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

HOXD12 Gene

protein-coding   GIFtS: 50
GCID: GC02P176930

homeobox D12

(Previous name: homeo box D12 )
(Previous symbol: HOX4H)
 Explore 7 diseases affiliated with
HOXD12 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for HOXD12    

Aliases
for HOXD12 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Homeobox D121 2
HOX4H1 2 3 5
Homeo Box D121 2
Homeobox Protein Hox-4H2 3
Homeobox Protein Hox-D122
Hox-4.7, Mouse, Homolog Of2

External Ids:    HGNC: 51351   Entrez Gene: 32382   Ensembl: ENSG000001701787   OMIM: 1429885   UniProtKB: P354523   

Export aliases for HOXD12 gene to outside databases

Previous GC identifers: GC02P175017 GC02P175625 GC02P177168 GC02P177169 GC02P176790 GC02P176672 GC02P168842


Summaries
for HOXD12 gene

(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 HOXD12:
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, located on different chromosomes, consisting of 9 to 11 genes
arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions
that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and
genital abnormalities. The exact role of this gene has not been determined. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: HXD12_HUMAN, P35452
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 HOXD12


Genomic Views
for HOXD12 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_005403.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HOXD12 gene promoter:
         TBP   PPAR-gamma1   E2F   E2F-2   PPAR-gamma2   c-Ets-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: HOXD12 promoter sequence
   Search SABiosciences Chromatin IP Primers for HOXD12

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXD12


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

Entrez Gene cytogenetic band: 2q31.1   Ensembl cytogenetic band:  2q31.1   HGNC cytogenetic band: 2q31.1

HOXD12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXD12 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P176930:  view genomic region     (about GC identifiers)

Start:
 176,964,458 bp from pter      End:
 176,966,408 bp from pter
Size:
 1,951 bases      Orientation:
 plus strand

Proteins
for HOXD12 gene

(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: HXD12_HUMAN, P35452 (See protein sequence)
Recommended Name: Homeobox protein Hox-D12  
Size: 270 amino acids; 29031 Da
Subcellular location: Nucleus
Secondary accessions: B5MCP0 Q9NS03

Explore the universe of human proteins at neXtProt for HOXD12: NX_P35452

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_P35452

    • HOXD12 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_067016.3  
    ENSEMBL proteins: 
     ENSP00000385586   ENSP00000385132  

    Human Recombinant Protein Products: 
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    Uscn Proteins for HOXD12

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000228nuclear chromosome NAS--
    GO:0005667transcription factor complex IEA--


    HOXD12 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for HOXD12 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HOXD12 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR020479 Homeobox_metazoa
     IPR017970 Homeobox_CS
     IPR001356 Homeodomain
     IPR009057 Homeodomain-like

    Graphical View of Domain Structure for InterPro Entry P35452

    ProtoNet protein and cluster: P35452

    1 Blocks protein family: IPB000047 Lambda and other repressor helix-turn-helix signature

    UniProtKB/Swiss-Prot: HXD12_HUMAN, P35452
    Similarity: Belongs to the Abd-B homeobox family
    Similarity: Contains 1 homeobox DNA-binding domain


    Function
    for HOXD12 gene

    (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: HXD12_HUMAN, P35452
    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 HOXD12:
    homeo box D12(4H),homologous to mouse Hox-4.7,interacting with HOD13 during mouse limb development

    miRNA
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    Gene Editing
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    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for HOXD12

    In Situ Assay
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    Gene Ontology (GO): 4 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 NAS--
    GO:0005515protein binding ----
    GO:0043565sequence-specific DNA binding IEA--


    HOXD12 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for HOXD12:
     Decreased Wnt reporter activit 

    Animal Models:
         Mouse knock-outs for HOXD12: Evx2/Hoxd11/Hoxd12/Hoxd13Evx2/Hoxd11/Hoxd12/tm1Ddu Hoxd12tm1Mrc
         8 MGI mutant phenotypes (inferred from 3 alleles) (MGI details for Hoxd12):
     digestive/alimentary  embryogenesis  limbs/digits/tail  mortality/aging  muscle 
     nervous system  reproductive system  skeleton 

    HOXD12 for phenotypes           About GeneDecksing


    Pathways & Interactions
    for HOXD12 gene

    (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 HOXD12

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/16 Interacting proteins for HOXD12 (P354523 ENSP000003855864) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAFGO155253, ENSP000003503694I2D: score=2 STRING: ENSP00000350369
    MEIS1O004703, ENSP000002723694I2D: score=2 STRING: ENSP00000272369
    MAFO754443, ENSP000003270484I2D: score=1 STRING: ENSP00000327048
    MAFBQ9Y5Q33, ENSP000003624104I2D: score=1 STRING: ENSP00000362410
    MAFFQ9ULX93, ENSP000003453934I2D: score=2 STRING: ENSP00000345393
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001501skeletal system development IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent NAS--
    GO:0007275multicellular organismal development NAS--
    GO:0007389pattern specification process IEA--


    HOXD12 for ontologies           About GeneDecksing



    Drugs & Compounds
    for HOXD12 gene

    (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 HOXD12
    Search CenterWatch for drugs/clinical trials and news about HOXD12 / HXD12 

    Transcripts
    for HOXD12 gene

    (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 HOXD12 gene: 
    NM_021193.3  

    Unigene Cluster for HOXD12:

    Homeobox D12
    Hs.450028  [show with all ESTs]
    Unigene Representative Sequence: BC121103
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000406506(uc010zev.1) ENST00000404162

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    Inhib. RNA
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    Clone
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    Primer
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    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat HOXD12
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HOXD12
      Search QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HOXD12

    Additional cDNA sequence: 

    BC069088.1 BC121103.1 BC121104.1 

    3 DOTS entries:

    DT.120958985  DT.91684853  DT.95086599 

    3 AceView cDNA sequences:

    BC069088 NM_021193 BG031716 

    GeneLoc Exon Structure


    Expression
    for HOXD12 gene

    (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

    HOXD12 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ACAGTGCAGG

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

    HOXD12 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)
    LimbAutopodPrechondrocytic Mesenchymal CellsBone, Cartilage
    LimbLimb BudLimb Bud Mesenchyme CellsMesoderm
    LimbLimb BudZone Of Polarizing Activity CellsMesoderm
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See HOXD12 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HOXD12

    SOURCE GeneReport for Unigene cluster: Hs.450028
        SABiosciences Expression via Pathway-Focused PCR Array including HOXD12: 
              Homeobox (HOX) Genes in human mouse rat

    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for HOXD12 gene

    (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 HOXD12 gene from 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves HOXD121 homeobox D12 66.29(n)
    66.17(a)    		   396178  NM_205249.1  NP_990580.1 
    lizard
    (Anolis carolinensis)    		 Reptilia HOXD126
    		 --
    		 80(a)
    		 1 ↔ 1
    		 GL343356.1(570379-570618)
    zebrafish
    (Danio rerio)    		 Actinopterygii hoxd12a1 homeo box D12a 52.9(n)
    45.83(a)    		   100006598  NM_001126486.1  NP_001119958.1 
    worm
    (Caenorhabditis elegans)    		 Secernentea nob-16
    		 kNOB-like posterior (NO Backside) family member (n...
    		 15(a)
    		 1 → many
    		 III(12077688-12084220)


    ENSEMBL Gene Tree for HOXD12 (if available)
    TreeFam Gene Tree for HOXD12 (if available) 

    Paralogs
    for HOXD12 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for HOXD12 gene
    HOXA92  HOXA132  HOXC92  HOXD112  HOXC122  HOXB132  ENSG000002571842  HOXC112  
    HOXD102  HOXD132  HOXC132  HOXA112  HOXB92  HOXC102  HOXD92  HOXA102  
    10 SIMAP similar genes for HOXD12 using alignment to 4 protein entries:     HXD12_HUMAN (see all proteins):
    HOXC13    HOX B6    HOXA4    HOXB1    MEOX1    NKX2-5
    HOXC12    POU6F1    HOXD8    HOXD11

    HOXD12 for paralogs           About GeneDecksing



    Genomic Variants
    for HOXD12 gene

    (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

    10/55 NCBI SNPs in HOXD12 are shown (see all 55)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 2 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1830213611,2
    		--176962553(+) TGTTCA/CATTCT 1 -- us2k10--------
    rs8471561,2
    		C,F,A,--176962561(+) TCTCTT/CAATCA 1 -- us2k112Minor allele frequency- C:0.35MN NA WA CSA EA 556
    rs8471551,2
    		C,F,--176962580(+) GCCACT/CCTCCC 1 -- us2k112Minor allele frequency- C:0.29MN NA WA CSA EA 556
    rs743586961,2
    		C,F,--176962648(+) TTGCCT/CGCCAG 1 -- us2k11Minor allele frequency- C:0.03EA 120
    rs1166406051,2
    		F,--176962695(+) AGACTG/ATCCAA 1 -- us2k11Minor allele frequency- A:0.07WA 118
    rs1868685191,2
    		--176962771(+) TAGTCC/TTGAGG 1 -- us2k10--------
    rs1431674791,2
    		--176962868(+) CGTGA-/GGA   
      GAGACT    GCAGG     		1 -- us2k10--------
    rs75730071,2
    		C,--176962873(+) GGAGAT/GACTGC 1 -- us2k11Minor allele frequency- G:0.00CSA 1
    rs8471541,2
    		C,F,A,--176962958(-) AAGAGC/TTCTTA 1 -- us2k111Minor allele frequency- T:0.31NA WA CSA EA 372
    rs8471531,2
    		C,F,A,H,--176962989(-) ATACTC/TAAGGG 1 -- us2k123Minor allele frequency- T:0.35NS EA NA WA CSA 2346

    HapMap Linkage Disequilibrium report for HOXD12 (176964458 - 176966408 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HOXD12: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HOXD12
    DNA2.0 Custom Variant and Variant Library Synthesis for HOXD12

    Disorders / Diseases
    for HOXD12 gene

    (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
    HOXD12 for disorders           About GeneDecksing

    OMIM gene information: 142988    OMIM disorders: --

    7 diseases for HOXD12:    About MalaCards
    brachydactyly-syndactyly syndrome    talipes equinovarus    syndactyly    synpolydactyly
    brachydactyly    clubfoot    polydactyly

    2 diseases from the University of Copenhagen DISEASES database for HOXD12:
    Polydactyly     Syndactyly
    Human Genome Epidemiology (HuGE) Navigator: HOXD12 (5 documents)

    Export disorders for HOXD12 gene to outside databases

    Publications
    for HOXD12 gene

    (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 HOXD12 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with HOXD12)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. EVX2, a human homeobox gene homologous to the even-skipped segmentation gene, is localized at the 5' end of HOX4 locus on chromosome 2. (PubMed id 1675198)1, 2, 3 D'Esposito M....Boncinelli E. (1991)
    2. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (1990)
    3. A region of the human HOXD cluster that confers polyc omb-group responsiveness. (PubMed id 20085705)1 Woo C.J....Kingston R.E. (2010)
    4. Altered transmission of HOX and apoptotic SNPs identi fy a potential common pathway for clubfoot. (PubMed id 19938081)1 Ester A.R....Hecht J.T. (2009)
    5. Study of HOXD genes in autism particularly regarding the ratio of second to fourth digit length. (PubMed id 19540081)1 Sugie Y....Osawa J. (2009)
    6. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PubMed id 19453261)1 Yerges L.M....Zmuda J.M. (2009)
    7. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PubMed id 17236141)1 Zhao X.... Zhang X. (2007)
    8. [Analysis of association between 5' HOXD gene and idiopathic congenital talipes equinovarus] (PubMed id 16331564)1 Wang L.L....Sun K.L. (2005)
    9. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    10. Complete mutation analysis panel of the 39 human HOX genes. (PubMed id 11857506)1 Kosaki K.... Matsuo N. (2002)

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    Genome Databases showing HOXD12 gene

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    Entrez Gene: 3238 HGNC: 5135 AceView: HOXD12 Ensembl:ENSG00000170178 euGenes: HUgn3238
    ECgene: HOXD12 H-InvDB: HOXD12

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