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    SSR1 signal sequence receptor subunit 1 [ Homo sapiens (human) ]

    Gene ID: 6745, updated on 3-Nov-2024

    Summary

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    Official Symbol
    SSR1provided by HGNC
    Official Full Name
    signal sequence receptor subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:11323
    See related
    Ensembl:ENSG00000124783 MIM:600868; AllianceGenome:HGNC:11323
    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
    TRAPA
    Summary
    The signal sequence receptor (SSR) is a glycosylated endoplasmic reticulum (ER) membrane receptor associated with protein translocation across the ER membrane. The SSR consists of 2 subunits, a 34-kD glycoprotein encoded by this gene and a 22-kD glycoprotein. This gene generates several mRNA species as a result of complex alternative polyadenylation. This gene is unusual in that it utilizes arrays of polyA signal sequences that are mostly non-canonical. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 19.2), appendix (RPKM 16.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SSR1 in Genome Data Viewer
    Location:
    6p24.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (7281143..7313199, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (7150204..7182261, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (7281376..7313432, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374904 Neighboring gene Sharpr-MPRA regulatory region 13455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7042699-7043587 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7051539-7052040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16885 Neighboring gene Sharpr-MPRA regulatory region 12169 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7119221-7119796 Neighboring gene NANOG hESC enhancer GRCh37_chr6:7124594-7125112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7140608-7141135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23937 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7145752-7146422 Neighboring gene ras responsive element binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23938 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:7151030-7151195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7156680-7157346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7160729-7161690 Neighboring gene VISTA enhancer hs2061 Neighboring gene Sharpr-MPRA regulatory region 4659 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7169201-7169702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7169703-7170202 Neighboring gene skeletal muscle cis-regulatory module in RREB1 intron Neighboring gene Sharpr-MPRA regulatory region 2698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7258615-7259114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7261311-7262102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7262103-7262894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7267569-7268070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:7273665-7274166 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_94357 Neighboring gene MPRA-validated peak5642 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7312596-7313464 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:7313465-7314331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16890 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:7342644-7342806 Neighboring gene cancer antigen 1 Neighboring gene ACCSL pseudogene 1 Neighboring gene ribosomal protein S3 pseudogene 4

    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. HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptides. Wei ML, et al. Nature, 1992 Apr 2. PMID 1557127
    2. Segregation of the signal sequence receptor protein in the rough endoplasmic reticulum membrane. Vogel F, et al. Eur J Cell Biol, 1990 Dec. PMID 1964414
    3. Translocon-associated protein alpha transcripts are induced by granulocyte-macrophage colony-stimulating factor and exhibit complex alternative polyadenylation. Hirama T, et al. FEBS Lett, 1999 Jul 23. PMID 10437777
    4. RP11‑156L14.1 regulates SSR1 expression by competitively binding to miR‑548ao‑3p in hypopharyngeal squamous cell carcinoma. Yan J, et al. Oncol Rep, 2020 Nov. PMID 33000261, Free PMC Article
    5. The N-terminal region of the alpha-subunit of the TRAP complex has a conserved cluster of negative charges. Hartmann E, et al. FEBS Lett, 1994 Aug 8. PMID 8050590

    See all (131) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RP11156L14.1 regulates SSR1 expression by competitively binding to miR548ao3p in hypopharyngeal squamous cell carcinoma.
      Title: RP11‑156L14.1 regulates SSR1 expression by competitively binding to miR‑548ao‑3p in hypopharyngeal squamous cell carcinoma.
    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
    Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of signal sequence receptor, alpha (SSR1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • FLJ14232, FLJ22100, FLJ23034, FLJ78242, FLJ93042, DKFZp781N23103

    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 cotranslational protein targeting to membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of cell population proliferation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    translocon-associated protein subunit alpha
    Names
    SSR alpha subunit
    SSR-alpha
    TRAP alpha
    signal sequence receptor subunit alpha
    signal sequence receptor, alpha
    translocon-associated protein alpha subunit

    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_001292008.2 → NP_001278937.1  translocon-associated protein subunit alpha isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1.The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL139095, AL550910, BC007710, BM685131
      Consensus CDS
      CCDS78109.1
      UniProtKB/TrEMBL
      C9JBX5
      Related
      ENSP00000420730.1, ENST00000489567.5
      Conserved Domains (1) summary
      pfam03896
      Location:14 → 212
      TRAP_alpha; Translocon-associated protein (TRAP), alpha subunit

    2. NM_003144.5 → NP_003135.2  translocon-associated protein subunit alpha isoform 1 precursor

      See identical proteins and their annotated locations for NP_003135.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL139095, BC007710, BM685131
      Consensus CDS
      CCDS4499.1
      UniProtKB/Swiss-Prot
      A8K685, P43307, Q53GX2, Q53H19, Q5TAM3, Q6IB43, Q8NBH9, Q96IA2, Q9TNQ8, Q9UN49
      UniProtKB/TrEMBL
      B2R6N9
      Related
      ENSP00000244763.4, ENST00000244763.9
      Conserved Domains (1) summary
      pfam03896
      Location:14 → 280
      TRAP_alpha; Translocon-associated protein (TRAP), alpha subunit

    RNA

    1. NR_120448.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL139095, BC007710, BM685131, BQ216448

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      7281143..7313199 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      7150204..7182261 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P43307.3 GenPept UniProtKB/Swiss-Prot:P43307

    Gene LinkOut

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

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