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    SCIMP SLP adaptor and CSK interacting membrane protein [ Homo sapiens (human) ]

    Gene ID: 388325, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SCIMPprovided by HGNC
    Official Full Name
    SLP adaptor and CSK interacting membrane proteinprovided by HGNC
    Primary source
    HGNC:HGNC:33504
    See related
    Ensembl:ENSG00000161929 MIM:614406; AllianceGenome:HGNC:33504
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UNQ5783; C17orf87
    Summary
    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]
    Expression
    Biased expression in spleen (RPKM 11.9), lymph node (RPKM 9.3) and 13 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCIMP in Genome Data Viewer
    Location:
    17p13.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (5208920..5234860, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (5102281..5128266, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (5112215..5138155, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11566 Neighboring gene ZNF232 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5033804-5034304 Neighboring gene zinc finger protein 232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040130-5040801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5040802-5041472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5042145-5042815 Neighboring gene ubiquitin specific peptidase 6 Neighboring gene MPRA-validated peak2704 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8065 Neighboring gene zinc finger protein 594 Neighboring gene ZNF594 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8066 Neighboring gene MPRA-validated peak2705 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11567 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11569 Neighboring gene Sharpr-MPRA regulatory region 14928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:5157813-5158318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:5187866-5188384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8068 Neighboring gene rabaptin, RAB GTPase binding effector protein 1 Neighboring gene uncharacterized LOC105371505 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:5265177-5265872 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:5316624-5317823 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:5322619-5323156 Neighboring gene nucleoporin 88

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SCIMP: A Novel Targeted Gene for Postmenopausal Osteoporosis Progression. Sun X, et al. Orthop Surg, 2023 May. PMID 37057624, Free PMC Article
    2. SCIMP, a transmembrane adaptor protein involved in major histocompatibility complex class II signaling. Draber P, et al. Mol Cell Biol, 2011 Nov. PMID 21930792, Free PMC Article
    3. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Lambert JC, et al. Nat Genet, 2013 Dec. PMID 24162737, Free PMC Article
    4. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Zhu J, et al. Nat Biotechnol, 2013 Apr. PMID 23503679, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SCIMP: A Novel Targeted Gene for Postmenopausal Osteoporosis Progression.
      Title: SCIMP: A Novel Targeted Gene for Postmenopausal Osteoporosis Progression.
    2. results suggest that SCIMP is involved in signal transduction after MHC-II stimulation and therefore serves as a regulator of antigen presentation and other APC functions.
      Title: SCIMP, a transmembrane adaptor protein involved in major histocompatibility complex class II signaling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32580, MGC163426, MGC163428

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular adaptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to molecule of fungal origin ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cytokine production involved in immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of dendritic cell cytokine production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of interleukin-12 production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of interleukin-6 production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of lipopolysaccharide-mediated signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of stress-activated MAPK cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in toll-like receptor 3 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in toll-like receptor 4 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in toll-like receptor 7 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in toll-like receptor TLR1:TLR2 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    colocalizes_with filopodium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in immunological synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in immunological synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in leading edge membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in phagocytic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    colocalizes_with ruffle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in tetraspanin-enriched microdomain IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in uropod membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SLP adapter and CSK-interacting membrane protein
    Names
    DTFT5783
    SLP65/SLP76, Csk-interacting membrane protein
    transmembrane protein C17orf87

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001271842.1 → NP_001258771.1  SLP adapter and CSK-interacting membrane protein isoform 2

      See identical proteins and their annotated locations for NP_001258771.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AC087500, AK310145
      Consensus CDS
      CCDS62044.1
      UniProtKB/Swiss-Prot
      Q6UWF3
      Related
      ENSP00000382509.4, ENST00000399600.8
      Conserved Domains (1) summary
      pfam15050
      Location:12 → 135
      SCIMP; SCIMP protein

    2. NM_001319190.2 → NP_001306119.1  SLP adapter and CSK-interacting membrane protein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and has multiple coding region differences, compared to variant 1, one of which results in a frameshift. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC087500
      Consensus CDS
      CCDS82046.1
      UniProtKB/Swiss-Prot
      Q6UWF3
      Related
      ENSP00000459605.1, ENST00000571800.5
      Conserved Domains (1) summary
      pfam15050
      Location:12 → 87
      SCIMP; SCIMP protein

    3. NM_207103.3 → NP_996986.1  SLP adapter and CSK-interacting membrane protein isoform 1

      See identical proteins and their annotated locations for NP_996986.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC087500, AK310145, BC130554
      Consensus CDS
      CCDS42242.1
      UniProtKB/Swiss-Prot
      A6XGL4, B4DLK1, Q6UWF3, Q96MD0
      Related
      ENSP00000461269.1, ENST00000574081.6
      Conserved Domains (1) summary
      pfam15050
      Location:12 → 142
      SCIMP; SCIMP protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      5208920..5234860 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435959.1 → XP_047291915.1  SLP adapter and CSK-interacting membrane protein isoform X1

      UniProtKB/TrEMBL
      I3L1W2
      Related
      ENSP00000459153.1, ENST00000574297.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      5102281..5128266 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054316028.1 → XP_054172003.1  SLP adapter and CSK-interacting membrane protein isoform X1

      UniProtKB/TrEMBL
      I3L1W2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6UWF3.1 GenPept UniProtKB/Swiss-Prot:Q6UWF3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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