HOXD11 Gene

Aliases
for HOXD11 gene

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, ¹⁰fRNAdb, ¹²H-InvDB, ¹³NCBI, ¹⁴NONCODE, and/or ¹⁵RNAdb)
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Previous GC identifers: GC02P175024 GC02P175633 GC02P177174 GC02P176797 GC02P176680 GC02P168849

Summaries
for HOXD11 gene

(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Genomic Views
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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:

NC_000002.11  NT_005403.18  NC_018913.2  

SwitchGear Promoter luciferase reporter plasmid: HOXD11 promoter sequence

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat HOXD11

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


GeneLoc information about chromosome 2         GeneLoc Exon Structure

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

Proteins
for HOXD11 gene

(According to ¹UniProtKB, HORDE, ²neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, antibodies-online, and/or GeneTex,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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Explore the universe of human proteins at neXtProt for HOXD11: NX_P31277

Explore proteomics data for HOXD11 at MOPED


See HOXD11 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

HOXD11 Human Recombinant Protein Products:

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	antibodies-online peptides for HOXD11

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Domains /
Families
for HOXD11 gene

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GenesLikeMe)
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ProtoNet protein and cluster: P31277

Find genes that share domains with HOXD11           About GenesLikeMe

Function
for HOXD11 gene

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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     Gene Ontology (GO): 3 molecular function terms:    About this table

(inferred from 7 alleles) (MGI details for Hoxd11)

genOway: Develop your customized and physiologically relevant rodent model for HOXD11

miRNA Products:		miRTarBase miRNAs that target HOXD11: hsa-let-7b-5p (MIRT051956), hsa-mir-744-5p (MIRT037516)
		Block miRNA regulation of human, mouse, rat HOXD11 using miScript Target Protectors
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		SwitchGear 3'UTR luciferase reporter plasmid: HOXD11 3' UTR sequence

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		Predesigned siRNA for gene silencing in human, mouse, rat HOXD11

Gene Editing Products:

DNA2.0 Custom Protein Engineering Service for HOXD11

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In Situ Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD11

Localization
for HOXD11 gene

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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Subcellular locations from COMPARTMENTS: 

Compartment	Confidence
nucleus	5

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Gene Ontology (GO): 1 cellular component term:    About this table

Pathways & Interactions
for HOXD11 gene

(SuperPaths according to PathCards, Pathways according to 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 GenesLikeMe, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene, Sets of similar genes according to GenesLikeMe)
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Gene Ontology (GO): Selected biological process terms (see all 19):    About this table

Drugs & Compounds
for HOXD11 gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, Sets of similar genes according to GenesLikeMe)
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Transcripts
for HOXD11 gene

(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Expression
for HOXD11 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 GenesLikeMe, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE ¹MOPED, ²PaxDb, and ³MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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HOXD11 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: CAACGCGAGC

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Kidney (Urinary System)    fully expand to see all 6 entries
Metanephric Mesenchyme Cells Metanephric Mesenchyme
Metanephros
mK3
Intermediate mesoderm derivatives
Limb (Muscoskeletal System)    fully expand to see all 4 entries
Limb Bud Mesenchyme Cells Limb Bud
Limb Bud
Bone (Muscoskeletal System)    fully expand to see all 3 entries
Sacral Sclerotome Cells Sacral Mesenchymal Sclerotome
Zeugopod Long Bone
Mesoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
Limb Bud Mesenchyme Cells Limb Bud
Cartilage (Muscoskeletal System)    fully expand to see all 2 entries
Sacral Sclerotome Cells Sacral Mesenchymal Sclerotome

Primer Products:		OriGene qSTAR qPCR primer pairs in human, mouse for HOXD11
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In Situ Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD11

Orthologs
for HOXD11 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)
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Paralogs
for HOXD11 gene

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68,Sets of similar genes according to GenesLikeMe)
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Paralogs for HOXD11 gene

ENSG00000257184²  HOXD10²  HOXC13²  HOXC10²  HOXD12²  HOXA9²  HOXA13²  HOXC9²  

HOXB13²  HOXC12²  HOXC11²  HOXD13²  HOXA11²  HOXB9²  HOXD9²  HOXA10²  

13 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    HOXB3    HOXD13    GBX1    HOXC11

HOXA10

Find genes that share paralogs with HOXD11           About GenesLikeMe

Genomic Variants
for HOXD11 gene

(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for HOXD11 (see all 96)    About this table

Genomic Data					Transcription Related Data				Allele Frequencies
SNP ID	Valid	Clinical significance	Chr 2 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
-1st2nd3rd	-1st2nd3rd	-1st2nd3rd	-1st2nd3rd	--	--	--	-1st2nd3rd	--	--	-1st2nd3rd	-1st2nd3rd	-1st2nd3rd
rs1888961351,2		--	176970117(+)	AAGGGG/TCGGAG	1	--	us2k1		0	--	--	--	--
rs1164253451,2	C,F	--	176970121(+)	GGCGGA/GGGAAG	1	--	us2k1		1		WA	118
rs2018287651,2	C	--	176970168(+)	AGGAA-/GGGGGG	1	--	us2k1		0	--	--	--	--
rs1172576371,2	C,F	--	176970185(+)	CAGCCA/GGAAAA	1	--	us2k1		1		EA	120
rs729234361,2	C,F	--	176970247(+)	CAGAGC/AGCACA	1	--	us2k1		2		WA NA	238
rs38138111,2	C,F,H	--	176970340(-)	CTGGGG/ACCTGG	1	--	us2k1		4		NS EA	418
rs730337201,2	C,F	--	176970401(+)	CCCTCG/TGTTCT	1	--	us2k1		2		WA	120
rs8471481,2	C,F,H	--	176970456(-)	CCGAGT/AGAGCA	1	--	us2k1		16		NS EA NA WA CSA	791
rs8471471,2	C,F,A,H	--	176970659(-)	TCAGCC/TCCTCC	1	--	us2k1 tfbs3 trp3		23		MN NS EA NA WA CSA	2417
rs803407311,2	C,F	--	176970735(+)	TTGGCG/CGGGCT	1	--	us2k1		2		CSA WA	119

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

Structural Variations
     Database of Genomic Variants (DGV) Selected 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

Site Specific Mutation Identification with PCR Assays

SeqTarget long-range PCR primers for resequencing HOXD11

DNA2.0 Custom Variant and Variant Library Synthesis for HOXD11

Disorders / Diseases
for HOXD11 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, Sets of similar genes according to GenesLikeMe)
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Publications
for HOXD11 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)
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1. 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. (amp 2010)
2. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PubMed id 19938081)^{1, 4} Ester A.R....Hecht J.T. (Am. J. Med. Genet. A 2009)
3. Absence of mutations in the HOXA11 and HOXD11 genes in children with congenital renal malformations. (PubMed id 19255789)^{1, 4} Bouba I....Georgiou I. (Pediatr. Nephrol. 2009)
4. 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. (J. Bone Miner. Res. 2009)
5. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. (PubMed id 17236141)^{1, 2} Zhao X.... Zhang X. (Am. J. Hum. Genet. 2007)
6. Vertebrate homeobox gene nomenclature. (PubMed id 1358459)^{1, 3} Scott M.P. (Cell 1992)
7. Nomenclature for human homeobox genes. (PubMed id 1973146)^{1, 3} McAlpine P.J. and Shows T.B. (Genomics 1990)
8. The human HOX gene family. (PubMed id 2574852)^{1, 2} Acampora D.... Boncinelli E. (Nucleic Acids Res. 1989)
9. 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. (Cancer Res. 2002)
10. A region of the human HOXD cluster that confers polycomb-group responsiveness. (PubMed id 20085705)¹ Woo C.J....Kingston R.E. (Cell 2010)

External Searches for HOXD11 gene

Genome Databases showing HOXD11 gene

Other Databases showing HOXD11 gene

Specialized Databases showing HOXD11 gene

Products
for HOXD11 gene

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, GeneTex, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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