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CCIN Gene

protein-coding   GIFtS: 51
GCID: GC09P036159

Calicin

  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
calicin1 2
BTBD202
KBTBD142

External Ids:    HGNC: 15681   Entrez Gene: 8812   Ensembl: ENSG000001859727   OMIM: 6039605   UniProtKB: Q139393   

Export aliases for CCIN gene to outside databases

Previous GC identifers: GC09P036481 GC09P036338


(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 CCIN Gene:
The protein encoded by this gene is a basic protein of the sperm head cytoskeleton. This protein contains kelch
repeats and a BTB/POZ domain and is necessary for normal morphology during sperm differentiation. This gene is
intronless. (provided by RefSeq, Jul 2008)

GeneCards Summary for CCIN Gene:
CCIN (calicin) is a protein-coding gene. Diseases associated with CCIN include varicocele, and shigellosis. GO annotations related to this gene include structural constituent of cytoskeleton. An important paralog of this gene is KLHL11.

UniProtKB/Swiss-Prot: CALI_HUMAN, Q13939
Function: Possible morphogenetic cytoskeletal element in spermiogenic differentiation




(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_000009.12  NC_018920.2  NT_008413.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the CCIN gene promoter:
         NF-1   Tal-1   AML1a   ATF-2   XBP-1   CUTL1   E47   C/EBPalpha   SEF-1 (1)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCIN promoter sequence
   Search Chromatin IP Primers for CCIN

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


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

Entrez Gene cytogenetic band: 9p13.3   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p13.1

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

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P036159:  view genomic region     (about GC identifiers)

Start:
36,169,389 bp from pter      End:
36,171,331 bp from pter
Size:
1,943 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: CALI_HUMAN, Q13939 (See protein sequence)
Recommended Name: Calicin  
Size: 588 amino acids; 66582 Da
Secondary accessions: Q9BXG7

Explore the universe of human proteins at neXtProt for CCIN: NX_Q13939

Explore proteomics data for CCIN at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_005884.2  
    ENSEMBL proteins: 
     ENSP00000334996  

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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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    HGNC Gene Families:
    BTBD: BTB/POZ domain containing

    Selected InterPro protein domains (see all 6):
     IPR000210 BTB/POZ-like
     IPR006652 Kelch_1
     IPR011333 BTB/POZ_fold
     IPR015916 Gal_Oxidase_b-propeller
     IPR013069 BTB_POZ

    Graphical View of Domain Structure for InterPro Entry Q13939

    ProtoNet protein and cluster: Q13939

    2 Blocks protein domains:
    IPB000210 BTB/POZ domain
    IPB011705 BTB/Kelch-associated


    UniProtKB/Swiss-Prot: CALI_HUMAN, Q13939
    Similarity: Contains 1 BACK (BTB/Kelch associated) domain
    Similarity: Contains 1 BTB (POZ) domain
    Similarity: Contains 6 Kelch repeats


    CCIN 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: CALI_HUMAN, Q13939
    Function: Possible morphogenetic cytoskeletal element in spermiogenic differentiation

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005200structural constituent of cytoskeleton ----
    GO:0005515protein binding ----
         
    CCIN for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for CCIN:
     Increased cell death in DLD-1   Synthetic lethal with Ras 

    Animal Models:
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    hsa-mir-424-5p (MIRT042434)

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    hsa-miR-629* hsa-miR-586 hsa-miR-532-3p
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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
    CALI_HUMAN, Q13939: Cytoplasm, cytoskeleton, perinuclear theca, calyx. Note=Sperm head cytoskeletal structure
    tightly associated to the nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton5
    cytosol2
    nucleus2
    plasma membrane1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005856cytoskeleton ----
    GO:0033150cytoskeletal calyx IEA--

    CCIN 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 CCIN
    Interactions:

        Search GeneGlobe Interaction Network for CCIN

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

    1 Interacting protein for CCIN (Q139393 ENSP000003349964) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ACTA1P681333, ENSP000003556454I2D: score=1 STRING: ENSP00000355645
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007283spermatogenesis IEA--
    GO:0030154cell differentiation IEA--

    CCIN 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
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    Browse Tocris compounds for CCIN (CALI)



    (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 CCIN gene: 
    NM_005893.2  

    Unigene Cluster for CCIN:

    Calicin
    Hs.115460  [show with all ESTs]
    Unigene Representative Sequence: NM_005893
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000335119(uc003zzb.4)
    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat CCIN

    Additional mRNA sequence: 

    AF333334.1 AK313763.1 BC019251.2 Z46967.1 

    4 DOTS entries:

    DT.407880  DT.100673016  DT.100676563  DT.121155343 

    Selected AceView cDNA sequences (see all 36):

    BM564063 BP371354 BI826975 BX106803 AA420997 NM_005893 BI829423 BI827210 
    BI827696 BM554512 BI831628 BP368804 CD251977 BM563612 BC019251 BI831707 
    BM564310 BG724007 BI828812 CD359506 BI825638 BI561092 Z46967 BI826408 

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

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

    CCIN Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.115460

    UniProtKB/Swiss-Prot: CALI_HUMAN, Q13939
    Tissue specificity: Testis. Not detectable or shows a drastically altered pattern of arrangement in the heads of
    malformed spermatozoa

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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 chordates.

    Orthologs for CCIN gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccin1 , 5 calicin1, 5 88.49(n)1
    93.03(a)1
      4 (23.08 cM)5
    4428291  NM_001002787.21  NP_001002787.11 
     439834835 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Uncharacterized protein
    60(a)
    59(a)
    many → 1
    many → 1
    GL343201.1(2362809-2364569)
    GL343201.1(2212547-2214310)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CCIN gene
    KLHL112  
    1 SIMAP similar gene for CCIN using alignment to 3 protein entries:     CALI_HUMAN (see all proteins):
    KBTBD3

    CCIN for paralogs           About GeneDecksing



    (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 CCIN (see all 172)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1474275861,2
    Cuntested136170096(+) CTCAGC/TGCACT 2 S syn11Minor allele frequency- T:0.00NA 4550
    rs1465850821,2
    C,Funtested136170278(+) GGACCG/ACAAGC 2 /H /R mis11Minor allele frequency- A:0.00NA 4546
    rs1834183081,2
    --36167472(+) TCAGGG/TGATCC 1 -- us2k10--------
    rs78608661,2
    C,A--36167497(+) cccaaA/Ggtgct 1 -- us2k10--------
    rs21828191,2
    C,F,A,H--36167569(+) CCCGGA/CGCATT 1 -- us2k18Minor allele frequency- C:0.44NS EA NA CSA 544
    rs21490071,2
    C,A--36167797(+) AGCACC/TGGCCG 1 -- us2k15Minor allele frequency- T:0.43NA CSA WA EA 361
    rs1886625561,2
    --36167802(+) CGGCCA/GGGCAC 1 -- us2k10--------
    rs21490081,2
    C,F,A--36167810(+) CACGGT/GGGCTC 1 -- us2k16Minor allele frequency- G:0.40NA WA CSA 10
    rs1129556901,2
    C--36168012(+) AGTTGG/AAGGTT 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1930167001,2
    --36168028(+) GAGCCA/GAGAAC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for CCIN (36169389 - 36171331 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for CCIN:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv34080CNV Loss18971310
    nsv528600CNV Loss19592680
    nsv893049CNV Gain21882294

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

    (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: 603960    OMIM disorders: --

    2 diseases for CCIN:    
    About MalaCards
    varicocele    shigellosis

    1 disease from the University of Copenhagen DISEASES database for CCIN:
    Varicocele

    CCIN for disorders           About GeneDecksing

    Genetic Association Database (GAD): CCIN

    Export disorders for CCIN 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 CCIN gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with CCIN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular nature of calicin, a major basic protein of the mammalian sperm head cytoskeleton. (PubMed id 7641791)1, 2, 3, 9 von Buelow M.... Franke W.W. (Exp. Cell Res. 1995)
    2. Actin-binding properties and colocalization with actin during spermiogenesis of mammalian sperm calicin. (PubMed id 11090452)1, 9 LAccuyer C....Rousseaux-PrAcvost R. (Biol. Reprod. 2000)
    3. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
    4. Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement. (PubMed id 20235792)4 Uhl G.R....MunafA^ M.R. (Pharmacogenomics 2010)
    5. 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)
    6. (PubMed id )2 
    7. Calicin in human sperm fertilizing zona-free hamster eggs in vitro. (PubMed id 7569061)9 Paranko J. and Salonen I. (Reprod. Fertil. Dev. 1995)
    8. Presence and localization of the 60 KD calicin in human spermatozoa presenting postacrosomal sheath defects: preliminary results. (PubMed id 2015086)9 Courtot A.M. (Mol. Reprod. Dev. 1991)
    9. CP beta3, a novel isoform of an actin-binding protein, is a component of the cytoskeletal calyx of the mammalian sperm head. (PubMed id 9184090)9 von BA1low M....Franke W.W. (Exp. Cell Res. 1997)
    10. The protein complexity of the cytoskeleton of bovine and human sperm heads: the identification and characterization of cylicin II. (PubMed id 7737358)9 Hess H.... Franke W.W. (Exp. Cell Res. 1995)

    (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: 881 HGNC: 1568 AceView: CCIN Ensembl:ENSG00000185972 euGenes: HUgn881
    ECgene: CCIN H-InvDB: CCIN

    (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 CCIN 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 CCIN gene:
    Search GeneIP for patents involving CCIN

    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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