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

HOXC11 Gene

protein-coding   GIFtS: 52
GCID: GC12P054366

homeobox C11

(Previous name: homeo box C11 )
(Previous symbol: HOX3H)
 Explore 6 diseases affiliated with
HOXC11 via our new
 Human Malady Compendium 
Biological research products
for HOXC11
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Homeobox C111 2
HOX3H1 2 3
Homeo Box C111 2
Homeobox Protein Hox-3H2 3
Homeobox Protein Hox-C112

External Ids:    HGNC: 51231   Entrez Gene: 32272   Ensembl: ENSG000001233887   OMIM: 6055595   UniProtKB: O432483   

Export aliases for HOXC11 gene to outside databases

Previous GC identifers: GC12M054415 GC12P054479 GC12P054083 GC12P052653 GC12P051405


(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 HOXC11:
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. The
product of this gene binds to a promoter element of the lactase-phlorizin hydrolase. It also may play a role in early
intestinal development. An alternatively spliced variant encoding a shorter isoform has been described but its
full-length nature has not been determined. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: HXC11_HUMAN, O43248
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. Binds to a promoter element of the
lactase-phlorizin hydrolase gene

Gene Wiki entry for HOXC11


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HOXC11 gene promoter:
         Max1   E2F-3a   E2F-4   C/EBPbeta   E2F-5   Lmo2   E2F-2   E2F   E2F-1   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHOXC11 promoter sequence
   Search SABiosciences Chromatin IP Primers for HOXC11

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXC11


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

HOXC11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXC11 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P054366:  view genomic region     (about GC identifiers)

Start:
54,366,910 bp from pter      End:
54,371,427 bp from pter
Size:
4,518 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HXC11_HUMAN, O43248 (See protein sequence)
Recommended Name: Homeobox protein Hox-C11  
Size: 304 amino acids; 33748 Da
Subcellular location: Nucleus
Secondary accessions: A8K7D1 Q96DH2

Explore the universe of human proteins at neXtProt for HOXC11: NX_O43248

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O43248

  • HOXC11 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_055027.1  
    ENSEMBL proteins: 
     ENSP00000446680   ENSP00000243082  

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    Uscn Proteins for HOXC11

    Gene Ontology (GO): 4 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:0005737cytoplasm IDA--
    GO:0005739mitochondrion IDA--


    HOXC11 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HOXC11 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR021918 DUF3528
     IPR020479 Homeobox_metazoa
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry O43248

    ProtoNet protein and cluster: O43248

    UniProtKB/Swiss-Prot: HXC11_HUMAN, O43248
    Similarity: Belongs to the Abd-B homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: HXC11_HUMAN, O43248
    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. Binds to a promoter element of the
    lactase-phlorizin hydrolase gene

         Genatlas biochemistry entry for HOXC11:
    homeo box C11(3H),homologous to mouse Hox-3.7,involved in mouse posterior limb patterning expressed in posterior limb

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    hsa-miR-21* hsa-miR-642a hsa-miR-3194-5p hsa-let-7d hsa-miR-1197 hsa-miR-513a-5p hsa-miR-15a hsa-miR-605
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    Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700sequence-specific DNA binding transcription factor activity IEA--
    GO:0043565sequence-specific DNA binding IEA--


    HOXC11 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for HOXC11:
     Synthetic lethal with Ras 

    Animal Models:
         Mouse knock-out Hoxc11tm1Mrc for HOXC11
         5 MGI mutant phenotypes (inferred from 1 allele(MGI details for Hoxc11):
     cellular  limbs/digits/tail  renal/urinary system  reproductive system  skeleton 

    HOXC11 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HOXC11

    STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

    5/12 Interacting proteins for HOXC11 (O432483 ENSP000002430824) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CD2APQ9Y5K63, ENSP000003522644I2D: score=1 STRING: ENSP00000352264
    GTF2A1LQ9UNN43, ENSP000003845974I2D: score=1 STRING: ENSP00000384597
    GTF2H1P327803, ENSP000002659634I2D: score=1 STRING: ENSP00000265963
    MEIS1O004703, ENSP000002723694I2D: score=1 STRING: ENSP00000272369
    SMAD3P840223, ENSP000003329734I2D: score=1 STRING: ENSP00000332973
    About this table

    Gene Ontology (GO): 5/10 biological process terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development ----
    GO:0001656metanephros development IEA--
    GO:0001759organ induction IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0007275multicellular organismal development ----


    HOXC11 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 HOXC11
    Search CenterWatch for drugs/clinical trials and news about HOXC11 / HXC11 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HOXC11 gene: 
    NM_014212.3  

    Unigene Cluster for HOXC11:

    Homeobox C11
    Hs.127562  [show with all ESTs]
    Unigene Representative Sequence: NM_014212
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000546378(uc001sem.3) ENST00000243082

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    hsa-miR-21* hsa-miR-642a hsa-miR-3194-5p hsa-let-7d hsa-miR-1197 hsa-miR-513a-5p hsa-miR-15a hsa-miR-605
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    Additional cDNA sequence: 

    AJ000041.1 AK291946.1 BC001543.1 X99630.1 

    1 DOTS entry:

    DT.86838844 

    20 AceView cDNA sequences:

    BX384375 X99630 CR602963 BM454815 AJ000041 BM792333 BE544348 NM_014212 
    BC001543 AL555641 AA953456 BP380768 BX095756 AU100254 BP380964 BM791522 
    BF315826 AU107978 BX384374 AW291236 

    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

    HOXC11 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGCACTCCCC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    HOXC11 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    3 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    LimbLimb BudLimb Bud Mesenchyme CellsMesoderm
    LimbZeugopodPrechondrocytic Mesenchymal CellsBone, Cartilage
    KidneyMetanephric MesenchymeMetanephric Mesenchyme CellsKidney
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    PureStem™ progenitor W8 (Embryonic Progenitor Cell)

    See HOXC11 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXC11

    SOURCE GeneReport for Unigene cluster: Hs.127562
        SABiosciences Expression via Pathway-Focused PCR Array including HOXC11: 
              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 HOXC11

    (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 HOXC11 gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves HOXC116
    --
    76(a)
    1 ↔ 1
    Un(11038119-11040351)
    lizard
    (Anolis carolinensis)
    Reptilia HOXC116
    --
    68(a)
    1 ↔ 1
    2(72099112-72102084)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.116032 Transcribed sequence with weak similarity to protein more 79.23(n)    BQ395576.1 
    zebrafish
    (Danio rerio)
    Actinopterygii hoxc11b1 homeo box C11b 62.78(n)
    66.67(a)
      570925  XM_694457.5  XP_699549.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Abd-B6
    Abdominal B
    10(a)
    1 → many
    3R(12752932-12797958)
    worm
    (Caenorhabditis elegans)
    Secernentea php-36
    Posterior Hox gene Paralog family member (php-3)
    17(a)
    1 → many
    III(12074190-12077456)


    ENSEMBL Gene Tree for HOXC11 (if available)
    TreeFam Gene Tree for HOXC11 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXC11 gene
    HOXA92  HOXA132  HOXC92  HOXD112  HOXC122  HOXB132  ENSG000002571842  HOXD102  
    HOXA112  HOXD132  HOXC132  HOXB92  HOXC102  HOXD122  HOXD92  HOXA102  
    2 SIMAP similar genes for HOXC11 using alignment to 2 protein entries:     HXC11_HUMAN (see all proteins):
    HOXA11    HOXD11

    HOXC11 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/93 NCBI SNPs in HOXC11 are shown (see all 93    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs57982921,2
    C,F,--51403502(+) AGCAAG/-CCAGA 1 -- us2k12Minor allele frequency- -:0.15MN EA 356
    rs340282551,2
    C--51404271(+) GTCAAC/GCTGGG 2 N K mis11Minor allele frequency- G:0.00NA 4548
    rs178494921,2
    C--51404396(+) GGTCTC/TCTCCT 2 S F mis1 ese3 trp32Minor allele frequency- T:0.00NA 4
    rs740898431,2
    C,--51405455(+) CGCTAT/AGATCC 1 -- int12Minor allele frequency- A:0.16WA 120
    rs788949921,2
    C,F,--51405628(+) GCCTTA/GGTGCT 1 -- int11Minor allele frequency- G:0.12WA 118
    rs755471421,2
    --51405788(+) GTTCTC/TAGCTT 1 -- int12Minor allele frequency- T:0.04CSA WA 119
    rs740898451,2
    C,--51406534(+) GGACTG/ATGGCC 1 -- ut312Minor allele frequency- A:0.15WA 120
    rs38161521,2
    C,H,--51407297(+) GAAAGG/CGGGGG 1 -- ut31 trp33Minor allele frequency- C:0.00NS EA 284
    rs786958161,2
    F,--51407480(+) ATTAAC/ACCCTC 1 -- ds50011Minor allele frequency- A:0.10WA 118
    rs774866301,2
    C,F,--51407677(+) TTCCAT/CAGCTA 1 -- ds50011Minor allele frequency- C:0.10WA 118

    HapMap Linkage Disequilibrium report for HOXC11 (54366910 - 54371427 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for HOXC11
         1 CNV: 3890

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for HOXC11

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    HOXC11 for disorders           About GeneDecksing

    OMIM gene information: 605559    OMIM disorders: --

    6 diseases for HOXC11:    About MalaCards
    lung carcinoma    breast cancer    neuroblastoma    carcinoma
    pancreatic cancer    pancreatitis


    Export disorders for HOXC11 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 HOXC11 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with HOXC11)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The HOXC11 homeodomain protein interacts with the lactase-phlorizin hydrolase promoter and stimulates HNF1alpha-dependent transcription. (PubMed id 9582375)1, 2, 9 Mitchelmore C.E.... Noren O. (1998)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete mutation analysis panel of the 39 human HOX genes. (PubMed id 11857506)1, 2 Kosaki K.... Matsuo N. (2002)
    4. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (1992)
    5. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (1990)
    6. Interaction of developmental transcription factor HOX C11 with steroid receptor coactivator SRC-1 mediates resistance to endocrine th erapy in breast cancer [corrected]. (PubMed id 20145129)1 McIlroy M....Young L.S. (2010)
    7. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (2010)
    8. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
    9. Identification of multi-SH3 domain-containing protein interactome in pancreatic cancer: a yeast two-hybrid approach. (PubMed id 18654987)1 Thalappilly S....Dusetti N.J. (2008)
    10. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 3227 HGNC: 5123 AceView: HOXC11 Ensembl:ENSG00000123388 euGenes: HUgn3227
    ECgene: HOXC11 H-InvDB: HOXC11

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for HOXC11 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for HOXC11 Genetics and Cytogenetics in Oncology and Haematology

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