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. Thi... See more...

Aliases for HOXC5 Gene

Aliases for HOXC5 Gene

  • Homeobox C5 2 3 5
  • Homeobox Protein Hox-3D 3 4
  • Homeobox Protein Hox-C5 3 4
  • Homeobox Protein CP11 3 4
  • Homeo Box C5 2 3
  • HOX3D 3 4
  • CP11 3
  • HOX3 3

External Ids for HOXC5 Gene

Previous HGNC Symbols for HOXC5 Gene

  • HOX3D
  • HOX3

Previous GeneCards Identifiers for HOXC5 Gene

  • GC12M054391
  • GC12P054539
  • GC12P054129
  • GC12P052713
  • GC12P054411
  • GC12P054379
  • GC12P051449
  • GC12P054471
  • GC12P054018
  • GC12P054115
  • GC12P054124
  • GC12P054040
  • GC12P054051
  • GC12P054060
  • GC12P054072
  • GC12P054084
  • GC12P054093
  • GC12P054104

Summaries for HOXC5 Gene

Entrez Gene Summary for HOXC5 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, HOXC5, is one of several homeobox HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Two alternatively spliced variants have been described for HOXC5. The transcript variant which includes the shared exon apparently doesn't encode a protein. The protein-coding transcript variant contains gene-specific exons only. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXC5 Gene

HOXC5 (Homeobox C5) is a Protein Coding gene. Diseases associated with HOXC5 include Lymphoma, Non-Hodgkin, Familial. 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 HOXB5.

UniProtKB/Swiss-Prot Summary for HOXC5 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 HOXC5 Gene

Additional gene information for HOXC5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HOXC5 Gene

Genomics for HOXC5 Gene

GeneHancer (GH) Regulatory Elements for HOXC5 Gene

Promoters and enhancers for HOXC5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J053971 Promoter/Enhancer 2.7 VISTA EPDnew FANTOM5 Ensembl ENCODE dbSUPER 752.9 -13.5 -13540 63 ZNF785 SIN3A ZBTB40 CTCF SREBF1 ZBTB6 RBPJ SMARCE1 POLR2A TCF7L2 HOXC8 HOXC11 HOXC4 HOXC9 HOXC6 HOXC10 HOXC5 HNRNPA1 ZNF740 PCBP2
GH12J054035 Promoter 0.4 EPDnew 750.4 +18.3 18292 0.1 EZH2 MIR615 HOXC5 piR-30124 NONHSAG011269.2 ENSG00000273046 HOXC4
GH12J053250 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 32.7 -764.8 -764801 3 CTCF SREBF1 ZBTB6 POLR2A TCF7L2 USF2 NR2F6 HCFC1 MYC ZNF701 MFSD5 piR-30800 lnc-RARG-1 piR-48880 ATF7 SP1 HOXC5 PCBP2 ZNF740 AAAS
GH12J054350 Promoter/Enhancer 2.4 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 24.1 +338.7 338739 11.2 ZNF785 SIN3A ZBTB40 SP1 CTCF ZBTB6 MLX FOXA1 RBPJ SMARCE1 ENSG00000258086 ENSG00000258137 LOC102724050 SP1 PCBP2 CBX5 ATF7 ENSG00000258344 HNRNPA1 GPR84
GH12J053320 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 22 -693.5 -693451 6.4 ZNF785 SIN3A SP1 ZBTB40 CTCF SREBF1 ZBTB6 RBPJ POLR2A TCF7L2 AAAS lnc-SP7-1 piR-40339 piR-45394 SP1 PCBP2 ATF7 ESPL1 MAP3K12 ENSG00000258344
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXC5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXC5 gene promoter:
  • c-Ets-1
  • Egr-3
  • Egr-4
  • FOXL1
  • Pax-5
  • Sp1

Genomic Locations for HOXC5 Gene

Genomic Locations for HOXC5 Gene
chr12:54,016,852-54,035,361
(GRCh38/hg38)
Size:
18,510 bases
Orientation:
Plus strand
chr12:54,410,642-54,429,145
(GRCh37/hg19)
Size:
18,504 bases
Orientation:
Plus strand

Genomic View for HOXC5 Gene

Genes around HOXC5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXC5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXC5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXC5 Gene

Proteins for HOXC5 Gene

  • Protein details for HOXC5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q00444-HXC5_HUMAN
    Recommended name:
    Homeobox protein Hox-C5
    Protein Accession:
    Q00444

    Protein attributes for HOXC5 Gene

    Size:
    222 amino acids
    Molecular mass:
    24976 Da
    Quaternary structure:
    No Data Available

neXtProt entry for HOXC5 Gene

Post-translational modifications for HOXC5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXC5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXC5 Gene

Domains & Families for HOXC5 Gene

Gene Families for HOXC5 Gene

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

Suggested Antigen Peptide Sequences for HOXC5 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein Hox-3D (HXC5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q00444

UniProtKB/Swiss-Prot:

HXC5_HUMAN :
  • Belongs to the Antp homeobox family.
Family:
  • Belongs to the Antp homeobox family.
genes like me logo Genes that share domains with HOXC5: view

Function for HOXC5 Gene

Molecular function for HOXC5 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.
GENATLAS Biochemistry:
homeo box C5(3D),homologous to mouse Hox-3.4,Drosophila antp,Ubx,abd-A ,expressed in first trimester trophoblast,involved in mouse anterior limb patterning, expressed in anterior limb

Phenotypes From GWAS Catalog for HOXC5 Gene

Gene Ontology (GO) - Molecular Function for HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity TAS 1346761
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXC5: view
genes like me logo Genes that share phenotypes with HOXC5: view

Animal Models for HOXC5 Gene

MGI Knock Outs for HOXC5:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXC5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for HOXC5 Gene

Localization for HOXC5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXC5 Gene

Subcellular locations from

COMPARTMENTS
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 HOXC5 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with HOXC5: view

Pathways & Interactions for HOXC5 Gene

PathCards logo

SuperPathways for HOXC5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II TAS 1346761
GO:0007275 multicellular organism development IEA --
GO:0009952 anterior/posterior pattern specification IBA,IEA 21873635
GO:0048706 embryonic skeletal system development IEA --
genes like me logo Genes that share ontologies with HOXC5: view

No data available for Pathways by source and SIGNOR curated interactions for HOXC5 Gene

Drugs & Compounds for HOXC5 Gene

No Compound Related Data Available

Transcripts for HOXC5 Gene

mRNA/cDNA for HOXC5 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(228) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HOXC5

Alternative Splicing Database (ASD) splice patterns (SP) for HOXC5 Gene

No ASD Table

Relevant External Links for HOXC5 Gene

GeneLoc Exon Structure for
HOXC5
ECgene alternative splicing isoforms for
HOXC5

Expression for HOXC5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXC5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXC5 Gene

This gene is overexpressed in Fallopian Tube (x6.5) and Ovary (x4.2).

NURSA nuclear receptor signaling pathways regulating expression of HOXC5 Gene:

HOXC5
genes like me logo Genes that share expression patterns with HOXC5: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXC5 Gene

Orthologs for HOXC5 Gene

This gene was present in the common ancestor of animals.

Orthologs for HOXC5 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Hoxc5 17 33 32
  • 98.5 (n)
rat
(Rattus norvegicus)
Mammalia Hoxc5 32
  • 98.5 (n)
cow
(Bos Taurus)
Mammalia HOXC5 32
  • 98.5 (n)
dog
(Canis familiaris)
Mammalia HOXC5 32
  • 97.45 (n)
chimpanzee
(Pan troglodytes)
Mammalia HOXC5 33 32
  • 97.11 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 65 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia hoxc5 32
  • 73.94 (n)
zebrafish
(Danio rerio)
Actinopterygii hoxc5a 33 32
  • 58.45 (n)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Scr 34
  • 75 (a)
ftz 33
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 33 (a)
OneToMany
Species where no ortholog for HOXC5 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)
  • chicken (Gallus gallus)
  • 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)
  • 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 HOXC5 Gene

ENSEMBL:
Gene Tree for HOXC5 (if available)
TreeFam:
Gene Tree for HOXC5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HOXC5: view image

Paralogs for HOXC5 Gene

(14) SIMAP similar genes for HOXC5 Gene using alignment to 1 proteins:

  • HXC5_HUMAN
genes like me logo Genes that share paralogs with HOXC5: view

Variants for HOXC5 Gene

Sequence variations from dbSNP and Humsavar for HOXC5 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000059230 -- 54,014,986(+) G/A upstream_transcript_variant
rs1000137595 -- 54,028,295(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000191769 -- 54,028,030(+) C/G genic_upstream_transcript_variant, intron_variant
rs1000269134 -- 54,022,527(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000396997 -- 54,033,853(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HOXC5 Gene

Variant ID Type Subtype PubMed ID
esv2672088 CNV deletion 23128226
esv2759900 CNV gain+loss 17122850
nsv428282 CNV gain 18775914
nsv558998 CNV loss 21841781
nsv826379 CNV gain 20364138
nsv832418 CNV loss 17160897

Variation tolerance for HOXC5 Gene

Residual Variation Intolerance Score: 45.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.09; 38.19% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXC5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HOXC5

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXC5 Gene

Disorders for HOXC5 Gene

MalaCards: The human disease database

(1) MalaCards diseases for HOXC5 Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
lymphoma, non-hodgkin, familial
  • non-hodgkin lymphoma; nhl
- elite association - COSMIC cancer census association via MalaCards
Search HOXC5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for HOXC5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXC5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXC5 Gene

Publications for HOXC5 Gene

  1. Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease. (PMID: 16215934) Gong LG … Sun KL (Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2005) 3 23 43 56
  2. The upstream region of the human homeobox gene HOX3D is a target for regulation by retinoic acid and HOX homeoproteins. (PMID: 1346761) Arcioni L … Mavilio F (The EMBO journal 1992) 3 4 23 56
  3. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott MP (Cell 1992) 2 3 56
  4. Nomenclature for human homeobox genes. (PMID: 1973146) McAlpine PJ … Shows TB (Genomics 1990) 2 3 56
  5. Organization of human class I homeobox genes. (PMID: 2576652) Boncinelli E … Simeone A (Genome 1989) 3 4 56

Products for HOXC5 Gene

Sources for HOXC5 Gene