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HOXC5 Gene(Protein Coding)

Homeobox C5

GCID:
GC12P054060
GIFtS:
48
Genes Participants
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Aliases for HOXC5 Gene

Aliases for HOXC5 Gene

  • Homeobox C5 2 3 5
  • Homeobox Protein Hox-3D 3 4
  • Homeobox Protein CP11 3 4
  • Homeo Box C5 2 3
  • HOX3D 3 4
  • Homeobox Protein Hox-C5 3
  • 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
  • GC12P054040
  • GC12P054051

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. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and sequence-specific DNA binding. An important paralog of this gene is HOXA5.

UniProtKB/Swiss-Prot 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

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXC5 Gene

Genomics for HOXC5 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HOXC5 Gene

Enhancers for HOXC5 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
GH12G053971 2.1 FANTOM5 Ensembl ENCODE dbSUPER 23.2 -26.6 -26610 36.8 CREB3L1 AGO1 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 ZNF263 SP3 ZNF740 MAP3K12 ENSG00000258344 LOC100652999 HOXC8 HOXC5 SP1 HOTAIR CBX5 HOXC4
GH12G053962 1.4 ENCODE dbSUPER 24.5 -50.2 -50174 7.5 CREB3L1 DMAP1 FEZF1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 MCM3 SP3 HOXC8 HOXC9 MAP3K12 HOXC5 HOTAIR HOXC6 HOXC4 SP1 SPRYD3 ENSG00000258086
GH12G054354 2.1 FANTOM5 Ensembl ENCODE dbSUPER 12 +341.2 341150 6.6 FEZF1 YBX1 YY1 ZNF143 ZNF263 SP3 MCM3 NFYC TBX21 MEF2D MAP3K12 CBX5 GPR84 ZNF385A HOXC8 HOXC9 SP1 ENSG00000258086 ENSG00000258344 MIR148B
GH12G054215 1.6 FANTOM5 Ensembl ENCODE 11.2 +200.2 200249 2.6 HDGF PKNOX1 ATF1 ARNT E2F7 SIN3A ZNF2 ETS1 ZNF121 GLIS2 GPR84 HOXC8 HOXC-AS1 HOXC6 HOXC-AS2 HOXC9 HOXC4 HOXC5 ENSG00000257534 FLJ12825
GH12G054195 1.5 FANTOM5 Ensembl ENCODE 11.8 +179.8 179824 3.1 HDGF PKNOX1 KLF17 ZNF121 GLIS2 ZNF366 SMARCC2 FOS KLF7 KDM4B MAP3K12 HOXC8 HOXC-AS1 HOXC-AS2 HOXC9 HOXC6 MIR196A2 MIR615 HOXC4 HOXC5
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HOXC5 on UCSC Golden Path with GeneCards custom track

Promoters for HOXC5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000052281 648 1801 HDGF PKNOX1 CREB3L1 ARNT SIN3A FEZF1 ZNF2 ZNF207 FOS ZNF263

Transcription factor binding sites by QIAGEN in the HOXC5 gene promoter:

Genomic Location for HOXC5 Gene

Chromosome:
12
Start:
54,016,852 bp from pter
End:
54,035,361 bp from pter
Size:
18,510 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 Structure • Gene Density

RefSeq DNA sequence for HOXC5 Gene

Proteins for HOXC5 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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:

Protein Domains for HOXC5 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HOXC5 Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HOXC5 Gene

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
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 HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding TAS,IEA --
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

Inhibitory RNA Products

Flow Cytometry Products

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

Nucleus.

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

Gene Ontology (GO) - Cellular Components for HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
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

SuperPathways for HOXC5 Gene

PathCards logo More details on SuperPathways for HOXC5
No Data Available

Gene Ontology (GO) - Biological Process for HOXC5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS 1346761
GO:0007275 multicellular organism development IEA --
GO:0009952 anterior/posterior pattern specification 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

Products:

  1. Drug
No Compound Related Data Available

Transcripts for HOXC5 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HOXC5 Gene

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

Inhibitory RNA Products

Flow Cytometry Products

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

Products:

  1. Primer

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

mRNA expression in normal human tissues for HOXC5 Gene
mRNA expression by BioGPS for HOXC5 GenemRNA expression by GTEx 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

Primer Products

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
cow
(Bos Taurus)
 Mammalia HOXC5 34
  • 98.5 (n)
mouse
(Mus musculus)
 Mammalia Hoxc5 34 16 35
  • 98.5 (n)
rat
(Rattus norvegicus)
 Mammalia Hoxc5 34
  • 98.5 (n)
dog
(Canis familiaris)
 Mammalia HOXC5 34
  • 97.45 (n)
chimpanzee
(Pan troglodytes)
 Mammalia HOXC5 34 35
  • 97.11 (n)
lizard
(Anolis carolinensis)
 Reptilia -- 35
  • 65 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia hoxc5 34
  • 73.94 (n)
zebrafish
(Danio rerio)
 Actinopterygii hoxc5a 34 35
  • 58.45 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Scr 36
  • 75 (a)
ftz 35
  • 18 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 35
  • 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)

Paralogs for HOXC5 Gene

Paralogs for HOXC5 Gene

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

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 Sequence Context AA Info Type
rs1000059230 -- 54,014,986(+) TCAAA(A/G)TGGCT upstream-variant-2KB
rs1000137595 -- 54,028,295(+) TTACT(G/T)TCAAA intron-variant, upstream-variant-2KB
rs1000191769 -- 54,028,030(+) CTTCC(C/G)TTGGA intron-variant, upstream-variant-2KB
rs1000269134 -- 54,022,527(+) TCTCT(C/T)TTTGC intron-variant
rs1000396997 -- 54,033,853(+) GGAGC(C/G)CGGGG intron-variant, upstream-variant-2KB

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)

Relevant External Links for HOXC5 Gene

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

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

Disorders for HOXC5 Gene

Relevant External Links for HOXC5

Genetic Association Database (GAD)
HOXC5
Human Genome Epidemiology (HuGE) Navigator
HOXC5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HOXC5

No disorders were found for HOXC5 Gene.

No data available for MalaCards , 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 L.G. … Sun K.L. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2005) 3 22 46 64
  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. (EMBO J. 1992) 3 4 22 64
  3. Vertebrate homeobox gene nomenclature. (PMID: 1358459) Scott M.P. (Cell 1992) 2 3 64
  4. Nomenclature for human homeobox genes. (PMID: 1973146) McAlpine P.J. … Shows T.B. (Genomics 1990) 2 3 64
  5. Organization of human class I homeobox genes. (PMID: 2576652) Boncinelli E. … Simeone A. (Genome 1989) 3 4 64

Products for HOXC5 Gene

  • Addgene plasmids for HOXC5

Sources for HOXC5 Gene

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