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

CLVS1 Gene

protein-coding   GIFtS: 48
GCID: GC08P061969

clavesin 1

(Previous name: retinaldehyde binding protein 1-like 1 )
(Previous symbol: RLBP1L1)
 Explore 5 diseases affiliated with
CLVS1 via our new
 Human Malady Compendium 
Biological research products
for CLVS1
    

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

Aliases
Clavesin 11 2     C6orf212L1
CRALBPL1 2 3     MGC346461
RLBP1L11 2 3     Clavesin-11
Retinaldehyde Binding Protein 1-Like 11 2     Cellular Retinaldehyde-Binding Protein-Like3
Retinaldehyde-Binding Protein 1-Like 12 3     

External Ids:    HGNC: 231391   Entrez Gene: 1578072   Ensembl: ENSG000001771827   OMIM: 6112925   UniProtKB: Q8IUQ03   

Export aliases for CLVS1 gene to outside databases

Previous GC identifers: GC08P062365 GC08P062201 GC08P057689


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: CLVS1_HUMAN, Q8IUQ0
Function: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds
phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)




(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_000008.10  NC_018919.1  NT_008183.19  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for CLVS1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLVS1 promoter sequence
   Search SABiosciences Chromatin IP Primers for CLVS1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CLVS1


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

Entrez Gene cytogenetic band: 8q12.3   Ensembl cytogenetic band:  8q12.2   HGNC cytogenetic band: 8q12.1

CLVS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLVS1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P061969:  view genomic region     (about GC identifiers)

Start:
61,969,717 bp from pter      End:
62,414,204 bp from pter
Size:
444,488 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: CLVS1_HUMAN, Q8IUQ0 (See protein sequence)
Recommended Name: Clavesin-1  
Size: 354 amino acids; 40788 Da
Subunit: Forms a complex with clathrin heavy chain and gamma-adaptin
Subcellular location: Golgi apparatus, trans-Golgi network membrane; Peripheral membrane protein (By similarity).
Cytoplasmic vesicle, clathrin-coated vesicle (By similarity). Early endosome membrane; Peripheral membrane protein
Miscellaneous: Binding to PtdIns(3,5)P2 is not required for localization
Secondary accessions: B2R7M5 C8UZT3 Q8NB32
Alternative splicing: 2 isoforms:  Q8IUQ0-1   Q8IUQ0-2   (No experimental confirmation available. May be due to an intron retention)

Explore the universe of human proteins at neXtProt for CLVS1: NX_Q8IUQ0

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IUQ0

  • CLVS1 Protein expression data from MOPED and PaxDb:    About this image 
    CLVS1 Protein Expression
    REFSEQ proteins: NP_775790.1  
    ENSEMBL proteins: 
     ENSP00000428986   ENSP00000428402   ENSP00000429244   ENSP00000429869   ENSP00000325506  
     ENSP00000428174   ENSP00000429544  

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    Uscn Proteins for CLVS1

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005768endosome IDA19651769
    GO:0005794Golgi apparatus IEA--
    GO:0005802trans-Golgi network ISS--
    GO:0030136clathrin-coated vesicle ISS--
    GO:0031901early endosome membrane IEA--

    CLVS1 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    CLVS1 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR001071 CRAL-bd_toc_tran
     IPR001251 CRAL-TRIO_dom
     IPR011074 CRAL/TRIO_N_dom

    Graphical View of Domain Structure for InterPro Entry Q8IUQ0

    ProtoNet protein and cluster: Q8IUQ0

    2 Blocks protein families:
    IPB001071 Cellular retinaldehyde-binding protein signature
    IPB001251 Cellular retinaldehyde-binding (CRAL)/Triple function domain (TRIO)


    UniProtKB/Swiss-Prot: CLVS1_HUMAN, Q8IUQ0
    Domain: The CRAL-TRIO domain is required for targeting to the membrane and for binding PtdIns(3,5)P2
    Similarity: Contains 1 CRAL-TRIO domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLVS1_HUMAN, Q8IUQ0
    Function: Required for normal morphology of late endosomes and/or lysosomes in neurons (By similarity). Binds
    phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity IEA--
    GO:0080025phosphatidylinositol-3,5-bisphosphate binding IDA19651769
         
    CLVS1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for CLVS1 

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    In Situ Assay
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    (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 CLVS1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007040lysosome organization ISS--

    CLVS1 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 CLVS1
    Search CenterWatch for drugs/clinical trials and news about CLVS1 

    (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,
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    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 CLVS1 gene: 
    NM_173519.2  

    Unigene Cluster for CLVS1:

    Clavesin 1
    Hs.591874  [show with all ESTs]
    Unigene Representative Sequence: BC042617
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000522621 ENST00000519846 ENST00000523868 ENST00000518592(uc003xui.3)
    ENST00000325897(uc003xuh.3) ENST00000521189(uc003xug.2) ENST00000524095
    ENST00000520712 ENST00000518426 ENST00000522928 ENST00000518858

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    hsa-miR-448 hsa-miR-181c hsa-miR-522 hsa-miR-4263 hsa-miR-16-1* hsa-miR-4299 hsa-miR-888* hsa-miR-3916
    SwitchGear 3'UTR luciferase reporter plasmidCLVS1 3' UTR sequence
    Inhib. RNA
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    Additional cDNA sequence: 

    AF445194.1 AK091641.1 AK094567.1 AK125153.1 AK313040.1 AY094971.1 BC042617.1 BC048992.1 

    15 DOTS entries:

    DT.97791318  DT.446703  DT.101983609  DT.100031690  DT.100828247  DT.100803424  DT.100828250  DT.121476279 
    DT.121476362  DT.121476177  DT.121476233  DT.91700552  DT.95266274  DT.100031677  DT.100828245 

    24/68 AceView cDNA sequences (see all 68):

    BI752656 AA330126 BE674107 BM726271 AY094971 CK820995 AI694510 AF445194 
    AL535513 Z38866 CR591744 BC042617 F06131 BG189420 AX747107 CR599613 
    BI793066 NM_173519 AK091641 AL567255 AL538323 BU622331 AL524447 CK820994 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for CLVS1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b
    SP1:              -                             -                 -               
    SP2:              -                                                               
    SP3:                                                                              
    SP4:                                                                              
    SP5:              -                                                               


    ECgene alternative splicing isoforms for CLVS1

    (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

    CLVS1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AACATTGAAT
    CLVS1 Expression
    About this image

    CLVS1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    OvaryOvigerous CordOvarian Somatic CellsOvary
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See CLVS1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLVS1

    SOURCE GeneReport for Unigene cluster: Hs.591874

    UniProtKB/Swiss-Prot: CLVS1_HUMAN, Q8IUQ0
    Tissue specificity: Expressed mainly in the brain

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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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for CLVS1 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 CLVS11 clavesin 1 85.44(n)
    94.58(a)
      421141  XM_419223.3  XP_419223.2 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    96(a)
    93(a)
    1 ↔ many
    1 ↔ many
    4(28860551-28879264)
    4(28924829-28934852)
    African clawed frog
    (Xenopus laevis)
    Amphibia BG810906.12   -- 77.25(n)    BG810906.1 
    zebrafish
    (Danio rerio)
    Actinopterygii clvs26
    clavesin 2
    77(a)
    1 → many
    20(40301718-40351606)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG106576
    CG339666
    (see all 18)
    --
    26(a)
    25(a)
    (see all 18)
    possible ortholog
    possible ortholog
    (see all 18)
    3L(12484930-12490316)
    3L(1234130-1235420)


    ENSEMBL Gene Tree for CLVS1 (if available)
    TreeFam Gene Tree for CLVS1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CLVS1 gene
    RLBP12  TTPAL2  CLVS22  TTPA2  
    5 SIMAP similar genes for CLVS1 using alignment to 5 protein entries:     CLVS1_HUMAN (see all proteins):
    CLVS2    RLBP1    DKFZp686E0870    TTPA    TTPAL

    CLVS1 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

    10/4010 NCBI SNPs in CLVS1 are shown (see all 4010    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1385635921,2
    C--62198586(+) GGCCA-/TTTTTT 1 -- us2k10--------
    rs1872860251,2
    --62198675(+) TTCCCA/GTAACT 1 -- us2k10--------
    rs1400345741,2
    --62198837(+) GGGCTA/GGAAAG 1 -- us2k10--------
    rs1899396961,2
    --62198842(+) GGAAAC/GTGTGG 1 -- us2k10--------
    rs1456714271,2
    --62198857(+) GCCTCA/GGGATA 1 -- us2k10--------
    rs29193071,2
    C,F,O,A,H--62198900(-) CCACTA/GGAGCA 1 -- us2k117Minor allele frequency- N:0.00EA NA NS WA 1416
    rs726570401,2
    C--62198936(+) GGAGCC/TATAGA 1 -- us2k10--------
    rs78150541,2
    C,F--62198937(+) GAGCCA/GTAGAG 1 -- us2k116Minor allele frequency- G:0.49NA NS EA WA CSA 932
    rs1487294361,2
    --62199076(+) GTGGAC/TTCTCT 1 -- us2k10--------
    rs101002711,2
    C,F--62199261(+) ACTTTA/TAAGTC 1 -- us2k13Minor allele frequency- T:0.19WA CSA 122

    HapMap Linkage Disequilibrium report for CLVS1 (61969717 - 62219717 bp, first 250kb of CLVS1)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for CLVS1
         1 CNV: 65149
         1 Indel: 60709

    SABiosciences Cancer Mutation PCR Assays
    1 SABiosciences qBiomarker Copy Number PCR Array containing CLVS1:
    Ovarian Cancer
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing CLVS1
    DNA2.0 Custom Variant and Variant Library Synthesis for CLVS1

    (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

    CLVS1 for disorders           About GeneDecksing

    OMIM gene information: 611292    OMIM disorders: --

    5 diseases for CLVS1:    About MalaCards
    duane retraction syndrome    hepatocellular carcinoma    alzheimer's disease    carcinoma
    neuronitis

    1 disease from the University of Copenhagen DISEASES database for CLVS1:
    Duane retraction syndrome
    Human Genome Epidemiology (HuGE) Navigator: CLVS1 (1 document)

    Export disorders for CLVS1 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 CLVS1 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with CLVS1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The clavesin family: neuron-specific lipid- and clathrin-binding Sec14 proteins regulating lysosomal morphology. (PubMed id 19651769)1, 2, 3 Katoh Y....McPherson P.S. (2009)
    2. Cloning and characterization of a novel, human cellular retinaldehyde-binding protein CRALBP-like (CRALBPL) gene. (PubMed id 16802092)1, 2, 3 Kong Y.-H....Yu L. (2006)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    5. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. (PubMed id 21116278)1 Furney S.J....Lovestone S. (2010)
    6. Cellular retinaldehyde-binding protein-like (CRALBPL), a novel human Sec14p-like gene that is upregulated in human hepatocellular carcinomas, may be used as a marker for human hepatocellular carcinomas. (PubMed id 18271718)1 Zhao S....Mao Y. (2008)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    10. 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. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 157807 HGNC: 23139 AceView: MGC34646 Ensembl:ENSG00000177182 euGenes: HUgn157807
    ECgene: CLVS1 H-InvDB: CLVS1

    (According to HUGE)
    About This Section
      --

    (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
    NameDescription
    PharmGKB entry for CLVS1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for CLVS1 gene:
    Search GeneIP for patents involving CLVS1

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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