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SCIMP Gene

protein-coding   GIFtS: 39
GCID: GC17M005113

SLP Adaptor And CSK Interacting Membrane Protein

(Previous name: chromosome 17 open reading frame 87)
(Previous symbol: C17orf87)
  Search for SCIMP
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
SLP Adaptor And CSK Interacting Membrane Protein1 2     Csk-Interacting Membrane Protein1
C17orf871 2 3 5     DTFT57832
SLP65/SLP76, Csk-Interacting Membrane Protein2 3     UNQ57832
SLP65/SLP761     SLP Adapter And CSK-Interacting Membrane Protein2
Chromosome 17 Open Reading Frame 871     Transmembrane Protein C17orf872

External Ids:    HGNC: 335041   Entrez Gene: 3883252   Ensembl: ENSG000001619297   OMIM: 6144065   UniProtKB: Q6UWF33   

Export aliases for SCIMP gene to outside databases


(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 SCIMP Gene:
This gene encodes a transmembrane adaptor protein that is expressed in antigen-presenting cells and is localized
in the immunologic synapse. The encoded protein is involved in major histocompatibility complex class II signal
transduction and immune synapse formation. Alternatively spliced transcript variants have been found for this
gene. (provided by RefSeq, Dec 2012)

GeneCards Summary for SCIMP Gene:
SCIMP (SLP adaptor and CSK interacting membrane protein) is a protein-coding gene.

UniProtKB/Swiss-Prot: SCIMP_HUMAN, Q6UWF3
Function: Lipid tetraspanin-associated transmembrane adapter/mediator involved in major histocompatibility complex
(MHC) class II signaling transduction. Required in generating the calcium response and enhancing ERK activity
upon MHC-II stimulation




(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_000017.11  NT_010718.17  NC_018928.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SCIMP
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCIMP promoter sequence
   Search Chromatin IP Primers for SCIMP

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


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

Entrez Gene cytogenetic band: 17p13.2   Ensembl cytogenetic band:  17p13.2   HGNC cytogenetic band: 17p13.2

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

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M005113:  view genomic region     (about GC identifiers)

Start:
5,112,256 bp from pter      End:
5,138,155 bp from pter
Size:
25,900 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: SCIMP_HUMAN, Q6UWF3 (See protein sequence)
Recommended Name: SLP adapter and CSK-interacting membrane protein  
Size: 145 amino acids; 16618 Da
Subunit: Interacts with CD37, CD53 and CD81. Interacts with BLNK and GRB2 isoform 1. Interacts (via prolin-rich
region) with LYN (via SH3 domain). Interacts with CSK (via SH2 domain)
Caution: It is uncertain whether Met-1 or Met-12 is the initiator
Secondary accessions: B4DLK1 Q96MD0
Alternative splicing: 2 isoforms:  Q6UWF3-1   Q6UWF3-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SCIMP: NX_Q6UWF3

Post-translational modifications: 

  • Phosphorylated. Phosphorylation occurs on tyrosine residues by tyrosine-protein kinases LYN and SRC upon MHC-II
    stimulation1
  • Palmitoylated1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • REFSEQ proteins (2 alternative transcripts): 
    NP_001258771.1  NP_996986.1  

    ENSEMBL proteins: 
     ENSP00000461269   ENSP00000382509   ENSP00000459605   ENSP00000459153  

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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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    1 InterPro protein domain:
     IPR028181 SCIMP

    Graphical View of Domain Structure for InterPro Entry Q6UWF3

    ProtoNet protein and cluster: Q6UWF3


    Find genes that share domains with SCIMP           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: SCIMP_HUMAN, Q6UWF3
    Function: Lipid tetraspanin-associated transmembrane adapter/mediator involved in major histocompatibility complex
    (MHC) class II signaling transduction. Required in generating the calcium response and enhancing ERK activity
    upon MHC-II stimulation

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
         
    Find genes that share ontologies with SCIMP           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for SCIMP:
     Decreased Wnt reporter activit 

         4 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Scimp):
     cellular  growth/size/body  hematopoietic system  homeostasis/metabolism 

    Find genes that share phenotypes with SCIMP           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Scimptm1Lex for SCIMP

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    hsa-mir-335-5p (MIRT017059)

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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
    SCIMP_HUMAN, Q6UWF3: Membrane; Single-pass membrane protein (Potential). Membrane; Lipid-anchor. Note=Together
    with MHC-II, associates with lipid-enriched microdomains called tetraspanin-enriched microdomains (TEMs). Rapidly
    translocates into immunological synapse (IS) at cell-cell contacts between antigen-presenting cells (APCs) and
    T-cells. Colocalized with tetraspanins CD37, CD53, and CD81 at the uropod. Present at regions of cell-cell
    contacts but also at the leading edge of migrating cells

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001772immunological synapse IDA--
    GO:0016020membrane IDA--
    GO:0016021integral component of membrane IEA--
    GO:0031256leading edge membrane IDA--
    GO:0031259uropod membrane IDA--

    Find genes that share ontologies with SCIMP           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 SCIMP
    Interactions:

        Search GeneGlobe Interaction Network for SCIMP

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0070374positive regulation of ERK1 and ERK2 cascade IDA--

    Find genes that share ontologies with SCIMP           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 SCIMP



    (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 SCIMP gene (2 alternative transcripts): 
    NM_001271842.1  NM_207103.3  

    Unigene Cluster for SCIMP:

    SLP adaptor and CSK interacting membrane protein
    Hs.462080  [show with all ESTs]
    Unigene Representative Sequence: NM_207103
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000574081(uc002gbh.2) ENST00000399600(uc010clb.1) ENST00000571800(uc002gbi.2)
    ENST00000574297
    miRNA
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    Additional mRNA sequence: 

    AK057142.1 AK297035.1 AK310145.1 AY358809.1 BC127925.1 BC130554.1 BC130556.1 BC144395.1 
    DQ778084.1 

    5 DOTS entries:

    DT.86844649  DT.40125945  DT.95158313  DT.120906940  DT.99993393 

    Selected AceView cDNA sequences (see all 32):

    CA394486 CR612993 AA827110 T95272 BX279842 AW575021 AA731090 BX411363 
    AI825110 AI823787 NM_207103 AW501476 AW401804 AK057142 CA306389 AY358809 
    BX410087 CA748490 CD366373 AW016164 AW662810 AI582365 BM152175 AL559654 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for SCIMP    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b
    SP1:        -                           
    SP2:                                    


    ECgene alternative splicing isoforms for SCIMP

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

    SCIMP Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.462080

    UniProtKB/Swiss-Prot: SCIMP_HUMAN, Q6UWF3
    Tissue specificity: Expressed in antigen-presenting cells, like peripheral blood leukocytes and monocyte-derived
    dendritic cells (MDDC) (at protein level). Highly expressed in lymph nodes and spleen. Expressed in
    antigen-presenting cells. Faintly expressed in the majority of nonimmune system tissues

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCIMP

    (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 human and mouse.

    Orthologs for SCIMP gene from Selected species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scimp1 , 5 RIKEN cDNA A430084P05 gene5
    SLP adaptor and CSK interacting membrane protein1
    76.92(n)1
    68.46(a)1
      11 (43.21 cM)5
    3279571  NM_001045526.21  NP_001038991.11 
     707909325 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCIMP gene
    Selected SIMAP similar genes for SCIMP using alignment to 2 protein entries:     SCIMP_HUMAN (see all proteins) (see all similar genes):
    COX7A2    C17orf87    KLHDC1    ZNF23    ZNF738    ATL2
    CNOT2    LRRC36    SENP7    FANCA    IFT122    NSD1
    LRTOMT    SCLT1    CES4A    ECD    C12orf23    CCPG1

    Find genes that share paralogs with SCIMP           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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    10 SNPs for SCIMP    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1843987251,2
    C--5139466(+) CAAGTA/GGCTGG 2 -- us2k10--------
    rs1884482481,2
    --5139506(+) TAATCC/TTTGTA 2 -- us2k10--------
    rs749742591,2
    C--5139736(+) CAGTGG/TCTCAC 2 -- us2k10--------
    rs574025201,2
    --5139807(+) GACCAA/GCCTGG 2 -- us2k10--------
    rs581240101,2
    --5139808(+) ACCAGC/TCTGGC 2 -- us2k10--------
    rs1127578581,2
    ----5139933(+) GGAGGC/GGGAGG 2 -- us2k10--------
    rs80704181,2
    ----5139526(+) gagacA/Ggggtt 2 -- us2k10--------
    rs129503591,2
    ----5140085(+) AGCTGG/TGACTT 2 -- us2k10--------
    rs80698371,2
    ----5139525(+) agagaC/Tagggt 2 -- us2k10--------
    rs3738183761,2
    ----5139463(+) TCCCAA/CTAGCT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for SCIMP (5112256 - 5138155 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for SCIMP: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SCIMP
    DNA2.0 Custom Variant and Variant Library Synthesis for SCIMP

    (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: 614406    OMIM disorders: --


    Find genes that share disorders with SCIMP           About GenesLikeMe


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

    1. SCIMP, a transmembrane adapter protein involved in major histocompatibility complex class II signaling. (PubMed id 21930792)1, 2, 3 Draber P....Brdicka T. (Mol. Cell. Biol. 2011)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    4. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). (PubMed id 23503679)1 Zhu J....Elledge S.J. (Nat. Biotechnol. 2013)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    6. 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. (Genome Res. 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)

    (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: 388325 HGNC: 33504 AceView: UNQ5783 Ensembl:ENSG00000161929 euGenes: HUgn388325
    ECgene: SCIMP H-InvDB: SCIMP

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for SCIMP 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 SCIMP gene:
    Search GeneIP for patents involving SCIMP

    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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