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    SPCS1 signal peptidase complex subunit 1 [ Homo sapiens (human) ]

    Gene ID: 28972, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SPCS1provided by HGNC
    Official Full Name
    signal peptidase complex subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:23401
    See related
    Ensembl:ENSG00000114902 MIM:610358; AllianceGenome:HGNC:23401
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SPC1; SPC12; HSPC033; YJR010C-A
    Summary
    Predicted to enable ribosome binding activity. Involved in signal peptide processing; viral protein processing; and virion assembly. Located in endoplasmic reticulum membrane. Part of signal peptidase complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 60.9), colon (RPKM 57.9) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See SPCS1 in Genome Data Viewer
    Location:
    3p21.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52706106..52711148)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52739017..52744058)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52740122..52745164)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene G protein nucleolar 3 Neighboring gene small nucleolar RNA, C/D box 69 Neighboring gene glycosyltransferase 8 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14452 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52749367-52749954 Neighboring gene NIMA related kinase 4 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:52765581-52766780 Neighboring gene zinc finger protein 610 pseudogene Neighboring gene AK3 pseudogene 7

    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. SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency. Alzahrani N, et al. PLoS Pathog, 2022 Feb. PMID 35130329, Free PMC Article
    2. Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1. Gee F, et al. BMC Med Genet, 2014 May 4. PMID 24886551, Free PMC Article
    3. Host Factor SPCS1 Regulates the Replication of Japanese Encephalitis Virus through Interactions with Transmembrane Domains of NS2B. Ma L, et al. J Virol, 2018 Jun 15. PMID 29593046, Free PMC Article
    4. Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2. Suzuki R, et al. PLoS Pathog, 2013. PMID 24009510, Free PMC Article
    5. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Liaci AM, et al. Mol Cell, 2021 Oct 7. PMID 34388369

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency.
      Title: SPCS1-Dependent E2-p7 processing determines HCV Assembly efficiency.
    2. the results demonstrate that SPCS1 affects viral replication by interacting with NS2B, thereby influencing the posttranslational processing of Japanese Encephalitis Virus proteins and the assembly of virions.
      Title: Host Factor SPCS1 Regulates the Replication of Japanese Encephalitis Virus through Interactions with Transmembrane Domains of NS2B.
    3. cis-acting regulatory polymorphisms acting on GNL3 and SPCS1 contribute to the OA association signal at chromosome 3p21, and these genes therefore merit further investigation.
      Title: Allelic expression analysis of the osteoarthritis susceptibility locus that maps to chromosome 3p21 reveals cis-acting eQTLs at GNL3 and SPCS1.
    4. SPCS1 plays a key role in the formation of the membrane-associated NS2-E2 complex via its interaction with NS2 and E2, which leads to a coordinating interaction between the structural and non-structural proteins
      Title: Signal peptidase complex subunit 1 participates in the assembly of hepatitis C virus through an interaction with E2 and NS2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
    EBI GWAS Catalog
    Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein targeting to ER IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in proteolysis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in signal peptide processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in signal peptide processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in viral protein processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in virion assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of signal peptidase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of signal peptidase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of signal peptidase complex TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    signal peptidase complex subunit 1
    Names
    SPase 12 kDa subunit
    microsomal signal peptidase 12 kDa subunit
    signal peptidase 12kDa
    signal peptidase complex 12 kDa subunit
    signal peptidase complex subunit 1 homolog
    NP_054760.4

    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_014041.5 → NP_054760.4  signal peptidase complex subunit 1

      Status: VALIDATED

      Source sequence(s)
      AC104446, AK027426, BC000884, CA309210, DB459917
      Consensus CDS
      CCDS33769.3
      UniProtKB/TrEMBL
      A0A5F9YFS9
      Related
      ENSP00000478310.2, ENST00000619898.5
      Conserved Domains (1) summary
      pfam06645
      Location:12 → 81
      SPC12; Microsomal signal peptidase 12 kDa subunit (SPC12)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      52706106..52711148
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      52739017..52744058
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y6A9.5 GenPept UniProtKB/Swiss-Prot:Q9Y6A9

    Gene LinkOut

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

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