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

Summary

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

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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 EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1472 (e-PCR)
- UniSTS:48907

NoName (e-PCR)
- UniSTS:9484

SHGC-32039 (e-PCR)
- UniSTS:65037

RH17553 (e-PCR)
- UniSTS:42004

WI-18513 (e-PCR)
- UniSTS:24614

G31079 (e-PCR)
- UniSTS:72239

D8S2279 (e-PCR)
- UniSTS:473907

RH104291 (e-PCR)
- UniSTS:98616

A006X18 (e-PCR)
- UniSTS:15163

D6S321E (e-PCR)
- UniSTS:147520

SHGC-86312 (e-PCR)
- UniSTS:104516

SHGC-36562 (e-PCR)
- UniSTS:82766

SGC35789 (e-PCR)
- UniSTS:17498

D6S321E (e-PCR)
- UniSTS:33379

D10S16 (e-PCR)
- UniSTS:155756

STS-N36801 (e-PCR)
- UniSTS:66161

RH93008 (e-PCR)
- UniSTS:90737

RH80030 (e-PCR)
- UniSTS:87680

RH103606 (e-PCR)
- UniSTS:97931

A006P22 (e-PCR)
- UniSTS:76690

SHGC-84014 (e-PCR)
- UniSTS:104635

D6S321E (e-PCR)
- UniSTS:147451

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)

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
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

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