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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HOXC5 Gene

protein-coding   GIFtS: 47
GCID: GC12P054379

Homeobox C5

(Previous name: homeo box C5)
(Previous symbols: HOX3D, HOX3)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Homeobox C51 2     Homeobox Protein CP112 3
HOX3D1 2 3 5     Homeobox Protein Hox-3D2 3
HOX31 2     CP112
Homeo Box C51 2     Homeobox Protein Hox-C52

External Ids:    HGNC: 51271   Entrez Gene: 32222   Ensembl: ENSG000001727897   OMIM: 1429735   UniProtKB: Q004443   

Export aliases for HOXC5 gene to outside databases

Previous GC identifers: GC12M054391 GC12P054539 GC12P054129 GC12P052713 GC12P054411 GC12P051449


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 anaplastic large cell lymphoma, and non-hodgkin lymphoma. GO annotations related to this gene include sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is GSX1.

UniProtKB/Swiss-Prot: HXC5_HUMAN, Q00444
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 Wiki entry for HOXC5 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HOXC5 gene promoter:
         Egr-3   Pax-5   Sp1   FOXL1   c-Ets-1   Egr-4   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for HOXC5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXC5


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13.3   Ensembl cytogenetic band:  12q13.13   HGNC cytogenetic band: 12q13.13

HOXC5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXC5 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P054379:  view genomic region     (about GC identifiers)

Start:
54,379,629 bp from pter      End:
54,429,145 bp from pter
Size:
49,517 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: HXC5_HUMAN, Q00444 (See protein sequence)
Recommended Name: Homeobox protein Hox-C5  
Size: 222 amino acids; 24976 Da
Subcellular location: Nucleus

Explore the universe of human proteins at neXtProt for HOXC5: NX_Q00444

Explore proteomics data for HOXC5 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q00444

  • HOXC5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    HOXC5 Protein Expression
    REFSEQ proteins: NP_061826.1  
    ENSEMBL proteins: 
     ENSP00000309336  

    Human Recombinant Protein Products for HOXC5: 
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    Cloud-Clone Corp. Proteins for HOXC5 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0030054cell junction IDA--

    HOXC5 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    HOXL: Homeoboxes / ANTP class : HOXL subclass

    5/6 InterPro protein domains (see all 6):
     IPR001827 Homeobox_Antennapedia_CS
     IPR020479 Homeobox_metazoa
     IPR017995 Homeobox_antennapedia
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain

    Graphical View of Domain Structure for InterPro Entry Q00444

    ProtoNet protein and cluster: Q00444

    1 Blocks protein domain: IPB001827 Homeobox protein

    UniProtKB/Swiss-Prot: HXC5_HUMAN, Q00444
    Similarity: Belongs to the Antp homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    HOXC5 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: HXC5_HUMAN, Q00444
    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 entry for HOXC5:
    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

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding ----
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding IEA--
         
    HOXC5 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for HOXC5:
     Decreased BPV1 E2 protein expr  Increased HPV18 LCR reporter a 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Hoxc5):
     skeleton 

    HOXC5 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Hoxc5tm1Mrc for HOXC5

       inGenious Targeting Laboratory - Custom generated mouse model solutions for HOXC5 
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    SwitchGear 3'UTR luciferase reporter plasmidHOXC5 3' UTR sequence
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXC5


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HOXC5

    3 Interacting proteins for HOXC5 (Q004443) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PBX1P404243I2D: score=1 
    PBX3P404263I2D: score=1 
    POLR2IP369543I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0006357regulation of transcription from RNA polymerase II promoter TAS1346761
    GO:0009952anterior/posterior pattern specification IEA--
    GO:0048706embryonic skeletal system development IEA--

    HOXC5 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HOXC5 (HXC5)

    Search CenterWatch for drugs/clinical trials and news about HOXC5 / HXC5

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HOXC5 gene: 
    NM_018953.3  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000513209 ENST00000512206(uc001set.3) ENST00000312492(uc001sew.3)

    miRNA
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    8/18 QIAGEN miScript miRNA Assays for microRNAs that regulate HOXC5 (see all 18):
    hsa-miR-185* hsa-miR-4288 hsa-miR-518e hsa-miR-632 hsa-miR-3121-3p hsa-miR-4273 hsa-miR-190 hsa-miR-1231
    SwitchGear 3'UTR luciferase reporter plasmidHOXC5 3' UTR sequence
    Inhib. RNA
    Products:
         
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HOXC5
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HOXC5

    24/228 AceView cDNA sequences (see all 228):

    BM836024 BQ684698 BX280842 CA432146 AW070489 AA813478 BE396026 AW469953 
    NM_017409 AW299598 BF434950 AA158947 AI174335 NM_014620 AW000987 BM832772 
    BF197458 BC074844 T28272 AI159844 BE464190 BU501253 AA888101 BQ949038 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HOXC5 expression in normal human tissues (normalized intensities)      HOXC5 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    HOXC5 Expression
    About this image


    HOXC5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/8 selected tissues (see all 8) fully expand
     
     Spinal Cord (Nervous System)    fully expand to see all 5 entries
             Lateral Motor Neurons Rostral Brachial Lateral Motor Column
             Motor neuron-like cells ( Generation of motor and gamma-aminobutyric acid (GABA)...
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Spinal Ventral Columns
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             umbilical cord reticulocytes   
     
     Limb (Muscoskeletal System)
             Limb Bud Mesenchyme Cells Limb Bud
     
     Umbilical Cord (Extraembryonic Tissues)
             umbilical cord reticulocytes   

    See HOXC5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXC5
        SABiosciences Expression via Pathway-Focused PCR Arrays including HOXC5: 
              Stem Cell Transcription Factors in human mouse rat
              Homeobox (HOX) Genes in human mouse rat

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXC5

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for HOXC5 gene from 6/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hoxc51 , 5 homeobox C51, 5 98.5(n)1
    99.55(a)1
      15 (58.07 cM)5
    154241  NM_175730.51  NP_783857.11 
     1029674435 
    chicken
    (Gallus gallus)
    Aves LOC1008585341 homeobox protein Hox-C5-like 71.81(n)
    64.43(a)
      100858534  XM_003643840.1  XP_003643888.1 
    lizard
    (Anolis carolinensis)
    Reptilia HOXC56
    Uncharacterized protein
    65(a)
    1 ↔ 1
    2(72020531-72022726)
    zebrafish
    (Danio rerio)
    Actinopterygii hoxc5a1 homeo box C5a 58.14(n)
    57.99(a)
      30379  NM_131144.1  NP_571219.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Scr3 midgut development specific RNA
    polymerase II more
    75(a)   3 84A5   --
    worm
    (Caenorhabditis elegans)
    Secernentea mab-56
    egl-56
    Homeobox protein egl-5
    27(a)
    14(a)
    many ↔ many
    many ↔ many
    III(7776907-7783454)
    III(7814382-7816451)


    ENSEMBL Gene Tree for HOXC5 (if available)
    TreeFam Gene Tree for HOXC5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXC5 gene
    GSX12  HOXA72  HOXA12  HOXB32  HOXD12  HOXA22  HOXB52  HOXC62  
    GSX22  HOXB42  HOXA52  HOXA42  HOXD32  HOXA62  HOXC82  HOXA32  
    HOXD82  HOXB62  HOXB12  HOXB82  HOXD42  HOXB22  PDX12  HOXB72  
    HOXC42  
    14 SIMAP similar genes for HOXC5 using alignment to 1 protein entry:     HXC5_HUMAN:
    HOXC6    HOXA4    HOXA-9    HOXA5    HOXB6    HOXD4
    HOXD8    HOXB5    HOXB7    HOXA7    HOXB8    HOXC8
    HOXD9    HOXA6

    HOXC5 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section
    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for HOXC5:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2672088CNV Deletion23128226
    nsv899102CNV Loss21882294
    nsv832418CNV Loss17160897
    nsv899100CNV Loss21882294
    nsv826379CNV Gain20364138
    nsv428282CNV Gain18775914
    dgv512e1CNV Complex17122850

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing HOXC5
    DNA2.0 Custom Variant and Variant Library Synthesis for HOXC5

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 142973    OMIM disorders: --

    7 diseases for HOXC5:    About MalaCards
    anaplastic large cell lymphoma    non-hodgkin lymphoma    hodgkin's lymphoma    b-cell lymphomas
    myeloid leukemia    thyroiditis    leukemia


    HOXC5 for disorders           About GeneDecksing

    4 Novoseek inferred disease relationships for HOXC5 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lymphoma t-cell 54.4 6 9327740 (3), 9354682 (1)
    lymphoma non-hodgkins 48.4 4 9354682 (2), 9327740 (1)
    leukemia 35.6 5 8634419 (3), 9823947 (2)
    lymphoma 24.7 11 9327740 (5), 9354682 (1)

    Genetic Association Database (GAD): HOXC5
    Human Genome Epidemiology (HuGE) Navigator: HOXC5 (1 document)

    Export disorders for HOXC5 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for HOXC5 gene, integrated from 9 sources (see all 23):
    (articles sorted by number of sources associating them with HOXC5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The upstream region of the human homeobox gene HOX3D is a target for regulation by retinoic acid and HOX homeoproteins. (PubMed id 1346761)1, 2, 9 Arcioni L....Mavilio F. (1992)
    2. Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease. (PubMed id 16215934)1, 4, 9 Gong L.G....Sun K.L. (2005)
    3. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (1992)
    4. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (1990)
    5. Organization of human class I homeobox genes. (PubMed id 2576652)1, 2 Boncinelli E.... Simeone A. (1989)
    6. Genome-wide meta-analysis identifies 56 bone mineral d ensity loci and reveals 14 loci associated with risk of fracture. (PubMed id 22504420)1 Estrada K....Rivadeneira F. (2012)
    7. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3222 HGNC: 5127 AceView: HOXC6 Ensembl:ENSG00000172789 euGenes: HUgn3222
    ECgene: HOXC5 H-InvDB: HOXC5

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HOXC5 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HOXC5 gene:
    Search GeneIP for patents involving HOXC5

    GeneCards and IP:
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