HOXD1 Gene
protein-coding GIFtS : 51
GCID: GC02 P177053
homeobox D1 (Previous name: homeo box D1 ) (Previous symbols: HOX4, HOX4G )
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Aliasesfor HOXD1 gene
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc ,
7 Ensembl ,
8 DME ,
9 miRBase ,
and/or 10 fRNAdb )About This Section Aliases Homeobox D1 1 2 Homeobox Protein Hox-GG2 3 HOX4G1 2 3 5 Hox-4.72 HOX41 2 3 Homeo Box 4G2 Homeo Box D11 2 Homeobox Protein Hox-D12
Export aliases for HOXD1 gene to outside databases Previous GC identifers: GC02P175105 GC02P175714 GC02P177017 GC02P177255 GC02P176878 GC02P176761 GC02P168930
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Summariesfor HOXD1 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 HOXD1 : This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. (provided by RefSeq, Jul 2008) UniProtKB/Swiss-Prot: HXD1_HUMAN, Q9GZZ0 Function : Sequence-specific transcription factor which is part of a developmental regulatory system that provides cellswith specific positional identities on the anterior-posterior axis. Acts on the anterior body structures Gene Wiki entry for HOXD1
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Genomic Viewsfor HOXD1 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 HOXD1 gene promoter: AhR Sox5 FOXF2 AP-4 Arnt POU2F1 POU2F1a HNF-1 Other transcription factors Search SABiosciences Chromatin IP Primers for HOXD1 Epigenetics: QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human , mouse , rat HOXD1
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 HOXD1 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 GC02P177053: view genomic region
(about GC identifiers )
Start:
177,053,307 bp from pter
End:
177,055,688 bp from pter
Size:
2,382 bases
Orientation:
plus strand
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Proteinsfor HOXD1 gene
(According to
1 UniProtKB ,
HORDE ,
neXtProt ,
Ensembl ,
and/or Reactome ,
Modification sites according to 2 PhosphoSitePlus ,
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: HXD1_HUMAN, Q9GZZ0 (See
protein sequence )Recommended Name: Homeobox protein Hox-D1 Size : 328 amino acids; 34093 Da
Subcellular location : Nucleus
Secondary accessions : B2RAB4Explore the universe of human proteins at neXtProt for HOXD1: NX_Q9GZZ0 HOXD1 Protein expression data from MOPED and PaxDb : About this image
REFSEQ proteins: NP_078777.1 ENSEMBL proteins: ENSP00000328598 Human Recombinant Protein Products: 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
IEA --
HOXD1 for ontologies About GeneDecksing HOXD1 Antibody Products: Assay Products for HOXD1:
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Protein
Domains / Familiesfor HOXD1 gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
About This Section
HOXD1 for domains About GeneDecksing 4 InterPro domains/families :
Graphical View of Domain Structure for InterPro Entry Q9GZZ0 ProtoNet protein and cluster: Q9GZZ0
1 Blocks protein family : IPB001827 Homeobox protein UniProtKB/Swiss-Prot: HXD1_HUMAN, Q9GZZ0 Similarity : Belongs to the Antp homeobox family. Labial subfamilySimilarity : Contains 1 homeobox DNA-binding domain
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Functionfor HOXD1 gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
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: HXD1_HUMAN, Q9GZZ0 Function : Sequence-specific transcription factor which is part of a developmental regulatory system that provides cellswith specific positional identities on the anterior-posterior axis. Acts on the anterior body structures
Genatlas biochemistry entry for HOXD1 : homeo box D1(4G),homologous to mouse Hox-4.9,Drosophila lab Clone Products: Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 (see all 3 ) OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 (see all 2 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector: HOXD1 (NM_024501 ) Browse Sino Biological Human cDNA Clones DNA2.0 Custom Codon Optimized Gene
Synthesis Service for HOXD1 Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat HOXD1
In Situ Assay Products: Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD1
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view) : About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0003700 sequence-specific DNA binding transcription factor activity
IEA -- GO:0043565 sequence-specific DNA binding
IEA --
HOXD1 for ontologies About GeneDecksing 2 GenomeRNAi human phenotypes for HOXD1 :Animal Models: Mouse knock-out Hoxd1 tm1Mrc for HOXD1 5 MGI mutant phenotypes (inferred from 2 alleles ) (MGI details for Hoxd1) :
HOXD1 for phenotypes About GeneDecksing
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Pathways & Interactionsfor HOXD1 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 1 UniProtKB ,
2 MINT ,
3 I2D , and/or
4 STRING ,
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 HOXD1 STRING Interaction
Network Preview (showing 1 interactants - click image to see more details)1 Interacting protein for HOXD1 (Q9GZZ0 3 ENSP00000328598 4 ) via UniProtKB, MINT, STRING , and/or I2D About this table Gene Ontology (GO): 2 biological process terms (GO ID links to tree view) : About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0006351 transcription, DNA-dependent
IEA -- GO:0048706 embryonic skeletal system development
IEA --
HOXD1 for ontologies About GeneDecksing
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Drugs & Compoundsfor HOXD1 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 Tocris compounds for HOXD1 Search CenterWatch for drugs/clinical trials and news about HOXD1 / HXD1
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Transcriptsfor HOXD1 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 HOXD1 gene: NM_024501.2 Unigene Cluster for HOXD1:
Homeobox D1 Hs.83465 [show with all ESTs ] Unigene Representative Sequence: AF241528 1 Ensembl transcript including schematic representation, and UCSC links where relevant : ENST00000331462 (uc002ukv.4 uc010fqy.3 uc021vsr.1 ) Clone Products: OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 (see all 3 ) OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 (see all 2 )OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling GenScript: all cDNA clones in your preferred vector: HOXD1 (NM_024501 ) DNA2.0 Custom Codon Optimized Gene
Synthesis Service for HOXD1 Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat HOXD1
Additional cDNA sequence: AF241528.1 AK314120.1 BC014477.1 BC028190.1
2 DOTS entries : DT.110725 DT.100748178
24/44 AceView cDNA sequences (see all 44 ):
AI640538 AI479390 BC028190 BC014477 AI088005 AW073903 AF241528 BQ687080 AW137557 BX101877 NM_024501 N68975 AW135647 BG766603 BF062946 BI829220 AW051981 BE464233 AW205452 BF439323 AI367262 AW300533 AI927994 BU149592 GeneLoc Exon Structure 2 Alternative Splicing Database (ASD) splice patterns (SP) for HOXD1 About this scheme ExUns: 1a · 1b ^ 2 ^ 3 SP1 :         SP2 :     -    
ECgene alternative splicing isoforms for HOXD1
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Expression for HOXD1 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 HOXD1 expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this image BioGPS CGAP TAG: TAAAGGGTTT
About this image HOXD1 expression in embryonic tissues and stem cells Expression by the Database of Embryonic development, Stem cell research, and
Regenerative medicine About this table See HOXD1 Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for HOXD1 SOURCE GeneReport for Unigene cluster: Hs.83465 SABiosciences Expression via Pathway-Focused PCR Arrays including HOXD1 : Primer Products: OriGene genome-wide validated SYBR primer pairs in human , mouse , rat for HOXD1Browse OriGene validated miRNA SYBR primer pairs SABiosciences RT2 qPCR Primer Assay in human , mouse , rat HOXD1 QIAGEN QuantiTect SYBR Green Assays in human , mouse , rat HOXD1 QIAGEN QuantiFast Probe-based Assays in human , mouse , rat HOXD1 In Situ Assay Products: Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD1
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Orthologsfor HOXD1 gene
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
,
5 MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase ,
and/or
6 Ensembl 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 HOXD1 gene from 5/17 species (see all 17 ) About this table
ENSEMBL Gene Tree for HOXD1 (if available)TreeFam Gene Tree for HOXD1 (if available)
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Paralogsfor HOXD1 gene (Paralogs according to
1 HomoloGene , 2 Ensembl , and 3 SIMAP , Pseudogenes according to 4 Pseudogene.org Build 68)About This Section Paralogs for HOXD1 gene GSX1 2 HOXA7 2 HOXA1 2 HOXA2 2 HOXB3 2 HOXC6 2 HOXB5 2 GSX2 2 HOXC5 2 HOXB4 2 HOXA5 2 HOXA4 2 HOXD3 2 HOXC8 2 HOXA6 2 HOXA3 2 HOXD8 2 HOXB1 2 HOXB6 2 HOXB8 2 HOXD4 2 HOXB2 2 HOXB7 2 PDX1 2 HOXC4 2 3 SIMAP similar genes for HOXD1 using alignment to 3 protein entries: HXD1_HUMAN (see all proteins ):HOX B6 HMX2 HOXA1
HOXD1 for paralogs About GeneDecksing
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Genomic Variantsfor HOXD1 gene (SNPs/Variants according to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE ,
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
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
HapMap Linkage Disequilibrium report for HOXD1 (177053307 - 177055688 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV) variations for HOXD1: --
SABiosciences Cancer Mutation PCR Assays
QIAGEN SeqTarget long-range PCR primers in human , mouse , rat for resequencing HOXD1
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Disorders
/ Diseasesfor HOXD1 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
HOXD1 for disorders About GeneDecksing
OMIM gene information: 142987
OMIM disorders : --5 diseases for HOXD1 : About MalaCards clubfoot syndactyly ovarian cancer neuroblastoma thyroiditis 1 disease from the University of Copenhagen DISEASES database for HOXD1 :Syndactyly Human Genome Epidemiology (HuGE) Navigator: HOXD1 (4 documents) Export disorders for HOXD1 gene to outside databases
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Publicationsfor HOXD1 gene (in
PubMed .
Associations of this gene to articles via
1 Entrez Gene ,
2 UniProtKB/Swiss-Prot ,
3 HGNC ,
4 GAD ,
5 PharmGKB ,
6 HMDB ,
7 DrugBank ,
8 UniProtKB/TrEMBL ,
9 Novoseek , and/or
10 fRNAdb )
About This Section PubMed articles for HOXD1 gene, integrated from 9 sources (see all 19 ): (articles sorted by number of sources associating them with HOXD1) Utopia : connect your pdf to the dynamic world of online information
Isolation and characterization of the human homeobox gene HOX D1. (PubMed id 11455954) 1 , 2 Appukuttan B.... Stout J.T. (2000) 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) Homeobox D1 regulates angiogenic functions of endothe lial cells via integrin I^1 expression. (PubMed id 21501586) 1 Park H....Kwon Y.G. (2011) A genome-wide association study identifies susceptibi lity loci for ovarian cancer at 2q31 and 8q24. (PubMed id 20852632) 1 Goode E.L....Pharoah P.D. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142) 1 Ravasi T....Hayashizaki Y. (2010) 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) 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) Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039) 2 Ota T.... Sugano S. (2004) Complete mutation analysis panel of the 39 human HOX genes. (PubMed id 11857506) 1 Kosaki K.... Matsuo N. (2002)
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External Searches for HOXD1 gene
(in PubMed ,
OMIM , and NCBI Bookshelf ) About This Section
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Genome Databases showing HOXD1 gene
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
Kegg ,
and/or
H-InvDB )
About This Section
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Other Databases showing HOXD1 gene
(According to HUGE )
About This Section --
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Specialized Databases showing HOXD1 gene (According to PharmGKB ,
ATLAS , HORDE , IMGT , LEIDEN , UniProtKB/Swiss-Prot , and/or UniProtKB/TrEMBL ,Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot )About This Section
Name Description
PharmGKB entry for HOXD1 Pharmacogenomics, SNPs, Pathways
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About This Section Patent Information for HOXD1 gene: Search GeneIP for patents involving HOXD1 GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Productsfor HOXD1 gene (Antibodies, recombinant proteins, and assays from EMD Millipore , R&D Systems , OriGene , QIAGEN , GenScript , Cell Signaling Technology , SABiosciences , Novus Biologicals , Sino Biological , Enzo Life Sciences , Abcam , ProSpec , Uscn , Thermo Fisher Scientific , Gene Editing from DNA2.0 , Clones from EMD Millipore , OriGene , GenScript , Sino Biological , DNA2.0 , SwitchGear Genomics , Vector BioLabs , Cell lines from GenScript and LifeMap BioReagents , PCR Arrays from SABiosciences , Drugs and/or compounds from EMD Millipore , Tocris Bioscience , and/or
Enzo Life Sciences ), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
Browse OriGene Antibodies OriGene shRNA RFP for HOXD1 OriGene 29mer shRNA kits in GFP-retroviral vector in human , mouse , rat for HOXD1 OriGene genome-wide validated SYBR primer pairs in human , mouse , rat for HOXD1 OriGene Protein Over-expression Lysate for HOXD1 Browse OriGene Fluorogenic Cell Assay Kits OriGene siRNA for HOXD1 OriGene 3'-UTR Clone for HOXD1 OriGene untagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human , mouse , rat for HOXD1 Browse OriGene GFP tagged cDNA clones in CMV expression vector Browse OriGene MicroRNA Expression Plasmids Browse OriGene basic RS shRNAs Browse OriGene validated miRNA SYBR primer pairs Browse OriGene full length recombinant human proteins expressed in human HEK293 cells OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling OriGene Custom Antibody Services for HOXD1 OriGene Custom Protein Services for HOXD1 OriGene Custom Immunoassay Development
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat HOXD1 QIAGEN SeqTarget long-range PCR primers in human , mouse , rat for resequencing HOXD1 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human , mouse , rat HOXD1 QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human , mouse , rat HOXD1 QIAGEN QuantiFast Probe-based Assays in human , mouse , rat HOXD1 QIAGEN QuantiTect SYBR Green Assays in human , mouse , rat HOXD1
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HOXD1 Proteins, Antibodies, CLIAs, and ELISAs
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HOXD1
Search ThermoFisher Antibodies for HOXD1
Vector BioLabs ready-to-use adenovirus/AAV for human , mouse , rat HOXD1
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Aliases for HOXD1
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Disorders / Diseases for HOXD1
Domains / Families for HOXD1
Drugs / Compounds for HOXD1
Expression for HOXD1
Function for HOXD1
Genomic Views for HOXD1
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