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AP5S1 Gene

protein-coding   GIFtS: 37
GCID: GC20P003804

Adaptor-Related Protein Complex 5, Sigma 1 Subunit

(Previous name: chromosome 20 open reading frame 29)
(Previous symbol: C20orf29)
  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
Adaptor-Related Protein Complex 5, Sigma 1 Subunit1 2     AP-5 Complex Subunit Sigma-12
C20orf291 2 3 5     Protein C20orf292
Adapter-Related Protein Complex 5 Sigma Subunit2 3     sigma52
Chromosome 20 Open Reading Frame 291     Sigma53

External Ids:    HGNC: 158751   Entrez Gene: 553172   Ensembl: ENSG000001258437   OMIM: 6148245   UniProtKB: Q9NUS53   

Export aliases for AP5S1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for AP5S1 Gene:
AP5S1 (adaptor-related protein complex 5, sigma 1 subunit) is a protein-coding gene. Diseases associated with AP5S1 include hereditary spastic paraplegia, and paraplegia.

UniProtKB/Swiss-Prot: AP5S1_HUMAN, Q9NUS5
Function: As part of AP-5, a probable fifth adapter protein complex it may be involved in endosomal transport.
According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break
repair




(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:
NC_000020.11  NC_018931.2  NT_011387.9  
Regulatory elements:
   Search for regulatory transcription factor binding sites for AP5S1
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for AP5S1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat AP5S1


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

Entrez Gene cytogenetic band: 20p13   Ensembl cytogenetic band:  20p13   HGNC cytogenetic band: 20p13

AP5S1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
AP5S1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P003804:  view genomic region     (about GC identifiers)

Start:
3,801,171 bp from pter      End:
3,805,954 bp from pter
Size:
4,784 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: AP5S1_HUMAN, Q9NUS5 (See protein sequence)
Recommended Name: AP-5 complex subunit sigma-1  
Size: 200 amino acids; 22522 Da
Subunit: Probably part of the adapter protein complex 5 (AP-5) a tetramer composed of AP5B1, AP5M1, AP5S1 and
AP5Z1. Interacts with ZFYVE26 and SPG11
Secondary accessions: B3KSD0 D3DVY7

Explore the universe of human proteins at neXtProt for AP5S1: NX_Q9NUS5

Explore proteomics data for AP5S1 at MOPED


See AP5S1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (3 alternative transcripts): 
NP_001191375.1  NP_001191376.1  NP_060817.1  

ENSEMBL proteins: 
 ENSP00000368892   ENSP00000368886   ENSP00000405487   ENSP00000246041  

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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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ProtoNet protein and cluster: Q9NUS5


(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: AP5S1_HUMAN, Q9NUS5
Function: As part of AP-5, a probable fifth adapter protein complex it may be involved in endosomal transport.
According to PubMed:20613862, it is required for efficient homologous recombination DNA double-strand break
repair

     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI--
     
AP5S1 for ontologies           About GeneDecksing


Phenotypes:
     2 GenomeRNAi human phenotypes for AP5S1:
 Decreased Wnt reporter activit  Increased gamma-H2AX phosphory 

Animal Models:
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miRNA
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hsa-mir-15b-5p (MIRT046383), hsa-mir-10a-5p (MIRT047741)

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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
AP5S1_HUMAN, Q9NUS5: Cytoplasm, cytosol. Late endosome membrane; Peripheral membrane protein; Cytoplasmic side
(Probable). Lysosome membrane; Peripheral membrane protein; Cytoplasmic side (Probable)

Gene Ontology (GO): Selected cellular component terms (see all 8):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA--
GO:0005737cytoplasm IDA--
GO:0005764lysosome IDA--
GO:0005765lysosomal membrane IEA--
GO:0005770late endosome IDA--

AP5S1 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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for AP5S1
Interactions:

    Search GeneGlobe Interaction Network for AP5S1

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

Selected Interacting proteins for AP5S1 (ENSP000002460414) via UniProtKB, MINT, STRING, and/or I2D (see all 31)
InteractantInteraction Details
GeneCardExternal ID(s)
AP5Z1ENSP000002975624STRING: ENSP00000297562
AFTPHENSP000002388554STRING: ENSP00000238855
AP1G2ENSP000003124424STRING: ENSP00000312442
AP1S1ENSP000003366664STRING: ENSP00000336666
AP2A1ENSP000003519264STRING: ENSP00000351926
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Gene Ontology (GO): 3 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000724double-strand break repair via homologous recombination IMP--
GO:0015031protein transport IEA--
GO:0016197endosomal transport IMP--

AP5S1 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 Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for AP5S1



(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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for AP5S1 gene (3 alternative transcripts): 
NM_001204446.1  NM_001204447.1  NM_018347.2  

Unigene Cluster for AP5S1:

Adaptor-related protein complex 5, sigma 1 subunit
Hs.104806  [show with all ESTs]
Unigene Representative Sequence: NM_001204446
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000379573(uc002wjt.3 uc002wju.2 uc002wjs.2 uc021wab.1)
ENST00000379567 ENST00000455742 ENST00000246041
miRNA
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Predesigned siRNA for gene silencing in human, mouse, rat AP5S1
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Primer
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  QuantiFast Probe-based Assays in human, mouse, rat AP5S1

Additional mRNA sequence: 

AK002030.1 AK093332.1 BC011985.1 BC043344.1 

4 DOTS entries:

DT.40275034  DT.92421454  DT.40129831  DT.92065030 

Selected AceView cDNA sequences (see all 474):

AA349951 BP372446 BM851732 BE393404 CD514332 BI906779 CF139346 BU171160 
AI377984 BF512205 BM451166 BQ668913 NM_021874 AI312048 BM992633 NM_212530 
CD671179 CR591656 T29904 BG109206 R34850 BQ961611 BP367080 AW245589 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for AP5S1 (see all 6)    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d · 4e
SP1:                    -     -           -                                 
SP2:                    -     -           -                                 
SP3:                          -           -                                 
SP4:                          -           -                                 
SP5:                                      -                                 


ECgene alternative splicing isoforms for AP5S1

(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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AP5S1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGAATCACTT
AP5S1 Expression
About this image


AP5S1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Skeletal Muscle (Muscoskeletal System)    fully expand to see all 4 entries
         Mononuclear Myocytes Hyoid Arch Muscles
AP5S1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

AP5S1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.104806
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for AP5S1

(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 chordates.

Orthologs for AP5S1 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ap5s11 , 5 RIKEN cDNA 2310035K24 gene5
adaptor-related protein 5 complex, sigma 1 subunit1
82.13(n)1
84.78(a)1
  2 (63.29 cM)5
695961  NM_027129.21  NP_081405.21 
 1312070785 
lizard
(Anolis carolinensis)
Reptilia AP5S16
adaptor-related protein complex 5, sigma 1 subunit...
44(a)
1 ↔ 1
GL343540.1(112220-118735)
tropical clawed frog
(Xenopus tropicalis)
Amphibia ap5s11 adaptor-related protein complex 5, sigma 1 subunit 52.55(n)
47.45(a)
  100135151  NM_001113860.1  NP_001107332.1 
zebrafish
(Danio rerio)
Actinopterygii BM529858.12   -- 72.38(n)    BM529858.1 


ENSEMBL Gene Tree for AP5S1 (if available)
TreeFam Gene Tree for AP5S1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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 AP5S1 (see all 214)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs775265461,2
C,F--3799191(+) GCCCTC/GTAGTG 3 -- us2k11Minor allele frequency- G:0.06WA 118
rs60520921,2
F,H--3799212(+) TGGTGT/CTGACT 3 -- us2k1 tfbs32Minor allele frequency- C:0.02NS WA 238
rs1902917691,2
--3799312(+) CTGCTA/GTAATC 3 -- us2k10--------
rs60520931,2
C,F,A,H--3799390(+) TCCCCA/CGCCTC 3 -- us2k118Minor allele frequency- C:0.21NS EA NA WA CSA 2342
rs1441302081,2
--3799496(+) CTTCCC/TTTCAG 3 -- us2k10--------
rs38105651,2
C,F--3799506(+) GTCACC/TTCCTA 3 -- us2k1 tfbs32Minor allele frequency- T:0.04EA 1600
rs1824925271,2
--3799509(+) ACCTCC/TTAACC 3 -- us2k10--------
rs1150140831,2
F--3799530(+) CCTATG/AGCTTA 3 -- us2k11Minor allele frequency- A:0.01WA 118
rs1482809731,2
--3799630(+) GAGCGC/TGTTCA 3 -- us2k10--------
rs1866798291,2
--3799631(+) AGCGTA/GTTCAA 3 -- us2k10--------

HapMap Linkage Disequilibrium report for AP5S1 (3801171 - 3805954 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for AP5S1: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing AP5S1
DNA2.0 Custom Variant and Variant Library Synthesis for AP5S1

(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.)
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OMIM gene information: 614824    OMIM disorders: --

3 diseases for AP5S1:    
About MalaCards
hereditary spastic paraplegia    paraplegia    spasticity


AP5S1 for disorders           About GeneDecksing


Export disorders for AP5S1 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 AP5S1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with AP5S1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The fifth adaptor protein complex. (PubMed id 22022230)1, 2, 3 Hirst J.... Robinson M.S. (PLoS Biol. 2011)
  2. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2, 3 Deloukas P....Rogers J. (Nature 2001)
  3. 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)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  6. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. (PubMed id 20613862)2 Slabicki M.... Buchholz F. (PLoS Biol. 2010)
  7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 55317 HGNC: 15875 AceView: CDC25BandC20orf29 Ensembl:ENSG00000125843 euGenes: HUgn55317
ECgene: AP5S1 H-InvDB: AP5S1

(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 AP5S1 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 AP5S1 gene:
Search GeneIP for patents involving AP5S1

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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