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RPTN Gene

protein-coding   GIFtS: 48
GCID: GC01M152126

Repetin

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(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
repetin1 2
Intermediate Filament-Associated Protein2

External Ids:    HGNC: 268091   Entrez Gene: 1266382   Ensembl: ENSG000002158537   OMIM: 6132595   UniProtKB: Q6XPR33   

Export aliases for RPTN gene to outside databases

Previous GC identifers: GC01M148940 GC01M150394 GC01M123503


(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 RPTN Gene:
RPTN (repetin) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is FLG2.

UniProtKB/Swiss-Prot: RPTN_HUMAN, Q6XPR3
Function: Involved in the cornified cell envelope formation. Multifunctional epidermal matrix protein. Reversibly
binds calcium




(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_000001.10  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the RPTN gene promoter:
         AML1a   GATA-3   POU2F1   POU2F1a   GATA-1   GATA-2   Evi-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPTN


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

Entrez Gene cytogenetic band: 1q21.3   Ensembl cytogenetic band:  1q21.3   HGNC cytogenetic band: 1q21.3

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

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M152126:  view genomic region     (about GC identifiers)

Start:
152,126,071 bp from pter      End:
152,131,704 bp from pter
Size:
5,634 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., 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: RPTN_HUMAN, Q6XPR3 (See protein sequence)
Recommended Name: Repetin  
Size: 784 amino acids; 90731 Da
Secondary accessions: B7ZBZ3

Explore the universe of human proteins at neXtProt for RPTN: NX_Q6XPR3

Explore proteomics data for RPTN at MOPED

Post-translational modifications: 

  • Potential substrate of transglutaminase. Some arginines are probably converted to citrullines by peptidylarginine
    deimidase1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

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

    REFSEQ proteins: NP_001116437.1  
    ENSEMBL proteins: 
     ENSP00000317895  

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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:
    EFHAND: EF-hand domain containing

    5 InterPro protein domains:
     IPR018247 EF_Hand_1_Ca_BS
     IPR011992 EF-hand-dom_pair
     IPR002048 EF_hand_dom
     IPR013787 S100_Ca-bd_sub
     IPR001751 S100/CaBP-9k_CS

    Graphical View of Domain Structure for InterPro Entry Q6XPR3

    ProtoNet protein and cluster: Q6XPR3

    1 Blocks protein domain: IPB001751 Calcium-binding protein

    UniProtKB/Swiss-Prot: RPTN_HUMAN, Q6XPR3
    Domain: Can be divided into a N-terminal domain with significant homology to S100-like calcium-binding proteins, a
    central domain containing a series of short tandem repeats, and two flanking segments with low homology to the
    consensus sequences of the central repeats
    Similarity: Belongs to the S100-fused protein family
    Similarity: Contains 2 EF-hand domains


    Find genes that share domains with RPTN           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RPTN_HUMAN, Q6XPR3
    Function: Involved in the cornified cell envelope formation. Multifunctional epidermal matrix protein. Reversibly
    binds calcium

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    Find genes that share ontologies with RPTN           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for RPTN:
     Decreased Tat-dependent transc  Decreased p24 protein expressi 

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

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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
    RPTN_HUMAN, Q6XPR3: Secreted, extracellular space, extracellular matrix
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    cytosol3
    cytoskeleton2
    nucleus2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001533cornified envelope IEA--
    GO:0005578proteinaceous extracellular matrix IEA--

    Find genes that share ontologies with RPTN           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 RPTN
    Interactions:

        Search GeneGlobe Interaction Network for RPTN

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

    Selected Interacting proteins for RPTN (Q6XPR33 ENSP000003178954) via UniProtKB, MINT, STRING, and/or I2D (see all 27)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    OTUD4Q018043, ENSP000004092794I2D: score=1 STRING: ENSP00000409279
    AMBRA1Q9C0C73I2D: score=1 
    ATG101Q9BSB43I2D: score=1 
    ATG3Q9NT623I2D: score=1 
    ATG7O953523I2D: score=1 
    About this table

    (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 RPTN

    1 HMDB Compound for RPTN    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (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 RPTN gene (2 alternative transcripts): 
    NM_152364.1  NM_001122965.1  

    Unigene Cluster for RPTN:

    Repetin
    Hs.376144  [show with all ESTs]
    Unigene Representative Sequence: AY396742
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000316073(uc001ezs.1)
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    Additional mRNA sequence: 

    AK096436.1 AY396742.1 BC112216.1 BC112218.1 

    2 DOTS entries:

    DT.75106896  DT.99998922 

    1 AceView cDNA sequence:

    AK096436 

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

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

    RPTN Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.376144

    UniProtKB/Swiss-Prot: RPTN_HUMAN, Q6XPR3
    Tissue specificity: Expression is scattered in the normal epidermis but strong in the acrosyringium, the inner
    hair root sheath and in the filiform papilli of the tongue

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    In Situ
    Assay Products:
     

     
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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 RPTN gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rptn1 , 5 repetin1, 5 72.93(n)1
    57.59(a)1
      3 (40.51 cM)5
    201291  NM_009100.21  NP_033126.21 
     933936995 
    chicken
    (Gallus gallus)
    Aves CRNN6
    Gallus gallus cornulin (CRNN), mRNA.
    19(a)
    1 → many
    25(1132880-1134156)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    17(a)
    1 → many
    GL343369.1(7-2795)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RPTN gene
    FLG22  TCHH2  HRNR2  CRNN2  FLG2  TCHHL12  
    14 SIMAP similar genes for RPTN using alignment to 3 protein entries:     RPTN_HUMAN (see all proteins):
    FLG    S100B    S100A1    S100G    S100A4    S100A8
    S100P    S100A9    S100A11    S100A12    S100A6    S100Z
    S100A2    S100A10

    Find genes that share paralogs with RPTN           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 RPTN (see all 234)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs112049261,2
    C,F,A,H--152125626(+) CCTGTC/TATGTG 1 -- ds500111Minor allele frequency- T:0.09NS EA NA 976
    rs1889098021,2
    --152125759(+) GGAGAC/TGTGAG 1 -- ds50010--------
    rs1390715961,2
    --152125785(+) TATGGA/GGATGT 1 -- ds50010--------
    rs1819322491,2
    --152125860(+) ACTCAC/GTAGAG 1 -- ds50010--------
    rs1862369451,2
    --152125923(+) ATTTGG/TTTTGT 1 -- ds50010--------
    rs1151660981,2
    C,F--152126061(+) AGGAGT/ACATGA 1 -- ds50011Minor allele frequency- A:0.06WA 118
    rs1914778251,2
    --152126067(+) CATGAA/CAGTTA 1 -- ds50010--------
    rs1831456181,2
    --152126194(+) ATTTGC/TAAACA 1 -- ut310--------
    rs1849985131,2
    --152126219(+) TCTCTC/TTATTT 1 -- ut310--------
    rs1899023211,2
    --152126377(+) CTCTTA/GTAGCA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for RPTN (152126071 - 152131704 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for RPTN:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2221423CNV Deletion18987734
    esv2718084CNV Deletion23290073
    esv2659441CNV Deletion23128226
    esv2718095CNV Deletion23290073
    nsv482125CNV Loss20164927
    nsv872442CNV Gain21882294

    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: 613259    OMIM disorders: --


    Find genes that share disorders with RPTN           About GenesLikeMe

    Genetic Association Database (GAD): RPTN
    Human Genome Epidemiology (HuGE) Navigator: RPTN (1 document)

    Export disorders for RPTN 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 RPTN gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with RPTN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation and characterization of human repetin, a member of the fused gene family of the epidermal differentiation complex. (PubMed id 15854042)1, 2, 3, 9 Huber M.... Hohl D. (J. Invest. Dermatol. 2005)
    2. Genetic associations of variants in genes encoding HIV-dependency factors required for HIV-1 infection. (PubMed id 21083371)4 Chinn L.W....O'Brien S.J. (J. Infect. Dis. 2010)
    3. Defining the human deubiquitinating enzyme interaction landscape. (PubMed id 19615732)1 Sowa M.E....Harper J.W. (Cell 2009)
    4. Identification of host proteins required for HIV infection through a functional genomic screen. (PubMed id 18187620)1 Brass A.L....Elledge S.J. (Science 2008)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (Nature 2006)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. 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)
    8. (PubMed id )2 
    9. Permeability barrier dysfunction in transgenic mice overexpressing claudin 6. (PubMed id 11923212)9 Turksen K. and Troy T.C. (Development 2002)
    10. Development of an ichthyosiform phenotype in Alox12b-deficient mouse skin transplants. (PubMed id 19122646)9 de Juanes S....Krieg P. (J. Invest. Dermatol. 2009)

    (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: 126638 HGNC: 26809 AceView: FLJ39117 Ensembl:ENSG00000215853 euGenes: HUgn126638
    ECgene: RPTN H-InvDB: RPTN

    (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 RPTN 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 RPTN gene:
    Search GeneIP for patents involving RPTN

    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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     OriGene Antibodies for RPTN   OriGene RNAi products in human, mouse, rat for RPTN  
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     Block miRNA regulation of human, mouse, rat RPTN using miScript Target Protectors SeqTarget long-range PCR primers for resequencing RPTN
     DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RPTN Predesigned siRNA for gene silencing in human, mouse, rat RPTN
     QuantiFast Probe-based Assays in human, mouse, rat RPTN QuantiTect SYBR Green Assays in human, mouse, rat RPTN
     Custom PCR Arrays for RPTN Search Chromatin IP Primers for RPTN
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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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