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

HOXD1 Gene

protein-coding   GIFtS: 51
GCID: GC02P177053

homeobox D1

(Previous name: homeo box D1 )
(Previous symbols: HOX4, HOX4G)
 Explore 5 diseases affiliated with
HOXD1 via our new
 Human Malady Compendium 
Biological research products
for HOXD1
    

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

Aliases
Homeobox D11 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

External Ids:    HGNC: 51321   Entrez Gene: 32312   Ensembl: ENSG000001286457   OMIM: 1429875   UniProtKB: Q9GZZ03   

Export aliases for HOXD1 gene to outside databases

Previous GC identifers: GC02P175105 GC02P175714 GC02P177017 GC02P177255 GC02P176878 GC02P176761 GC02P168930


(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 cells
with specific positional identities on the anterior-posterior axis. Acts on the anterior body structures

Gene Wiki entry for HOXD1


(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

SwitchGear Promoter luciferase reporter plasmidHOXD1 promoter sequence
   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)
HOXD1 gene location

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

(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: HXD1_HUMAN, Q9GZZ0 (See protein sequence)
Recommended Name: Homeobox protein Hox-D1  
Size: 328 amino acids; 34093 Da
Subcellular location: Nucleus
Secondary accessions: B2RAB4

Explore the universe of human proteins at neXtProt for HOXD1: NX_Q9GZZ0

HOXD1 Protein expression data from MOPED and PaxDb:    About this image 

Estimated protein expression log10 (pmol).

REFSEQ proteins: NP_078777.1  
ENSEMBL proteins: 
 ENSP00000328598  

Human Recombinant Protein Products: 
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Uscn Proteins for HOXD1

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

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


HOXD1 for ontologies           About GeneDecksing



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Uscn ELISAs and CLIAs for HOXD1


(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:
 IPR020479 Homeobox_metazoa
 IPR017970 Homeobox_CS
 IPR001356 Homeodomain
 IPR009057 Homeodomain-like

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 subfamily
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: HXD1_HUMAN, Q9GZZ0
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. Acts on the anterior body structures

     Genatlas biochemistry entry for HOXD1:
homeo box D1(4G),homologous to mouse Hox-4.9,Drosophila lab

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SwitchGear 3'UTR luciferase reporter plasmidHOXD1 3' UTR sequence
Inhib. RNA
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Gene Editing
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In Situ Assay
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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 IDQualified GO termEvidencePubMed IDs
GO:0003700sequence-specific DNA binding transcription factor activity IEA--
GO:0043565sequence-specific DNA binding IEA--


HOXD1 for ontologies           About GeneDecksing


2 GenomeRNAi human phenotypes for HOXD1:
 Increased G2M DNA content  Synthetic lethal with Ras 

Animal Models:
     Mouse knock-out Hoxd1tm1Mrc for HOXD1
     5 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Hoxd1):
 behavior/neurological  craniofacial  integument  nervous system  skeleton 

HOXD1 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 HOXD1

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for HOXD1 (Q9GZZ03 ENSP000003285984) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
HOXC9P312743, ENSP000003028364I2D: score=1 STRING: ENSP00000302836
About this table

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

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-dependent IEA--
GO:0048706embryonic skeletal system development IEA--


HOXD1 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 HOXD1
Search CenterWatch for drugs/clinical trials and news about HOXD1 / HXD1 

(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)

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hsa-let-7d hsa-miR-503 hsa-miR-301a hsa-miR-508-3p hsa-let-7g hsa-miR-9 hsa-let-7a hsa-miR-133a
SwitchGear 3'UTR luciferase reporter plasmidHOXD1 3' UTR sequence
Inhib. RNA
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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

(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 imageBioGPS
CGAP TAG: TAAAGGGTTT

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

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
4 LifeMap In Vivo Development Anatomical Compartments/Cells 
Tissue Anatomical Compartment CellCategory (developmental path)
KidneyUreteric BudUreteric Bud CellsKidney
KidneyUreteric BudUreteric Bud Tip CellsKidney
Yolk SacDefinitive Yolk SacDefinitive Hematopoietic Stem CellsBlood
KidneyUreteric BudKidney
Expression: Positive    Negative     Selective marker
Experimental details: Curated     Microarrays     In-situ hybridization
Stem Cell Differentiation: 2 LifeMap Cells 
NameCategory
PureStem™ endothelial Progenitor 30-SM2-3 (Embryonic Progenitor Cell)Blood, Endothelium
PureStem™ endothelial progenitor 30-SM2-1 (Embryonic Progenitor Cell)Endothelium

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: 
          Stem Cell Transcription Factors in human mouse rat
          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 HOXD1

(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 HOXD1 gene from 5/17 species (see all 17)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves F1P4V0_CHICK6
Q804C5_CHICK6
Uncharacterized protein
67(a)
30(a)
1 ↔ 1
possible ortholog
7(17361519-17361719)
2(32513652-32519213)
lizard
(Anolis carolinensis)
Reptilia HOXD16
--
65(a)
1 ↔ 1
GL343356.1(360930-363482)
zebrafish
(Danio rerio)
Actinopterygii hoxc1a6
homeo box C1a
25(a)
1 ↔ 1
23(36229648-36235041)
fruit fly
(Drosophila melanogaster)
Insecta lab6
labial
12(a)
1 → many
3R(2487149-2504312)
worm
(Caenorhabditis elegans)
Secernentea ceh-136
Homeobox protein ceh-13
25(a)
1 → many
III(7555594-7558142)


ENSEMBL Gene Tree for HOXD1 (if available)
TreeFam Gene Tree for HOXD1 (if available) 

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for HOXD1 gene
GSX12  HOXA72  HOXA12  HOXA22  HOXB32  HOXC62  HOXB52  GSX22  
HOXC52  HOXB42  HOXA52  HOXA42  HOXD32  HOXC82  HOXA62  HOXA32  
HOXD82  HOXB12  HOXB62  HOXB82  HOXD42  HOXB22  HOXB72  PDX12  
HOXC42  
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



(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

10/78 NCBI SNPs in HOXD1 are shown (see all 78    About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 2 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1821801161,2
--177051320(+) CGGGCA/GCGGTG 2 -- us2k1 int10--------
rs1462377241,2
--177051476(+) TAGTAA/CCAGCT 2 -- int1 us2k10--------
rs2017471571,2
--177051574(+) AAAAT-/TAAA  
        
TAAAT
2 -- us2k1 int10--------
rs1872937291,2
--177051623(+) GGCTAC/TAGCAC 2 -- us2k1 int10--------
rs1391677991,2
--177051709(+) CCAGCA/TGTGCA 2 -- us2k1 int10--------
rs1499037651,2
--177051727(+) CAGACC/TTCTTT 2 -- int1 us2k10--------
rs130116031,2
C,F,A,--177051871(+) CCACAA/TCCCTG 2 -- int1 us2k17Minor allele frequency- T:0.38NA WA CSA 247
rs1917559691,2
--177051888(+) ACTGGC/TTCCCT 2 -- us2k1 int10--------
rs1838557521,2
--177051895(+) CCCTGA/GGCTGT 2 -- int1 us2k10--------
rs1152929441,2
F,--177051916(+) ATTCTA/GAAGAC 2 -- int1 us2k11Minor allele frequency- G:0.06WA 118

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
DNA2.0 Custom Variant and Variant Library Synthesis for HOXD1

(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

(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 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

  1. Isolation and characterization of the human homeobox gene HOX D1. (PubMed id 11455954)1, 2 Appukuttan B.... Stout J.T. (2000)
  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. Homeobox D1 regulates angiogenic functions of endothe lial cells via integrin I^1 expression. (PubMed id 21501586)1 Park H....Kwon Y.G. (2011)
  5. 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)
  6. An atlas of combinatorial transcriptional regulation in mouse and man. (PubMed id 20211142)1 Ravasi T....Hayashizaki Y. (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. 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)
  9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
  10. Complete mutation analysis panel of the 39 human HOX genes. (PubMed id 11857506)1 Kosaki K.... Matsuo N. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 3231 HGNC: 5132 AceView: HOXD1 Ensembl:ENSG00000128645 euGenes: HUgn3231
ECgene: HOXD1 H-InvDB: HOXD1

(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 HOXD1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for HOXD1 gene:
Search GeneIP for patents involving HOXD1

GeneCards and IP:
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