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

CCDC88B Gene

protein-coding   GIFtS: 43
GCID: GC11P064107

Coiled-Coil Domain Containing 88B

(Previous name: coiled-coil domain containing 88)
(Previous symbol: CCDC88)
  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)
About This Section

Aliases
Coiled-Coil Domain Containing 88B1 2     Coiled-Coil Domain Containing 881
CCDC881 2     78 KDa Glucose-Regulated Protein [GRP78]-Interacting Protein Induced By ER
Stress2
Brain Leucine Zipper Protein1 2     HKRP32
GRP78-Interacting Protein Induced By ER Stress1 2     Coiled-Coil Domain-Containing Protein 88B2
Brain Leucine Zipper Domain-Containing Protein2 3     gipie2
Hook-Related Protein 32 3     HkRP33
BRLZ2 3     

External Ids:    HGNC: 267571   Entrez Gene: 2832342   Ensembl: ENSG000001680717   OMIM: 6112055   UniProtKB: A6NC983   

Export aliases for CCDC88B gene to outside databases

Previous GC identifers: GC11P063866 GC11P060435


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

Entrez Gene summary for CCDC88B Gene:
This gene encodes a member of the hook-related protein family. Members of this family are characterized by an
N-terminal potential microtubule binding domain, a central coiled-coiled and a C-terminal Hook-related domain.
The encoded protein may be involved in linking organelles to microtubules. (provided by RefSeq, Oct 2009)

GeneCards Summary for CCDC88B Gene: 
CCDC88B (coiled-coil domain containing 88B) is a protein-coding gene. Diseases associated with CCDC88B include sarcoidosis, and endotheliitis. GO annotations related to this gene include microtubule binding. An important paralog of this gene is HOOK2.




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NC_018922.2  NT_167190.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CCDC88B gene promoter:
         CREB   Tal-1   deltaCREB   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCCDC88B promoter sequence
   Search SABiosciences Chromatin IP Primers for CCDC88B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat CCDC88B


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

Entrez Gene cytogenetic band: 11q12.3   Ensembl cytogenetic band:  11q13.1   HGNC cytogenetic band: 11q13.1

CCDC88B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CCDC88B gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P064107:  view genomic region     (about GC identifiers)

Start:
64,107,690 bp from pter      End:
64,125,006 bp from pter
Size:
17,317 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: CC88B_HUMAN, A6NC98 (See protein sequence)
Recommended Name: Coiled-coil domain-containing protein 88B  
Size: 1476 amino acids; 164809 Da
Sequence caution: Sequence=BAC03417.1; Type=Erroneous initiation;
Secondary accessions: A5D8Y5 B5MDM2 Q05BL2 Q6RUV3 Q8N1Q6 Q8NF44 Q9H0H1
Alternative splicing: 6 isoforms:  A6NC98-1   A6NC98-2   A6NC98-3   A6NC98-4   A6NC98-5   A6NC98-6   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CCDC88B: NX_A6NC98

Explore proteomics data for CCDC88B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_A6NC98

  • CCDC88B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CCDC88B Protein Expression
    REFSEQ proteins: NP_115627.6  
    ENSEMBL proteins: 
     ENSP00000349238   ENSP00000352974   ENSP00000301897  

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    Cloud-Clone Corp. Proteins for CCDC88B 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm ----

    CCDC88B for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR008636 HOOK/CCDC88

    Graphical View of Domain Structure for InterPro Entry A6NC98

    ProtoNet protein and cluster: A6NC98

    UniProtKB/Swiss-Prot: CC88B_HUMAN, A6NC98
    Similarity: Belongs to the CCDC88 family


    CCDC88B 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, 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, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003779actin binding IEA--
    GO:0008017microtubule binding ----
         
    CCDC88B for ontologies           About GeneDecksing


    Animal Models:
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    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CCDC88B

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    5/11 Interacting proteins for CCDC88B (A6NC983 ENSP000003492384) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000237344P404253, ENSP000003971774I2D: score=3 STRING: ENSP00000397177
    PBX2P404253, ENSP000003641904I2D: score=3 STRING: ENSP00000364190
    ENSG00000206315P404253I2D: score=3 
    ENSG00000224952P404253I2D: score=3 
    ENSG00000225987P404253I2D: score=3 
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000226microtubule cytoskeleton organization ----
    GO:0016477cell migration IEA--
    GO:0032956regulation of actin cytoskeleton organization IEA--

    CCDC88B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 CCDC88B (CC88B)

    Search CenterWatch for drugs/clinical trials and news about CCDC88B / CC88B

    (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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for CCDC88B gene: 
    NM_032251.5  

    Unigene Cluster for CCDC88B:

    Coiled-coil domain containing 88B
    Hs.98564  [show with all ESTs]
    Unigene Representative Sequence: BC151218
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000463837 ENST00000356786(uc009ypo.2 uc001nzy.3 uc001oac.3)
    ENST00000494080 ENST00000494566(uc001nzz.1) ENST00000492980 ENST00000359902(uc001oaa.3)
    ENST00000479965(uc001oab.1) ENST00000473405 ENST00000472524 ENST00000301897

    miRNA
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    hsa-miR-661 hsa-miR-1207-3p hsa-miR-339-5p hsa-miR-635
    SwitchGear 3'UTR luciferase reporter plasmidCCDC88B 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AK095289.1 AL136799.1 AY491401.1 BC030194.1 BC040232.1 BC140822.1 BC140824.1 BC141866.1 
    BC151218.1 BC151222.1 

    10 DOTS entries:

    DT.99943095  DT.100754779  DT.92052105  DT.97804907  DT.100715851  DT.308479  DT.95374527  DT.120714958 
    DT.95103402  DT.97839231 

    24/77 AceView cDNA sequences (see all 77):

    BQ706508 BU542529 BQ053526 CR623413 CD672940 NM_032251 BQ056644 BC030194 
    BC040232 BX280238 BQ052264 CA428241 BE674671 BQ944786 AK074126 BI518766 
    BI836637 AK090436 AA515594 BX372241 BM046183 BM150271 AI684384 BE222756 

    GeneLoc Exon Structure

    5/15 Alternative Splicing Database (ASD) splice patterns (SP) for CCDC88B (see all 15)    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18a ·
    SP1:                                                              -                                                                                             
    SP2:                                                                                                                                                            
    SP3:                                                              -                       -                                                                     
    SP4:                                                                                      -                                                                     
    SP5:                                                                                                                                                            

    ExUns: 18b ^ 19 ^ 20 ^ 21a · 21b · 21c ^ 22a · 22b ^ 23a · 23b · 23c · 23d
    SP1:                                                                        
    SP2:                                                                        
    SP3:                                                                        
    SP4:                                                                        
    SP5:                                                                        


    ECgene alternative splicing isoforms for CCDC88B

    (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

    CCDC88B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CCDC88B Expression
    About this image


    See CCDC88B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CCDC88B

    SOURCE GeneReport for Unigene cluster: Hs.98564
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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 CCDC88B gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ccdc88b1 , 5 coiled-coil domain containing 88B1, 5 80.51(n)1
    78.49(a)1
      19 (5.08 cM)5
    783171  NM_001081291.11  NP_001074760.11 
     68446235 
    lizard
    (Anolis carolinensis)
    Reptilia CCDC88B6
    Uncharacterized protein
    27(a)
    1 ↔ 1
    GL343739.1(1131-23266)
    zebrafish
    (Danio rerio)
    Actinopterygii ccdc88b6
    coiled-coil domain containing 88B
    26(a)
    1 ↔ 1
    14(48637640-48707554)
    fruit fly
    (Drosophila melanogaster)
    Insecta Girdin6
    Girdin
    20(a)
    1 → many
    3L(3178930-3185287)
    worm
    (Caenorhabditis elegans)
    Secernentea Y51A2D.156
    Protein Y51A2D.15, isoform a
    16(a)
    possible ortholog
    V(18592757-18613944)


    ENSEMBL Gene Tree for CCDC88B (if available)
    TreeFam Gene Tree for CCDC88B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for CCDC88B gene
    HOOK22  HOOK12  CCDC88C2  CCDC88A2  HOOK32  
    3 SIMAP similar genes for CCDC88B using alignment to 3 protein entries:     CC88B_HUMAN (see all proteins):
    FLJ00214    FLJ00198    CCDC88A

    CCDC88B 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) 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

    10/553 SNPs in CCDC88B are shown (see all 553)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1467046351,2
    C--64105750(+) ATTCTC/TATCAT 1 -- us2k10--------
    rs776104941,2
    C--64105777(+) CACATA/GAAAAG 1 -- us2k10--------
    rs1908853821,2
    --64105810(+) GGTTAA/CCATGT 1 -- us2k10--------
    rs752315631,2
    C,F--64105852(+) TTGTTT/CGAATC 1 -- us2k11Minor allele frequency- C:0.02EA 120
    rs1818843271,2
    --64105908(+) CTTCTC/TTGAGT 1 -- us2k10--------
    rs4994251,2
    C,F,A,H--64105929(-) CTCTCC/TGTAGA 1 -- us2k122Minor allele frequency- T:0.21NS EA NA WA CSA 2347
    rs746783621,2
    F--64105984(+) GCCAGC/ATTTAC 1 -- us2k11Minor allele frequency- A:0.01EA 120
    rs1458163801,2
    --64106039(+) AGTGTC/TACTGA 1 -- us2k10--------
    rs1481566501,2
    --64106050(+) CAGGCC/TGGGCG 1 -- us2k10--------
    rs4770741,2
    C--64106056(-) ccaccG/Acgccc 1 -- us2k111Minor allele frequency- A:0.05NA WA CSA EA 254

    HapMap Linkage Disequilibrium report for CCDC88B (64107690 - 64125006 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for CCDC88B:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv358CNV Insertion18451855
    nsv832187CNV Loss17160897
    dgv1169n71CNV Loss21882294
    nsv897685CNV Loss21882294
    dgv1166n71CNV Loss21882294
    dgv1156n71CNV Loss21882294
    dgv1170n71CNV Loss21882294
    dgv13n64CNV Loss17921354
    nsv832186CNV Loss17160897
    dgv1163n71CNV Loss21882294

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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.)
    About This Section
    OMIM gene information: 611205    OMIM disorders: --

    2 diseases for CCDC88B:    About MalaCards
    sarcoidosis    endotheliitis


    CCDC88B for disorders           About GeneDecksing


    Export disorders for CCDC88B 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 CCDC88B gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with CCDC88B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Protective role of Gipie, a Girdin family protein, in endoplasmic reticulum stress responses in endothelial cells. (PubMed id 21289099)1, 3 Matsushita E....Takahashi M. (2011)
    2. A novel hook-related protein family and the characterization of hook- related protein 1. (PubMed id 15882442)1, 3 Simpson F.... Wicking C. (2005)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    5. A novel sarcoidosis risk locus for Europeans on chromo some 11q13.1. (PubMed id 22837380)1 Fischer A....Schreiber S. (2012)
    6. Host-microbe interactions have shaped the genetic arch itecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (2012)
    7. A human MAP kinase interactome. (PubMed id 20936779)1 Bandyopadhyay S....Ideker T. (2010)
    8. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
    9. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (2006)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 283234 HGNC: 26757 AceView: FLJ37970 Ensembl:ENSG00000168071 euGenes: HUgn283234
    ECgene: CCDC88B H-InvDB: CCDC88B

    (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 CCDC88B 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 CCDC88B gene:
    Search GeneIP for patents involving CCDC88B

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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