene

This gene is overexpressed in Bone (32.2), Spleen (25.0), and Testis (11.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HOXC12 Gene

Protein tissue co-expression partners for HOXC12 Gene

NURSA nuclear receptor signaling pathways regulating expression of HOXC12 Gene:


SOURCE GeneReport for Unigene cluster for HOXC12 Gene:

genes like me logo Genes that share expression patterns with HOXC12: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXC12 Gene

Orthologs for HOXC12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXC12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXC12 33 34
  • 98.57 (n)
(Bos Taurus)
Mammalia HOXC12 33 34
  • 95.1 (n)
(Ornithorhynchus anatinus)
Mammalia HOXC12 34
  • 95 (a)
(Canis familiaris)
Mammalia HOXC12 33 34
  • 92.61 (n)
(Rattus norvegicus)
Mammalia Hoxc12 33
  • 90.12 (n)
(Mus musculus)
Mammalia Hoxc12 33 16 34
  • 90 (n)
(Gallus gallus)
Aves HOXC12 33 34
  • 73.99 (n)
(Anolis carolinensis)
Reptilia HOXC12 34
  • 99 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxc12 33
  • 71.28 (n)
African clawed frog
(Xenopus laevis)
Amphibia hoxc12-A 33
(Danio rerio)
Actinopterygii hoxc12a 33 34
  • 66.79 (n)
hoxc12b 34
  • 53 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 16 (a)
Species where no ortholog for HOXC12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 HOXC12 Gene

Gene Tree for HOXC12 (if available)
Gene Tree for HOXC12 (if available)

Paralogs for HOXC12 Gene

(1) SIMAP similar genes for HOXC12 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with HOXC12: view

Variants for HOXC12 Gene

Sequence variations from dbSNP and Humsavar for HOXC12 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000727625 -- 53,957,040(+) G/A/T downstream_transcript_variant
rs1001086354 -- 53,956,829(+) G/C downstream_transcript_variant
rs1002566040 -- 53,956,360(+) C/A/G coding_sequence_variant, missense_variant, synonymous_variant
rs1002849613 -- 53,955,293(+) G/A coding_sequence_variant, missense_variant
rs1003793257 -- 53,955,448(+) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXC12 Gene

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

Variation tolerance for HOXC12 Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.64; 45.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXC12 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 HOXC12 Gene

Disorders for HOXC12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HOXC12 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
  • congenital clubfoot
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOXC12

genes like me logo Genes that share disorders with HOXC12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXC12 Gene

Publications for HOXC12 Gene

  1. Complete mutation analysis panel of the 39 human HOX genes. (PMID: 11857506) Kosaki K … Matsuo N (Teratology 2002) 3 4 58
  2. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott MP (Cell 1992) 2 3 58
  3. Nomenclature for human homeobox genes. (PMID: 1973146) McAlpine PJ … Shows TB (Genomics 1990) 2 3 58
  4. The human HOX gene family. (PMID: 2574852) Acampora D … Boncinelli E (Nucleic acids research 1989) 3 4 58
  5. Deletions of 5' HOXC genes are associated with lower extremity malformations, including clubfoot and vertical talus. (PMID: 26729820) Alvarado DM … Gurnett CA (Journal of medical genetics 2016) 3 58

Products for HOXC12 Gene

Sources for HOXC12 Gene

Loading form....