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HOXC13 (homeobox C13)

Written2009-06Toshiyuki Yamada, Shigeki Tsuchida
Department of Biochemistry, Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-Cho, Hirosaki 036-8562, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias_namesHOX3
HOX3G
homeo box C13
Other alias
HGNC (Hugo) HOXC13
LocusID (NCBI) 3229
Atlas_Id 473
Location 12q13.13  [Link to chromosome band 12q13]
Location_base_pair Starts at 54332576 and ends at 54340328 bp from pter ( according to hg19-Feb_2009)  [Mapping HOXC13.png]
Fusion genes
(updated 2016)
HOXC13 (12q13.13) / NUP98 (11p15.4)NUP98 (11p15.4) / HOXC13 (12q13.13)

DNA/RNA

Description Spans around 7.7 kb genomic region, contains 2 exons, homeodomain is located in exon 2.
Transcription Transcript; 2.2 kb, open reading frame; 990 bp.

Protein

 
Description 330 amino acids, DNA binding protein with a 60 aa of homeodomain (helix-turn-helix domain) in the C-terminal.
Expression In nail, hair follicle, tongue (filiform papilla), AML cells, erythroleukemia cells.
Localisation Nucleus.
Function Important for patterning of embryo, role in hair follicular formation and hair cycle control, role in leukemogenesis of myeloid cells and differentiation of erythroleukemia cells.
Homology With homeodomain proteins, ABD-B homeodomain proteins.

Mutations

Germinal Not known.
Somatic Not known.

Implicated in

Note
  
Entity t(11;12)(p15;q13)
Disease AML-M2
Cytogenetics Chromosome translocation formimg a fusion transcript of 5' NUP98 gene and 3' HOXC13 gene.
Hybrid/Mutated Gene 5' NUP98-3' HOXC13.
Abnormal Protein Fusion between FG motifs of NUP98 and the homeodomain of HOXC13.
 
  
  
Entity Erythroleukemia
Cytogenetics Not examined.
Hybrid/Mutated Gene Not examined.
Oncogenesis Expressed in human and mouse erythroleukemia cells, overexpression of HOXC13 inhibits differentiation of murine erythroleukemia (MEL) cells.
  

Bibliography

Hoxc13 mutant mice lack external hair.
Godwin AR, Capecchi MR.
Genes Dev. 1998 Jan 1;12(1):11-20.
PMID 9420327
 
Human homeobox gene HOXC13 is the partner of NUP98 in adult acute myeloid leukemia with t(11;12)(p15;q13).
La Starza R, Trubia M, Crescenzi B, Matteucci C, Negrini M, Martelli MF, Pelicci PG, Mecucci C.
Genes Chromosomes Cancer. 2003 Apr;36(4):420-3.
PMID 12619167
 
Coordinate regulation of HOX genes in human hematopoietic cells.
Magli MC, Barba P, Celetti A, De Vita G, Cillo C, Boncinelli E.
Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6348-52.
PMID 1712489
 
Fusion of the NUP98 gene and the homeobox gene HOXC13 in acute myeloid leukemia with t(11;12)(p15;q13).
Panagopoulos I, Isaksson M, Billstrom R, Strombeck B, Mitelman F, Johansson B.
Genes Chromosomes Cancer. 2003 Jan;36(1):107-12. (REVIEW)
PMID 12461755
 
Overexpression of Hoxc13 in differentiating keratinocytes results in downregulation of a novel hair keratin gene cluster and alopecia.
Tkatchenko AV, Visconti RP, Shang L, Papenbrock T, Pruett ND, Ito T, Ogawa M, Awgulewitsch A.
Development. 2001 May;128(9):1547-58.
PMID 11290294
 
Interaction between the homeodomain protein HOXC13 and ETS family transcription factor PU.1 and its implication in the differentiation of murine erythroleukemia cells.
Yamada T, Shimizu T, Suzuki M, Kihara-Negishi F, Nanashima N, Sakurai T, Fan Y, Akita M, Oikawa T, Tsuchida S.
Exp Cell Res. 2008 Feb 15;314(4):847-58. Epub 2007 Nov 17.
PMID 18076876
 

Citation

This paper should be referenced as such :
Yamada, T ; Tsuchida, S
HOXC13 (homeobox C13)
Atlas Genet Cytogenet Oncol Haematol. 2010;14(5):452-453.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/HOXC13ID473ch12q13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(1;11)(q23;p15) NUP98/PRRX1


External links

Nomenclature
HGNC (Hugo)HOXC13   5125
Cards
AtlasHOXC13ID473ch12q13
Entrez_Gene (NCBI)HOXC13  3229  homeobox C13
AliasesECTD9; HOX3; HOX3G
GeneCards (Weizmann)HOXC13
Ensembl hg19 (Hinxton)ENSG00000123364 [Gene_View]  chr12:54332576-54340328 [Contig_View]  HOXC13 [Vega]
Ensembl hg38 (Hinxton)ENSG00000123364 [Gene_View]  chr12:54332576-54340328 [Contig_View]  HOXC13 [Vega]
ICGC DataPortalENSG00000123364
TCGA cBioPortalHOXC13
AceView (NCBI)HOXC13
Genatlas (Paris)HOXC13
WikiGenes3229
SOURCE (Princeton)HOXC13
Genetics Home Reference (NIH)HOXC13
Genomic and cartography
GoldenPath hg19 (UCSC)HOXC13  -     chr12:54332576-54340328 +  12q13.13   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)HOXC13  -     12q13.13   [Description]    (hg38-Dec_2013)
EnsemblHOXC13 - 12q13.13 [CytoView hg19]  HOXC13 - 12q13.13 [CytoView hg38]
Mapping of homologs : NCBIHOXC13 [Mapview hg19]  HOXC13 [Mapview hg38]
OMIM142976   614931   
Gene and transcription
Genbank (Entrez)AA722686 AF255676 AF263466 AK024027 BC002754
RefSeq transcript (Entrez)NM_017410
RefSeq genomic (Entrez)NC_000012 NC_018923 NG_033026 NT_029419 NW_004929384
Consensus coding sequences : CCDS (NCBI)HOXC13
Cluster EST : UnigeneHs.118608 [ NCBI ]
CGAP (NCI)Hs.118608
Alternative Splicing GalleryENSG00000123364
Gene ExpressionHOXC13 [ NCBI-GEO ]   HOXC13 [ EBI - ARRAY_EXPRESS ]   HOXC13 [ SEEK ]   HOXC13 [ MEM ]
Gene Expression Viewer (FireBrowse)HOXC13 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3229
GTEX Portal (Tissue expression)HOXC13
Protein : pattern, domain, 3D structure
UniProt/SwissProtP31276   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP31276  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP31276
Splice isoforms : SwissVarP31276
PhosPhoSitePlusP31276
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox_CS    Homeobox_dom    Homeodomain-like    HoxA13_N   
Domain families : Pfam (Sanger)Homeobox (PF00046)    HoxA13_N (PF12284)   
Domain families : Pfam (NCBI)pfam00046    pfam12284   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)HOXC13
DMDM Disease mutations3229
Blocks (Seattle)HOXC13
SuperfamilyP31276
Human Protein AtlasENSG00000123364
Peptide AtlasP31276
HPRD00862
IPIIPI00010759   
Protein Interaction databases
DIP (DOE-UCLA)P31276
IntAct (EBI)P31276
FunCoupENSG00000123364
BioGRIDHOXC13
STRING (EMBL)HOXC13
ZODIACHOXC13
Ontologies - Pathways
QuickGOP31276
Ontology : AmiGOtranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  hair follicle development  chromatin binding  protein binding  nucleus  transcription from RNA polymerase II promoter  anatomical structure morphogenesis  anterior/posterior pattern specification  nail development  sequence-specific DNA binding  tongue morphogenesis  positive regulation of transcription from RNA polymerase II promoter  
Ontology : EGO-EBItranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding  hair follicle development  chromatin binding  protein binding  nucleus  transcription from RNA polymerase II promoter  anatomical structure morphogenesis  anterior/posterior pattern specification  nail development  sequence-specific DNA binding  tongue morphogenesis  positive regulation of transcription from RNA polymerase II promoter  
NDEx NetworkHOXC13
Atlas of Cancer Signalling NetworkHOXC13
Wikipedia pathwaysHOXC13
Orthology - Evolution
OrthoDB3229
GeneTree (enSembl)ENSG00000123364
Phylogenetic Trees/Animal Genes : TreeFamHOXC13
HOVERGENP31276
HOGENOMP31276
Homologs : HomoloGeneHOXC13
Homology/Alignments : Family Browser (UCSC)HOXC13
Gene fusions - Rearrangements
Fusion : MitelmanNUP98/HOXC13 [11p15.4/12q13.13]  [t(11;12)(p15;q13)]  
Fusion : TICdbNUP98 [11p15.4]  -  HOXC13 [12q13.13]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHOXC13 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HOXC13
dbVarHOXC13
ClinVarHOXC13
1000_GenomesHOXC13 
Exome Variant ServerHOXC13
ExAC (Exome Aggregation Consortium)HOXC13 (select the gene name)
Genetic variants : HAPMAP3229
Genomic Variants (DGV)HOXC13 [DGVbeta]
DECIPHER (Syndromes)12:54332576-54340328  ENSG00000123364
CONAN: Copy Number AnalysisHOXC13 
Mutations
ICGC Data PortalHOXC13 
TCGA Data PortalHOXC13 
Broad Tumor PortalHOXC13
OASIS PortalHOXC13 [ Somatic mutations - Copy number]
Cancer Gene: CensusHOXC13 
Somatic Mutations in Cancer : COSMICHOXC13  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHOXC13
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HOXC13
DgiDB (Drug Gene Interaction Database)HOXC13
DoCM (Curated mutations)HOXC13 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HOXC13 (select a term)
intoGenHOXC13
NCG5 (London)HOXC13
Cancer3DHOXC13(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142976    614931   
Orphanet10918   
MedgenHOXC13
Genetic Testing Registry HOXC13
NextProtP31276 [Medical]
TSGene3229
GENETestsHOXC13
Huge Navigator HOXC13 [HugePedia]
snp3D : Map Gene to Disease3229
BioCentury BCIQHOXC13
ClinGenHOXC13
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3229
Chemical/Pharm GKB GenePA29400
Clinical trialHOXC13
Miscellaneous
canSAR (ICR)HOXC13 (select the gene name)
Probes
Litterature
PubMed33 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHOXC13
EVEXHOXC13
GoPubMedHOXC13
iHOPHOXC13
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Apr 12 11:33:07 CEST 2017

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