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ISM1 Gene

protein-coding   GIFtS: 45
GCID: GC20P013202

Isthmin 1, Angiogenesis Inhibitor

(Previous names: chromosome 20 open reading frame 82, isthmin 1 homolog (zebrafish))
(Previous symbol: C20orf82)
  See ISM1-related disease
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
Isthmin 1, Angiogenesis Inhibitor1 2     Isthmin2
C20orf821 2 3     bA149I18.12
ISM2 3     dJ1077I2.12
Chromosome 20 Open Reading Frame 821     Isthmin 1 Homolog2
Isthmin 1 Homolog (Zebrafish)1     isthmin-12

External Ids:    HGNC: 162131   Entrez Gene: 1408622   Ensembl: ENSG000001012307   UniProtKB: B1AKI93   

Export aliases for ISM1 gene to outside databases

Previous GC identifer: GC20P013150


(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 ISM1 Gene:
ISM1 (isthmin 1, angiogenesis inhibitor) is a protein-coding gene. Diseases associated with ISM1 include indolent systemic mastocytosis. An important paralog of this gene is ISM2.


(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 at NCBI GenBank:
NC_000020.10  NC_018931.2  NT_011387.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the ISM1 gene promoter:
         GR   AML1a   Sp1   Pax-5   GR-beta   p300   Olf-1   Egr-2   ARP-1   GR-alpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ISM1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ISM1


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

Entrez Gene cytogenetic band: 20p12.1   Ensembl cytogenetic band:  20p12.1   HGNC cytogenetic band: 20p12.1

ISM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ISM1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P013202:  view genomic region     (about GC identifiers)

Start:
13,202,418 bp from pter      End:
13,281,298 bp from pter
Size:
78,881 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ISM1_HUMAN, B1AKI9 (See protein sequence)
Recommended Name: Isthmin-1 precursor  
Size: 464 amino acids; 52107 Da
Sequence caution: Sequence=CAC16127.3; Type=Erroneous gene model prediction; Sequence=CAC36074.2; Type=Erroneous
gene model prediction; Sequence=EAX10318.1; Type=Erroneous gene model prediction;
Secondary accessions: Q8WVH9

Explore the universe of human proteins at neXtProt for ISM1: NX_B1AKI9

Explore proteomics data for ISM1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn39

  • See ISM1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_543016.1  
    ENSEMBL proteins: 
     ENSP00000262487  

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    antibodies-online proteins for ISM1 (4 products) 

     
    antibodies-online peptides for ISM1

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    Cloud-Clone Corp. CLIAs for ISM1
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    antibodies-online kits for ISM1 (4 products) 


    (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:
     IPR000884 Thrombospondin_1_rpt
     IPR005533 AMOP

    Graphical View of Domain Structure for InterPro Entry B1AKI9

    ProtoNet protein and cluster: B1AKI9

    UniProtKB/Swiss-Prot: ISM1_HUMAN, B1AKI9
    Similarity: Belongs to the isthmin family
    Similarity: Contains 1 AMOP domain
    Similarity: Contains 1 TSP type-1 domain


    Find genes that share domains with ISM1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Phenotypes:
         1 GenomeRNAi human phenotype for ISM1:
     Decreased Wnt reporter activit 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ISM1

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate ISM1 (see all 44):
    hsa-miR-302d hsa-miR-520e hsa-miR-106a hsa-miR-507 hsa-miR-372 hsa-miR-93 hsa-miR-508-5p hsa-miR-23a
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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
    ISM1_HUMAN, B1AKI9: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    plasma membrane2
    lysosome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with ISM1           About GenesLikeMe


    (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 ISM1
    Interactions:

        Search GeneGlobe Interaction Network for ISM1

    (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 ISM1



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for ISM1 gene: 
    NM_080826.1  

    Unigene Cluster for ISM1:

    Isthmin 1 homolog (zebrafish)
    Hs.559353  [show with all ESTs]
    Unigene Representative Sequence: NM_080826
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000262487(uc010gce.1)
    miRNA
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    hsa-miR-302d hsa-miR-520e hsa-miR-106a hsa-miR-507 hsa-miR-372 hsa-miR-93 hsa-miR-508-5p hsa-miR-23a
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for ISM1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat ISM1
      QuantiTect SYBR Green Assays in human, mouse, rat ISM1
      QuantiFast Probe-based Assays in human, mouse, rat ISM1

    Additional mRNA sequence: 

    AK307409.1 BC017997.1 

    4 DOTS entries:

    DT.97796194  DT.219229  DT.100741069  DT.75185749 

    Selected AceView cDNA sequences (see all 28):

    BF971101 AI886394 BM978234 BM932119 AI082824 AI346444 AV708785 CA406451 
    W07772 W86257 AK095658 AA633473 CB989845 BC017997 BQ771595 AL732077 
    AI191256 BF437897 CB961129 AK074473 AI816793 BQ370885 R52250 CF994326 

    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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    ISM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCCTAGCAGG
    ISM1 Expression
    About this image


    ISM1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Zeugopod Epiphyseal End
             TGFbeta3+BMP7-induced chondrocytes
     
     Endothelium (Cardiovascular System)    fully expand to see all 2 entries
             Adult Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Adult Endothelial Cells Blood Brain Barrier
     
     Cartilage (Muscoskeletal System)
             TGFbeta3+BMP7-induced chondrocytes
    ISM1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ISM1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.559353
        Custom PCR Arrays for ISM1
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for ISM1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ISM1

    (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 ISM1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ism11 , 5 isthmin 1 homolog (zebrafish)1, 5 89.15(n)1
    93.49(a)1
      2 (69.06 cM)5
    3199091  NM_001276489.11  NP_001263418.11 
     1396781785 
    chicken
    (Gallus gallus)
    Aves ISM11 isthmin 1 homolog (zebrafish) 74.74(n)
    82.81(a)
      416740  XM_415036.4  XP_415036.4 
    lizard
    (Anolis carolinensis)
    Reptilia ISM16
    isthmin 1, angiogenesis inhibitor
    78(a)
    1 ↔ 1
    1(129062140-129113179)
    African clawed frog
    (Xenopus laevis)
    Amphibia Ism2 secreted protein Isthmin 76.86(n)    AY091635.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ism11 isthmin 1 67.77(n)
    70.04(a)
      497617  NM_001012376.1  NP_001012376.1 


    ENSEMBL Gene Tree for ISM1 (if available)
    TreeFam Gene Tree for ISM1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ISM1 gene
    ISM22  
    1 SIMAP similar gene for ISM1 using alignment to 1 protein entry:     ISM1_HUMAN:
    ISM2

    Find genes that share paralogs with ISM1           About GenesLikeMe



    (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 ISM1 (see all 1741)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1163560751,2
    C,F--13154512(+) TCCTCT/ACCCGG 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1400398641,2
    --13200624(+) CCGTCA/TAGAAA 1 -- us2k10--------
    rs1121751501,2
    F--13200882(+) TCCGAG/CTCACT 1 -- us2k11Minor allele frequency- C:0.50CSA 2
    rs1178941771,2
    F--13200942(+) CACGGA/TCCGAC 1 -- us2k11Minor allele frequency- T:0.01NA 120
    rs592586341,2
    C,F--13201111(+) GACGCC/TAGCCC 1 -- us2k12Minor allele frequency- T:0.25WA EA 238
    rs345023351,2
    C,F--13201177(+) CACTAA/C/GAGCTG 1 -- us2k19NA CSA WA 251
    rs359073051,2
    C,F--13201238(+) CAGCTT/CCCAGC 1 -- us2k19Minor allele frequency- C:0.31NA CSA WA EA 369
    rs1836446321,2
    --13201290(+) GACTCC/GCCTCC 1 -- us2k10--------
    rs1883551121,2
    --13201304(+) CCCAGA/GCTCTA 1 -- us2k10--------
    rs1822803011,2
    --13201335(+) AACAGA/CCGTGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ISM1 (13202418 - 13281298 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for ISM1:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2722201CNV Deletion23290073
    esv27679CNV Loss19812545
    nsv912684CNV Loss21882294
    nsv912686CNV Gain21882294
    esv29075CNV Gain19812545
    nsv912685CNV Gain21882294
    nsv518184CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing ISM1
    DNA2.0 Custom Variant and Variant Library Synthesis for ISM1

    (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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    1 disease for ISM1:    
    About MalaCards
    indolent systemic mastocytosis

    2 diseases from the University of Copenhagen DISEASES database for ISM1:
    Indolent systemic mastocytosis     Arrhythmogenic right ventricular dysplasia

    Find genes that share disorders with ISM1           About GenesLikeMe

    Genetic Association Database (GAD): ISM1

    Export disorders for ISM1 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 ISM1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ISM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide association study reveals genetic risk underlying Parkinson's disease. (PubMed id 19915575)1, 4 SimA^n-SA!nchez J....Gasser T. (Nat. Genet. 2009)
    2. 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)
    3. Isthmin is a novel secreted protein expressed as part of the Fgf-8 synexpression group in the Xenopus midbrain-hindbrain organizer. (PubMed id 12128218)1, 2 Pera E.M....De Robertis E.M. (Mech. Dev. 2002)
    4. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (Nature 2001)
    5. Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. (PubMed id 23934736)1 Yu B....Boerwinkle E. (Genet. Epidemiol. 2013)
    6. Isthmin exerts pro-survival and death-promoting effect on endothelial cells through alphavbeta5 integrin depending on its physical state. (PubMed id 21544092)1 Zhang Y....Ge R. (amp 2011)
    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: 140862 HGNC: 16213 AceView: C20orf82 Ensembl:ENSG00000101230 euGenes: HUgn140862
    ECgene: ISM1 H-InvDB: ISM1

    (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 ISM1 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 ISM1 gene:
    Search GeneIP for patents involving ISM1

    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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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 genOway)
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     antibodies-online antibodies for ISM1 (9 products)
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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 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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