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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

HOXD11 Gene

protein-coding GIFtS: 51
GCID: GC02P176936

Homeobox D11

(Previous name: homeo box D11)
(Previous symbols: HOX4, HOX4F)

9 related diseases
at

MalaCards

(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 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 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, 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)

GeneCards Summary for HOXD11 Gene:

HOXD11 (homeobox D11) is a protein-coding gene. Diseases associated with HOXD11 include brachydactyly-syndactyly syndrome, and syndactyly. 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 ENSG00000257184.

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 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

RefSeq DNA sequence:

NC_000002.11 NT_005403.17 NC_018913.2

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 plasmid: HOXD11 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 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: 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

Explore proteomics data for HOXD11 at MOPED

HOXD11 Protein expression data from MOPED¹, PaxDb² and MAXQB³ : About this image

REFSEQ proteins: NP_067015.2

ENSEMBL proteins:

ENSP00000249504

Human Recombinant Protein Products for HOXD11:

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	Cloud-Clone Corp. Proteins for HOXD11

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	NAS	--

HOXD11 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 InterPro protein domains:

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

HOXD11 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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, 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: 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

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003677	DNA binding	--	--
GO:0003700	sequence-specific DNA binding transcription factor activity	NAS	--
GO:0043565	sequence-specific DNA binding	IEA	--

HOXD11 for ontologies About GeneDecksing

Phenotypes:
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

Animal Models:
Mouse knock-outs for HOXD11: Evx2/Hoxd11/Hoxd12/Hoxd13^{Evx2/Hoxd11/Hoxd12/tm1Ddu} Hoxd11^tm2.1Ddu Hoxd11^tm1Mrc Hoxd11^tm2Ddu Hoxd11^tm1Ipc

inGenious Targeting Laboratory - Custom generated mouse model solutions for HOXD11

inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for HOXD11

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD11

(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 Central^TM 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

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
MEIS1	O00470³, ENSP00000272369⁴	I2D: score=1 STRING: ENSP00000272369
HMGB1	P09429³, ENSP00000343040⁴	I2D: score=1 STRING: ENSP00000343040

About this table

Gene Ontology (GO): 5/19 biological process terms (GO ID links to tree view) (see all 19): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001501	skeletal system development	--	--
GO:0001656	metanephros development	IEA	--
GO:0001658	branching involved in ureteric bud morphogenesis	ISS	--
GO:0001759	organ induction	IEA	--
GO:0006351	transcription, 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, IUPHAR, 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 (HXD11)

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

(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,
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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 Products:
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Additional mRNA sequence:

AK309681.1 BC109394.1

4 DOTS entries:

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

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

BF510955 AI095929 AW205221 AW206798 BC074760 NM_021192 BC069619 AA653427

AI139039 NM_002148 CD614162 AW243295 X59373 AL526269 AI277208 AW195017

BX117343 BM903736 AI423516 CB151522 BF526767 CA431276 AA479366 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) HOXD11 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CAACGCGAGC

About this image

HOXD11 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database

5/16 selected tissues (see all 16) fully expand


Kidney (Urinary System) fully expand to see all 5 entries
Metanephric Mesenchyme Cells Metanephric Mesenchyme
Metanephros
mK3
Intermediate mesoderm derivatives (Generation of intermediate mesoderm cells from...

Limb (Muscoskeletal System) fully expand to see all 4 entries
Limb Bud Mesenchyme Cells Limb Bud
Limb Bud

Mesoderm (Gastrulation Derivatives) fully expand to see all 3 entries
Limb Bud Mesenchyme Cells Limb Bud
Intermediate mesoderm derivatives (Generation of intermediate mesoderm cells from...

Bone (Muscoskeletal System) fully expand to see all 3 entries
Sacral Sclerotome Cells Sacral Mesencymal Sclerotome
Zeugopod Long Bone

Lower Urinary Tract (Urinary System) fully expand to see all 2 entries
visceral organ

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 chordates.

Orthologs for HOXD11 gene from 3/9 species (see all 9) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Hoxd11^{1 , 5}	homeobox D11^{1, 5}	90.28(n)¹ 94.64(a)¹		2 (44.13 cM)⁵ 15431¹ NM_008273.2¹ NP_032299.1¹ 74679392⁵
chicken (Gallus gallus)	Aves	HOXD11¹	homeobox D11	74.76(n) 75(a)		395328 NM_204620.1 NP_989951.1
lizard (Anolis carolinensis)	Reptilia	HOXD11⁶	Uncharacterized protein	58(a)	1 ↔ 1	GL343356.1(556257-559822)

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

ENSG00000257184² HOXD10² HOXC13² HOXC10² HOXD12² HOXA9² HOXA13² HOXC9²

HOXB13² HOXC12² HOXC11² HOXD13² HOXA11² HOXB9² HOXD9² HOXA10²

14 SIMAP similar genes for HOXD11 using alignment to 2 protein entries: HXD11_HUMAN (see all proteins):

CDX1 HOX B6 HOXC13 HOXB1 HOXA4 HOXB8

HOXA-9 HOXA11 CDX2 HOXB3 HOXD13 GBX1

HOXC11 HOXA10

HOXD11 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

SNP ID	Valid	Clinical significance	Chr 2 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
VAR_031647⁴		--	--	see VAR_031647	2	G D	mis⁴		0	--	--	--	--
rs188896135^1,2		--	176970117(+)	`AAGGGG/TCGGAG`	1	--	us2k¹		0	--	--	--	--
rs116425345^1,2	C,F	--	176970121(+)	`GGCGGA/GGGAAG`	1	--	us2k¹		1		WA	118
rs201828765^1,2	C	--	176970168(+)	`AGGAA-/GGGGGG`	1	--	us2k¹		0	--	--	--	--
rs117257637^1,2	C,F	--	176970185(+)	`CAGCCA/GGAAAA`	1	--	us2k¹		1		EA	120
rs72923436^1,2	C,F	--	176970247(+)	`CAGAGC/AGCACA`	1	--	us2k¹		2		WA NA	238
rs3813811^1,2	C,F,H	--	176970340(-)	`CTGGGG/ACCTGG`	1	--	us2k¹		4		NS EA	418
rs73033720^1,2	C,F	--	176970401(+)	`CCCTCG/TGTTCT`	1	--	us2k¹		2		WA	120
rs847148^1,2	C,F,H	--	176970456(-)	`CCGAGT/AGAGCA`	1	--	us2k¹		16		NS EA NA WA CSA	791
rs847147^1,2	C,F,A,H	--	176970659(-)	`TCAGCC/TCCTCC`	1	--	us2k¹ tfbs³ trp³		23		MN NS EA NA WA CSA	2417

HapMap Linkage Disequilibrium report for HOXD11 (176968944 - 176974722 bp)

Structural Variations
Database of Genomic Variants (DGV) 10/13 variations for HOXD11 (see all 13): About this table

Variant ID	Type	Subtype	PubMed ID
nsv520227	CNV	Loss	19592680
nsv875441	CNV	Loss	21882294
nsv875447	CNV	Loss	21882294
nsv875442	CNV	Loss	21882294
dgv4368n71	CNV	Loss	21882294
nsv524250	CNV	Loss	19592680
nsv875438	CNV	Loss	21882294
nsv875446	CNV	Loss	21882294
nsv875437	CNV	Loss	21882294
dgv4369n71	CNV	Loss	21882294

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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

HOXD11 for disorders           About GeneDecksing

OMIM gene information: 142986    OMIM disorders: --

9 diseases for HOXD11:    About MalaCards

brachydactyly-syndactyly syndrome syndactyly clubfoot renal agenesis

brachydactyly polydactyly acute myeloid leukemia myeloid leukemia

leukemia

2 diseases from the University of Copenhagen DISEASES database for HOXD11:

Polydactyly Renal agenesis

Genetic Association Database (GAD): HOXD11
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

Altered transmission of HOX and apoptotic SNPs identi fy a potential common pathway for clubfoot. (PubMed id 19938081)^{1, 4} Ester A.R....Hecht J.T. (2009)
Absence of mutations in the HOXA11 and HOXD11 genes in children with congenital renal malformations. (PubMed id 19255789)^{1, 4} Bouba I....Georgiou I. (2009)
Study of HOXD genes in autism particularly regarding the ratio of second to fourth digit length. (PubMed id 19540081)^{1, 4} Sugie Y....Osawa J. (2009)
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, 4} Yerges L.M....Zmuda J.M. (2009)
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PubMed id 17236141)^{1, 2} Zhao X.... Zhang X. (2007)
Vertebrate homeobox gene nomenclature. (PubMed id 1358459)^{1, 3} Scott M.P. (1992)
Nomenclature for human homeobox genes. (PubMed id 1973146)^{1, 3} McAlpine P.J. and Shows T.B. (1990)
The human HOX gene family. (PubMed id 2574852)^{1, 2} Acampora D.... Boncinelli E. (1989)
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)
A region of the human HOXD cluster that confers polyc omb-group responsiveness. (PubMed id 20085705)¹ Woo C.J....Kingston R.E. (2010)

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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,
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PharmGKB entry for HOXD11	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for HOXD11	Genetics and Cytogenetics in Oncology and Haematology

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