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RTL1 Gene

protein-coding   GIFtS: 39
GCID: GC14M101347

Retrotransposon-Like 1

  See RTL1-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
Retrotransposon-Like 11 2     MART12 3
PEG112 3 5     Mar12
Mammalian Retrotransposon Derived Protein 12 3     Retrotransposon-Like Protein 12
Paternally Expressed Gene 11 Protein2 3     MAR13
Retrotransposon-Derived Protein PEG112 3     

External Ids:    HGNC: 146651   Entrez Gene: 3880152   Ensembl: ENSG000002546567   OMIM: 6118965   UniProtKB: A6NKG53   

Export aliases for RTL1 gene to outside databases

Previous GC identifers: GC14M100417 GC14M081528


(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 RTL1 Gene:
This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late
fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript,
which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi)
mechanism. This gene is essential for maintenance of the fetal capillaries. (provided by RefSeq, Jul 2009)

GeneCards Summary for RTL1 Gene:
RTL1 (retrotransposon-like 1) is a protein-coding gene. Diseases associated with RTL1 include maternal uniparental disomy, chromosome 14, and uniparental disomy, paternal, chromosome 14.

UniProtKB/Swiss-Prot: RTL1_HUMAN, A6NKG5
Function: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface
and for development of the placenta (By similarity)




(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_000014.8  NC_018925.2  NT_026437.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the RTL1 gene promoter:
         AML1a   Pax-5   Olf-1   MyoD   E4BP4   C/EBPalpha   FOXJ2 (long isoform)   FOXJ2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RTL1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RTL1


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

Entrez Gene cytogenetic band: 14q32.2   Ensembl cytogenetic band:  14q32.2   HGNC cytogenetic band: 14q32.2

RTL1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RTL1 gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M101347:  view genomic region     (about GC identifiers)

Start:
101,346,992 bp from pter      End:
101,351,184 bp from pter
Size:
4,193 bases      Orientation:
minus 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: RTL1_HUMAN, A6NKG5 (See protein sequence)
Recommended Name: Retrotransposon-like protein 1  
Size: 1358 amino acids; 155048 Da
Miscellaneous: Rtl1 is one of at least 11 genes called Mar or Mart related to long terminal repeat
retrotransposons. They do not correspond to functional retrotransposons, but rather to neofunctionalized
retrotransposons genes
Miscellaneous: RTL1 is an imprinted gene located in a cluster of imprinted genes on chromosome 14. It is expressed
from the paternal chromosome and has an antisense transcript with full complementarity to RTL1, RTL1as, expressed
from the maternal chromosome, which acts as a repressor for RTL1. Excessive RTL1 expression and decreased RTL1
expression are relevant to upd(14)pat-like and upd(14)mat-like phenotypes, respectively. Paternal and maternal
uniparental disomy for chromosome 14 (upd(14)pat and upd(14)mat) cause distinct phenotypes; Upd(14)pat results in
a unique phenotype characterized by facial abnormality, a small, bell-shaped thorax and abdominal wall defects,
and upd(14)mat leads to pre- and postnatal growth failure and early onset of puberty
Secondary accessions: E9PKS8

Explore the universe of human proteins at neXtProt for RTL1: NX_A6NKG5

Explore proteomics data for RTL1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RTL1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001128360.1  
    ENSEMBL proteins: 
     ENSP00000435342  

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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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    2 InterPro protein domains:
     IPR021109 Peptidase_aspartic_dom
     IPR005162 Retrotrans_gag_dom

    Graphical View of Domain Structure for InterPro Entry A6NKG5

    ProtoNet protein and cluster: A6NKG5


    Find genes that share domains with RTL1           About GenesLikeMe


    (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, 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RTL1_HUMAN, A6NKG5
    Function: Plays an essential role in capillaries endothelial cells for the maintenance of feto-maternal interface
    and for development of the placenta (By similarity)

    Phenotypes:
         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rtl1):

     embryogenesis  growth/size/body  mortality/aging  other 

    Find genes that share phenotypes with RTL1           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Rtl1tm1Fuis for RTL1

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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
    RTL1_HUMAN, A6NKG5: Membrane; Multi-pass membrane protein (Potential)

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with RTL1           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 RTL1
    Interactions:

        Search GeneGlobe Interaction Network for RTL1

    5 Interacting proteins for RTL1 (A6NKG53) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    FNBP1LQ5T0N53I2D: score=2 
    CCT4P509913I2D: score=1 
    GSK3BP498413I2D: score=1 
    HSP90AA1P079003I2D: score=1 
    SRPK2P783623I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--

    Find genes that share ontologies with RTL1           About GenesLikeMe



    (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 RTL1



    (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 RTL1 gene: 
    NM_001134888.2  

    Unigene Cluster for RTL1:

    Retrotransposon-like 1
    Hs.298602  [show with all ESTs]
    Unigene Representative Sequence: NM_001134888
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000534062(uc010txj.1)
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    Additional mRNA sequence: BC150617.1 

    2 DOTS entries:

    DT.120754501  DT.97811948 

    2 AceView cDNA sequences:

    AI338830 BF514033 

    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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    RTL1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACGGCCTGCA
    RTL1 Expression
    About this image

    RTL1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RTL1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.298602
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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 RTL1 gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rtl11 , 5 retrotransposon-like 11, 5 74.35(n)1
    66.69(a)1
      12 (60.38 cM)5
    3533261  NM_184109.11  NP_908998.11 
     1095901695 
    lizard
    (Anolis carolinensis)
    Reptilia RTL16
    retrotransposon-like 1
    19(a)
    1 ↔ 1
    2(103314668-103317011)


    ENSEMBL Gene Tree for RTL1 (if available)
    TreeFam Gene Tree for RTL1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RTL1 gene
    3 SIMAP similar genes for RTL1 using alignment to 2 protein entries:     RTL1_HUMAN (see all proteins):
    FAM127B    FAM127C    FAM127A

    Find genes that share paralogs with RTL1           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 RTL1 (see all 34)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1490839141,2
    --101351689(+) CTTGGC/TTGTGG 1 -- us2k10--------
    rs1421408461,2
    --101351697(+) TGGAGC/TGGGAA 1 -- us2k10--------
    rs19506251,2
    --101351848(+) GGTGTG/TTACAG 1 -- us2k10--------
    rs58110141,2
    C--101351861(+) CTGGG-/TTTTTT 1 -- us2k10--------
    rs588082451,2
    C--101351861(+) CTGGGTT/-TTTTT 1 -- us2k11Minor allele frequency- -:0.50NA 2
    rs1512273241,2
    C--101351893(+) ATAACA/GTACCT 1 -- us2k10--------
    rs1403635211,2
    --101352324(+) CTGACA/GGTCCC 1 -- us2k10--------
    rs1153450931,2
    C,F--101352487(+) TACTGC/ATCTTT 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1503055211,2
    --101352584(+) CCTTAC/TGTGAA 1 -- us2k10--------
    rs733493551,2
    C,F--101352661(+) AAGTAC/AACCCT 1 -- us2k12Minor allele frequency- A:0.05WA 120

    HapMap Linkage Disequilibrium report for RTL1 (101346992 - 101351184 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RTL1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509549CNV Insertion20534489
    nsv902241CNV Loss21882294
    nsv902240CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
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    (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: 611896    OMIM disorders: --

    2 diseases for RTL1:    
    About MalaCards
    maternal uniparental disomy, chromosome 14    uniparental disomy, paternal, chromosome 14


    Find genes that share disorders with RTL1           About GenesLikeMe

    Genetic Association Database (GAD): RTL1

    Export disorders for RTL1 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 RTL1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with RTL1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. (PubMed id 19966805)1, 4 Wallace C....Clayton D.G. (Nat. Genet. 2010)
    2. Deletions and epimutations affecting the human 14q32.2 imprinted region in individuals with paternal and maternal upd(14)-like phenotypes. (PubMed id 18176563)1, 2 Kagami M.... Ogata T. (Nat. Genet. 2008)
    3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PubMed id 16093683)1, 2 Brandt J.... Volff J.-N. (Cytogenet. Genome Res. 2005)
    4. A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. (PubMed id 16155747)1, 3 Youngson N.A....Ferguson-Smith A.C. (J. Mol. Evol. 2005)
    5. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. (PubMed id 15854907)1, 3 Davis E....Charlier C. (Curr. Biol. 2005)
    6. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)1, 2 Heilig R.... Weissenbach J. (Nature 2003)
    7. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. (PubMed id 12796779)1, 3 Seitz H....CavaillAc J. (Nat. Genet. 2003)
    8. Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia. (PubMed id 24389010)1 Bundo M....Iwamoto K. (Neuron 2013)
    9. Identification of rtl1, a retrotransposon-derived imprinted gene, as a novel driver of hepatocarcinogenesis. (PubMed id 23593033)1 Riordan J.D....Dupuy A.J. (PLoS Genet. 2013)
    10. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. (PubMed id 17463248)4 Scott L.J....Boehnke M. (Science 2007)

    (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: 388015 HGNC: 14665 AceView: LOC388015 Ensembl:ENSG00000254656 euGenes: HUgn388015
    ECgene: RTL1 H-InvDB: RTL1

    (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 RTL1 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 RTL1 gene:
    Search GeneIP for patents involving RTL1

    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, eBioscience, 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 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 , 21 Aug 2014 , 8 Sep 2014

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