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

HOXD11 Gene

protein-coding   GIFtS: 49
GCID: GC02P176936

homeobox D11

(Previous name: homeo box D11 )
(Previous symbols: HOX4, HOX4F)
 Explore 10 diseases affiliated with
HOXD11 via our new
 Human Malady Compendium 
Biological research products
for HOXD11
    

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

Aliases
Homeobox D111 2     Homeobox Protein Hox-4F2 3
HOX4F1 2 3 5     Homeo Box 4F2
HOX41 2     Homeobox Protein Hox-D112
Homeo Box D111 2     Hox-4.6, Mouse, Homolog Of2

External Ids:    HGNC: 51341   Entrez Gene: 32372   Ensembl: ENSG000001287137   OMIM: 1429865   UniProtKB: P312773   

Export aliases for HOXD11 gene to outside databases

Previous GC identifers: GC02P175024 GC02P175633 GC02P177174 GC02P176797 GC02P176680 GC02P168849


(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 HOXD11:
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 product of the mouse Hoxd11 gene plays a role in forelimb morphogenesis. (provided by
RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: HXD11_HUMAN, P31277
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 HOXD11


(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 HOXD11 gene promoter:
         E2F-4   E2F-3a   PPAR-gamma1   E2F-2   Nkx2-5   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHOXD11 promoter sequence
   Search SABiosciences Chromatin IP Primers for HOXD11

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HOXD11


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

HOXD11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HOXD11 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P176936:  view genomic region     (about GC identifiers)

Start:
176,968,944 bp from pter      End:
176,974,722 bp from pter
Size:
5,779 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: HXD11_HUMAN, P31277 (See protein sequence)
Recommended Name: Homeobox protein Hox-D11  
Size: 338 amino acids; 35197 Da
Subcellular location: Nucleus
Secondary accessions: A6NIS4 Q9NS02

Explore the universe of human proteins at neXtProt for HOXD11: NX_P31277

HOXD11 Protein expression data from MOPED and PaxDb:    About this image 

Estimated protein expression log10 (pmol).

REFSEQ proteins: NP_067015.2  
ENSEMBL proteins: 
 ENSP00000249504  

Human Recombinant Protein Products: 
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OriGene Protein Over-expression Lysate: HOXD11
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Novus Biologicals HOXD11 Protein
Novus Biologicals HOXD11 Lysate
Browse Sino Biological Recombinant Proteins
Browse ProSpec Recombinant Proteins
Uscn Proteins for HOXD11

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus NAS--


HOXD11 for ontologies           About GeneDecksing



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Uscn ELISAs and CLIAs for HOXD11


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

HOXD11 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 P31277

ProtoNet protein and cluster: P31277

UniProtKB/Swiss-Prot: HXD11_HUMAN, P31277
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: HXD11_HUMAN, P31277
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 HOXD11:
homeo box D11(4F),homologous to mouse Hox-4.6

miRNA
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Inhib. RNA
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OriGene siRNA: HOXD11
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In Situ Assay
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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 NAS--
GO:0043565sequence-specific DNA binding IEA--


HOXD11 for ontologies           About GeneDecksing


Animal Models:
     Mouse knock-outs for HOXD11: Evx2/Hoxd11/Hoxd12/Hoxd13Evx2/Hoxd11/Hoxd12/tm1Ddu Hoxd11tm2.1Ddu Hoxd11tm1Mrc Hoxd11tm2Ddu Hoxd11tm1Ipc
     9 MGI mutant phenotypes (inferred from 7 alleles(MGI details for Hoxd11):
 cellular  embryogenesis  limbs/digits/tail  mortality/aging  nervous system 
 no phenotypic analysis  renal/urinary system  reproductive system  skeleton 

HOXD11 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 HOXD11

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for HOXD11 (P312773 ENSP000002495044) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
MEIS1O004703, ENSP000002723694I2D: score=1 STRING: ENSP00000272369
HMGB1P094293, ENSP000003430404I2D: score=1 STRING: ENSP00000343040
About this table

Gene Ontology (GO): 5/17 biological process terms (GO ID links to tree view) (see all 17):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0001501skeletal system development ----
GO:0001656metanephros development IEA--
GO:0001658branching involved in ureteric bud morphogenesis ISS--
GO:0001759organ induction IEA--
GO:0006351transcription, DNA-dependent IEA--


HOXD11 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 HOXD11
Search CenterWatch for drugs/clinical trials and news about HOXD11 / HXD11 

(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 HOXD11 gene: 
NM_021192.2  

Unigene Cluster for HOXD11:

Homeobox D11
Hs.421136  [show with all ESTs]
Unigene Representative Sequence: NM_021192
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000498438(uc010fqx.3) ENST00000249504(uc002uki.3)

miRNA
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Inhib. RNA
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Clone
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Additional cDNA sequence: 

AK309681.1 BC109394.1 

4 DOTS entries:

DT.70105486  DT.97771570  DT.408703  DT.100707782 

24/56 AceView cDNA sequences (see all 56):

AW205221 NM_021192 BF510955 NM_002148 AW206798 BC074760 AI095929 BC069619 
AA653427 AI139039 BX117343 CB151522 CD614162 X59373 BF939744 AA442532 
AW630600 AL526269 AA479366 AA256875 BM903736 BX114645 BF680250 BP380736 

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

HOXD11 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: CAACGCGAGC

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

About this image

HOXD11 expression in embryonic tissues and stem cells
Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
5 LifeMap In Vivo Development Anatomical Compartments/Cells 
Tissue Anatomical Compartment CellCategory (developmental path)
LimbLimb BudLimb Bud Mesenchyme CellsMesoderm
LimbLimb BudZone Of Polarizing Activity CellsMesoderm
LimbZeugopodPrechondrocytic Mesenchymal CellsBone, Cartilage
SomiteSacral Mesencymal SclerotomeSacral Sclerotome CellsBone, Cartilage, Tendons & Ligaments
KidneyMetanephric MesenchymeMetanephric Mesenchyme CellsKidney
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization
Stem Cell Differentiation: 3 LifeMap Cells 
NameCategory
mK3 (Cell line)Kidney
mK4 (Cell line)Kidney
Intermediate mesoderm derivatives (Generation of interm...)

See HOXD11 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for HOXD11

SOURCE GeneReport for Unigene cluster: Hs.421136
    SABiosciences Expression via Pathway-Focused PCR Array including HOXD11: 
          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 HOXD11

(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 HOXD11 gene from 5/13 species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves HOXD111 homeobox D11 74.76(n)
75(a)
  395328  NM_204620.1  NP_989951.1 
lizard
(Anolis carolinensis)
Reptilia HOXD116
--
96(a)
1 ↔ 1
GL343356.1(556826-557062)
zebrafish
(Danio rerio)
Actinopterygii hoxd11a6
homeo box D11a
52(a)
1 ↔ 1
9(1966617-1968889)
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)
19(a)
1 → many
III(12074190-12077456)


ENSEMBL Gene Tree for HOXD11 (if available)
TreeFam Gene Tree for HOXD11 (if available) 

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for HOXD11 gene
HOXA92  HOXA132  HOXC92  HOXC122  HOXB132  ENSG000002571842  HOXC112  HOXD102  
HOXD132  HOXC132  HOXA112  HOXB92  HOXC102  HOXD122  HOXD92  HOXA102  
16 SIMAP similar genes for HOXD11 using alignment to 2 protein entries:     HXD11_HUMAN (see all proteins):
CDX1    HOX B6    HOXC13    MEOX1    HOXB1    HOXA4
HOXB8    HOXA-9    HOXA11    CDX2    HOXB3    HOXD13
GBX1    HOXC11    HOXA10    HOXD12

HOXD11 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

10/73 NCBI SNPs in HOXD11 are shown (see all 73    About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1888961351,2
--176970117(+) AAGGGG/TCGGAG 1 -- us2k10--------
rs1164253451,2
F,--176970121(+) GGCGGA/GGGAAG 1 -- us2k11Minor allele frequency- G:0.06WA 118
rs2018287651,2
--176970168(+) AGGAA-/GGGGGG 1 -- us2k10--------
rs1172576371,2
C,F,--176970185(+) CAGCCA/GGAAAA 1 -- us2k11Minor allele frequency- G:0.02EA 120
rs729234361,2
C,F,--176970247(+) CAGAGC/AGCACA 1 -- us2k12Minor allele frequency- A:0.07WA NA 238
rs38138111,2
C,F,H,--176970340(-) CTGGGG/ACCTGG 1 -- us2k14Minor allele frequency- A:0.01NS EA 418
rs730337201,2
C,--176970401(+) CCCTCG/TGTTCT 1 -- us2k12Minor allele frequency- T:0.06WA 120
rs8471481,2
C,F,H,--176970456(-) CCGAGT/AGAGCA 1 -- us2k116Minor allele frequency- A:0.29NS EA NA WA CSA 791
rs8471471,2
C,F,A,H,--176970659(-) TCAGCC/TCCTCC 1 -- us2k1 tfbs3 trp323Minor allele frequency- T:0.26MN NS EA NA WA CSA 2417
rs803407311,2
--176970735(+) TTGGCG/CGGGCT 1 -- us2k12Minor allele frequency- C:0.04CSA WA 119

HapMap Linkage Disequilibrium report for HOXD11 (176968944 - 176974722 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for HOXD11: --

SABiosciences Cancer Mutation PCR Assays
QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HOXD11
DNA2.0 Custom Variant and Variant Library Synthesis for HOXD11

(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

HOXD11 for disorders           About GeneDecksing

OMIM gene information: 142986    OMIM disorders: --

10 diseases for HOXD11:    About MalaCards
brachydactyly-syndactyly syndrome    syndactyly    synpolydactyly    brachydactyly
renal agenesis    acute myeloid leukemia    myeloid leukemia    clubfoot
polydactyly    leukemia

2 diseases from the University of Copenhagen DISEASES database for HOXD11:
Polydactyly     Renal agenesis
Human Genome Epidemiology (HuGE) Navigator: HOXD11 (5 documents)

Export disorders for HOXD11 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 HOXD11 gene, integrated from 9 sources (see all 33):
(articles sorted by number of sources associating them with HOXD11)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PubMed id 17236141)1, 2 Zhao X.... Zhang X. (2007)
  2. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)1, 3 Scott M.P. (1992)
  3. Nomenclature for human homeobox genes. (PubMed id 1973146)1, 3 McAlpine P.J. and Shows T.B. (1990)
  4. The human HOX gene family. (PubMed id 2574852)1, 2 Acampora D.... Boncinelli E. (1989)
  5. The HOXD11 gene is fused to the NUP98 gene in acute myeloid leukemia with t(2;11)(q31;p15). (PubMed id 11782354)1, 9 Taketani T....Hayashi Y. (2002)
  6. A region of the human HOXD cluster that confers polyc omb-group responsiveness. (PubMed id 20085705)1 Woo C.J....Kingston R.E. (2010)
  7. 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)
  8. Absence of mutations in the HOXA11 and HOXD11 genes in children with congenital renal malformations. (PubMed id 19255789)1 Bouba I....Georgiou I. (2009)
  9. 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)
  10. 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)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 3237 HGNC: 5134 AceView: HOXD10andHOXD11 Ensembl:ENSG00000128713 euGenes: HUgn3237
ECgene: HOXD11 H-InvDB: HOXD11

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for HOXD11 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for HOXD11 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HOXD11 gene:
Search GeneIP for patents involving HOXD11

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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