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

Gene ID: 6745, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (7281143..7313199, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (7150204..7182261, complement)
105.20220307 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. 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
  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. HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptides. Wei ML, et al. Nature, 1992 Apr 2. PMID 1557127
  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 (110) 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)

Genotypes

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_2023_10

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

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