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Aliases for HOXC9 Gene

Aliases for HOXC9 Gene

  • Homeobox C9 2 3
  • HOX3B 3 4 6
  • Homeobox Protein Hox-3B 3 4
  • Homeo Box C9 2 3
  • 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

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. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is HOXD10.

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

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

Genomics for HOXC9 Gene

Regulatory Elements for HOXC9 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for HOXC9 Gene

53,994,895 bp from pter
54,003,337 bp from pter
8,443 bases
Plus strand

Genomic View for HOXC9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for HOXC9 Gene at MOPED

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 for HOXC9 Gene

Gene Families for HOXC9 Gene

  • HOXL :Homeoboxes / ANTP class : HOXL subclass

Suggested Antigen Peptide Sequences for HOXC9 Gene

Graphical View of Domain Structure for InterPro Entry



  • P31274
  • Contains 1 homeobox DNA-binding domain.
  • 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

Gene Ontology (GO) - Molecular Function for HOXC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXC9: view

Phenotypes for HOXC9 Gene

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

Animal Models for HOXC9 Gene

MGI Knock Outs for HOXC9:

Animal Model Products

CRISPR Products

miRNA for HOXC9 Gene

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

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HOXC9

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting for HOXC9 Gene

Localization for HOXC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXC9 Gene

Subcellular locations from

Jensen Localization Image for HOXC9 Gene COMPARTMENTS Subcellular localization image for HOXC9 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXC9 Gene

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

Pathways for HOXC9 Gene

SuperPathways for HOXC9 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Homeobox (HOX) Genes in human,mouse,rat
    • Stem Cell Transcription Factors in human,mouse,rat

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:0009952 anterior/posterior pattern specification IEA --
GO:0048704 embryonic skeletal system morphogenesis IEA --
GO:0048706 embryonic skeletal system development --
genes like me logo Genes that share ontologies with HOXC9: view

No data available for Pathways by source for HOXC9 Gene

Transcripts for HOXC9 Gene

mRNA/cDNA for HOXC9 Gene

Unigene Clusters for HOXC9 Gene

Homeobox C9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for HOXC9

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry 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 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 (9.9), Adipose - Subcutaneous (4.5), and Fallopian Tube (4.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for HOXC9 Gene

SOURCE GeneReport for Unigene cluster for HOXC9 Gene Hs.658823

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

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt 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 35
  • 99.87 (n)
  • 100 (a)
HOXC9 36
  • 100 (a)
(Bos Taurus)
Mammalia HOXC9 35
  • 97.69 (n)
  • 99.62 (a)
HOXC9 36
  • 98 (a)
(Canis familiaris)
Mammalia -- 36
  • 42 (a)
(Mus musculus)
Mammalia Hoxc9 35
  • 96.03 (n)
  • 99.62 (a)
Hoxc9 16
Hoxc9 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Hoxc9 35
  • 95.64 (n)
  • 99.62 (a)
(Gallus gallus)
Aves HOXC9 35
  • 75.93 (n)
  • 84.17 (a)
HOXC9 36
  • 83 (a)
(Anolis carolinensis)
Reptilia HOXC9 36
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733557 35
  • 74.9 (n)
  • 84.17 (a)
(Danio rerio)
Actinopterygii hoxc9a 35
  • 67.05 (n)
  • 73.64 (a)
hoxc9a 36
  • 66 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 19 (a)
Species with no ortholog for HOXC9:
  • 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

Selected 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 MAF
rs1047374 -- 54,002,886(+) GTTAG(G/T)TCTAC utr-variant-3-prime
rs1867297 -- 54,003,187(-) CGACC(C/T)AGCCC utr-variant-3-prime
rs58302615 -- 54,003,677(+) TGAGT(A/G)CATGA downstream-variant-500B
rs75955917 -- 54,003,756(+) CTGGC(A/G)GCATT downstream-variant-500B
rs116659696 -- 54,003,014(+) TCGCT(A/G)TATTT utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv826379 CNV Gain 20364138
nsv899100 CNV Loss 21882294
dgv512e1 CNV Complex 17122850
nsv428282 CNV Gain 18775914
nsv899101 CNV Loss 21882294
nsv899102 CNV Loss 21882294

Relevant External Links for HOXC9 Gene

HapMap Linkage Disequilibrium report

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

Disorders for HOXC9 Gene

No disorders were found for HOXC9 Gene.

No data available for UniProtKB/Swiss-Prot for HOXC9 Gene

Publications for HOXC9 Gene

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

Products for HOXC9 Gene

Sources for HOXC9 Gene

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