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

Gene ID: 388325, updated on 27-Nov-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
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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
  • 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)

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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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

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