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SLX1A Gene

protein-coding   GIFtS: 34
GCID: GC16P030218

SLX1 Structure-Specific Endonuclease Subunit Homolog A (S....

(Previous name: GIY-YIG domain containing 1)
(Previous symbol: GIYD1)
  See related diseases
at  

(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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Aliases
SLX1 Structure-Specific Endonuclease Subunit Homolog A (S.
Cerevisiae)1 2
     Structure-Specific Endonuclease Subunit SLX12
GIYD11 2 3     EC 3.6.1.-3
GIY-YIG Domain-Containing Protein 12 3     GIYD23
GIY-YIG Domain Containing 11     SLX13

External Ids:    HGNC: 209221   Entrez Gene: 5485932   Ensembl: ENSG000001322077   UniProtKB: Q9BQ833   

Export aliases for SLX1A gene to outside databases

Previous GC identifers: GC16P030208 GC16P030210 GC16P030215


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SLX1A Gene:
This gene encodes a protein that is an important regulator of genome stability. The protein represents the
catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures
that are formed during repair and recombination processes. Two identical copies of this gene are located on the p
arm of chromosome 16 due to a segmental duplication; this record represents the more centromeric copy.
Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this
gene and the downstream SULT1A3 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3) gene.
(provided by RefSeq, Nov 2010)

GeneCards Summary for SLX1A Gene:
SLX1A (SLX1 structure-specific endonuclease subunit homolog A (S. cerevisiae)) is a protein-coding gene. Diseases associated with SLX1A include fanconi's anemia, and malaria. GO annotations related to this gene include 5'-flap endonuclease activity and crossover junction endodeoxyribonuclease activity. An important paralog of this gene is SLX1B.

UniProtKB/Swiss-Prot: SLX1_HUMAN, Q9BQ83
Function: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary
structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA
substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for
5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves
HJs by generating two pairs of ligatable, nicked duplex products




(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for SLX1A
         Other transcription factors

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   Search Chromatin IP Primers for SLX1A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLX1A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p11.2   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p11.2

SLX1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLX1A gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P030218:  view genomic region     (about GC identifiers)

Start:
30,205,164 bp from pter      End:
30,208,887 bp from pter
Size:
3,724 bases      Orientation:
plus strand

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SLX1_HUMAN, Q9BQ83 (See protein sequence)
Recommended Name: Structure-specific endonuclease subunit SLX1  
Size: 275 amino acids; 30771 Da
Cofactor: Divalent cation
Subunit: Forms a heterodimer with SLX4
Caution: Found in a segmental duplication on p arm of chromosome 16 giving rise to two identical copies of this
gene sharing exons with SULT1A3 and SULT1A4
Secondary accessions: B7ZME1 Q6NTG6
Alternative splicing: 2 isoforms:  Q9BQ83-1   Q9BQ83-2   

Explore the universe of human proteins at neXtProt for SLX1A: NX_Q9BQ83

Explore proteomics data for SLX1A at MOPED


See SLX1A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001014999.1  NP_001015000.1  

ENSEMBL proteins: 
 ENSP00000333945   ENSP00000251303   ENSP00000455250  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR000305 GIY-YIG_SF
 IPR027520 Slx1

Graphical View of Domain Structure for InterPro Entry Q9BQ83

ProtoNet protein and cluster: Q9BQ83

UniProtKB/Swiss-Prot: SLX1_HUMAN, Q9BQ83
Similarity: Belongs to the SLX1 family
Similarity: Contains 1 GIY-YIG domain
Similarity: Contains 1 SLX1-type zinc finger


SLX1A 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, 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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SLX1_HUMAN, Q9BQ83
Function: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary
structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA
substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for
5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves
HJs by generating two pairs of ligatable, nicked duplex products

     Enzyme Number (IUBMB): EC 3.6.1.-1

     Gene Ontology (GO): 4 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI19595721
GO:0008821crossover junction endodeoxyribonuclease activity IDA19595721
GO:00171085'-flap endonuclease activity IDA19596235
GO:0046872metal ion binding IEA--
     
SLX1A for ontologies           About GeneDecksing


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
SLX1_HUMAN, Q9BQ83: Nucleus

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

GO IDQualified GO termEvidencePubMed IDs
GO:0033557Slx1-Slx4 complex IDA19595721

SLX1A for ontologies           About GeneDecksing


(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 GeneDecks, 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).
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SuperPaths for SLX1A About    
See pathways by source

SuperPathContained pathways About
1Fanconi anemia pathway (KEGG)
Fanconi anemia pathway

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



1 Kegg Pathway  (Kegg details for SLX1A):
    Fanconi anemia pathway


SLX1A for pathways           About GeneDecksing

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLX1A
Interactions:

    Search GeneGlobe Interaction Network for SLX1A

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for SLX1A (Q9BQ831, 3 ENSP000002513034) via UniProtKB, MINT, STRING, and/or I2D (see all 80)
InteractantInteraction Details
GeneCardExternal ID(s)
SLX4Q8IY921, 3, ENSP000002940084EBI-2370858,EBI-2370740 I2D: score=3 STRING: ENSP00000294008
CALM1P621583I2D: score=2 
CALM2P621583I2D: score=2 
CALM3P621583I2D: score=2 
CUL1Q136163, ENSP000003268044I2D: score=2 STRING: ENSP00000326804
About this table

Gene Ontology (GO): 4 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000724double-strand break repair via homologous recombination IMP19595721
GO:0000737DNA catabolic process, endonucleolytic IDA19595721
GO:0006281DNA repair IMP19595721
GO:0010792DNA double-strand break processing involved in repair via single-strand annealing IMP19595721

SLX1A for ontologies           About GeneDecksing



(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)
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Browse Tocris compounds for SLX1A (SLX1)



(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,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for SLX1A gene (2 alternative transcripts): 
NM_001014999.2  NM_001015000.2  

6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000565081 ENST00000345535(uc002dxh.3) ENST00000251303(uc002dxg.3)
ENST00000563995 ENST00000564268 ENST00000563616
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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™, 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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SLX1A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SLX1A Expression
About this image

SLX1A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SLX1A Protein Expression
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In Situ
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(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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This gene was present in the common ancestor of animals and fungi.

Orthologs for SLX1A gene from Selected species (see all 17)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Slx1b1 SLX1 structure-specific endonuclease subunit homolog more 77.53(n)
78.28(a)
  75764  NM_029420.4  NP_083696.2 
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
31(a)
1 → many
8(28728161-28734974)
lizard
(Anolis carolinensis)
Reptilia --
Structure-specific endonuclease subunit SLX1
51(a)
1 → many
GL343279.1(450819-455485)
tropical clawed frog
(Xenopus tropicalis)
Amphibia slx1a1 SLX1 structure-specific endonuclease subunit homolog more 61.03(n)
53.85(a)
  100127194  XM_002943431.2  XP_002943477.2 
zebrafish
(Danio rerio)
Actinopterygii LOC1000018451 structure-specific endonuclease subunit slx1-like 56.13(n)
52.8(a)
  100001845  XM_001337088.4  XP_001337124.1 
fruit fly
(Drosophila melanogaster)
Insecta slx11 nuclease slx1 52.46(n)
46.41(a)
  40578  NM_141227.3  NP_649484.3 
worm
(Caenorhabditis elegans)
Secernentea slx-11 slx-1 46.9(n)
42.04(a)
  172157  NM_059140.4  NP_491541.1 
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SLX16
Subunit of a complex, with Slx4p, that hydrolyzes ...
21(a)
1 → many
II(675313-676227) YBR228W


ENSEMBL Gene Tree for SLX1A (if available)
TreeFam Gene Tree for SLX1A (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SLX1A gene
SLX1B1 2  
2 SIMAP similar genes for SLX1A using alignment to 2 protein entries:     SLX1_HUMAN (see all proteins):
SLX1B    SLX1

SLX1A for paralogs           About GeneDecksing


2 Pseudogenes.org Pseudogenes for SLX1A
PGOHUM00000248777 PGOHUM00000248778


(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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Structural Variations
     Database of Genomic Variants (DGV) Selected variations for SLX1A (see all 17):    About this table    
Variant IDTypeSubtypePubMed ID
esv2714183CNV Deletion23290073
nsv471388CNV Duplication19718026
nsv471387CNV Duplication19718026
nsv821543CNV Duplication20802225
nsv471389CNV Duplication19718026
nsv820959CNV Duplication20802225
nsv905723CNV Loss21882294
nsv498862CNV Loss21111241
nsv905720CNV Loss21882294
nsv9426CNV Gain18304495

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(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.)
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3 diseases for SLX1A:    
About MalaCards
fanconi's anemia    malaria    retinitis


SLX1A for disorders           About GeneDecksing


Export disorders for SLX1A 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)
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PubMed articles for SLX1A gene, integrated from 10 sources (see all 12):
(articles sorted by number of sources associating them with SLX1A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. (PubMed id 19595721)1, 2, 3 Munoz I.M.... Rouse J. (Mol. Cell 2009)
  2. Human SULT1A3 pharmacogenetics: gene duplication and functional genomic studies. (PubMed id 15358107)1, 2, 3 Hildebrandt M.A.T.... Weinshilboum R.M. (Biochem. Biophys. Res. Commun. 2004)
  3. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. (PubMed id 19596235)1, 2 Svendsen J.M.... Harper J.W. (Cell 2009)
  4. Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. (PubMed id 19596236)1, 2 Fekairi S.... Gaillard P.-H.L. (Cell 2009)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Coordinated actions of SLX1-SLX4 and MUS81-EME1 for Holliday junction resolution in human cells. (PubMed id 24076221)1 Wyatt H.D....West S.C. (Mol. Cell 2013)
  7. Regulation of multiple DNA repair pathways by the Fanconi anemia protein SLX4. (PubMed id 23093618)1 Kim Y....Smogorzewska A. (Blood 2013)
  8. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
  9. Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. (PubMed id 19595722)1 Andersen S.L....Sekelsky J. (Mol. Cell 2009)
  10. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (Nature 2004)

(in PubMed, OMIM, and NCBI Bookshelf)
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 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: 548593 HGNC: 20922 Ensembl:ENSG00000132207 euGenes: HUgn548593 ECgene: SLX1A Kegg: 548593
H-InvDB: SLX1A

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SLX1A 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 SLX1A gene:
Search GeneIP for patents involving SLX1A

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



(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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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 inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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