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SSR4 signal sequence receptor subunit 4 [ Homo sapiens (human) ]

Gene ID: 6748, updated on 26-Nov-2024

Summary

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Official Symbol
SSR4provided by HGNC
Official Full Name
signal sequence receptor subunit 4provided by HGNC
Primary source
HGNC:HGNC:11326
See related
Ensembl:ENSG00000180879 MIM:300090; AllianceGenome:HGNC:11326
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
CDG1Y; TRAPD
Summary
This gene encodes the delta subunit of the translocon-associated protein complex which is involved in translocating proteins across the endoplasmic reticulum membrane. The encoded protein is located in the Xq28 region and is arranged in a compact head-to-head manner with the isocitrate dehydrogenase 3 (NAD+) gamma gene and both genes are driven by a CpG-embedded bidirectional promoter. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in pancreas (RPKM 97.6), stomach (RPKM 67.4) and 25 other tissues See more
Orthologs
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Genomic context

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See SSR4 in Genome Data Viewer
Location:
Xq28
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153794159..153798512)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152067822..152072175)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153059614..153063967)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PLXNB3 antisense RNA 1 Neighboring gene plexin B3 Neighboring gene uncharacterized LOC124905227 Neighboring gene SRSF protein kinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153059193-153059920 Neighboring gene isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma Neighboring gene CRISPRi-validated cis-regulatory element chrX.2654 Neighboring gene PDZ domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21072 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:153092379-153092957 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153099642-153099888 Neighboring gene CYCS pseudogene 45

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. Expanding the Molecular and Clinical Phenotype of SSR4-CDG. Ng BG, et al. Hum Mutat, 2015 Nov. PMID 26264460, Free PMC Article
  2. Expanding the phenotype of X-linked SSR4-CDG: Connective tissue implications. Castiglioni C, et al. Hum Mutat, 2021 Feb. PMID 33300232
  3. Cloning and molecular characterization of a human ortholog of Monodelphis TRAPD in ultraviolet B-induced melanoma. Wang Z, et al. Melanoma Res, 2004 Apr. PMID 15057039
  4. Translocon-associated protein TRAP delta and a novel TRAP-like protein are coordinately expressed with pro-opiomelanocortin in Xenopus intermediate pituitary. Holthuis JC, et al. Biochem J, 1995 Nov 15. PMID 7492314, Free PMC Article
  5. Oligomeric complexes involved in translocation of proteins across the membrane of the endoplasmic reticulum. Wang L, et al. FEBS Lett, 1999 Sep 3. PMID 10471800

See all (137) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expanding the phenotype of X-linked SSR4-CDG: Connective tissue implications.
    Title: Expanding the phenotype of X-linked SSR4-CDG: Connective tissue implications.
  2. We now report eight affected males with either de novo (4) or inherited (4) loss of function mutations in SSR4.
    Title: Expanding the Molecular and Clinical Phenotype of SSR4-CDG.
  3. results of this study implicate TRAPD as a candidate gene with potential functions that might be associated with ultraviolet-induced melanomagenesis and metastasis
    Title: Cloning and molecular characterization of a human ortholog of Monodelphis TRAPD in ultraviolet B-induced melanoma.
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

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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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with signal sequence receptor, delta (SSR4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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

Gene Ontology Provided by GOA

Component Evidence Code Pubs
part_of Sec61 translocon complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in extracellular exosome HDA PubMed 

General protein information

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

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.

Genomic

  1. NG_041795.1 RefSeqGene

    Range
    5494..9325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001204526.1 → NP_001191455.1  translocon-associated protein subunit delta isoform 1 precursor

    See identical proteins and their annotated locations for NP_001191455.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK094395, BC003371, BE791319, BP202705, U52111
    UniProtKB/TrEMBL
    A6NLM8
    Conserved Domains (1) summary
    pfam05404
    Location:35 → 183
    TRAP-delta; Translocon-associated protein, delta subunit precursor (TRAP-delta)

  2. NM_001204527.2 → NP_001191456.1  translocon-associated protein subunit delta isoform 3 precursor

    See identical proteins and their annotated locations for NP_001191456.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate exon in the 5' UTR and coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC032351, BG165852, BI754091, U52111
    UniProtKB/TrEMBL
    A6NLM8
    Conserved Domains (1) summary
    pfam05404
    Location:32 → 180
    TRAP-delta; Translocon-associated protein, delta subunit precursor (TRAP-delta)

  3. NM_006280.3 → NP_006271.1  translocon-associated protein subunit delta isoform 2 precursor

    See identical proteins and their annotated locations for NP_006271.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate segment in the 5' UTR and coding region and uses a downstream start codon, compared to variant 1. Isoform 2 has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    Z69043
    Consensus CDS
    CCDS14731.1
    UniProtKB/Swiss-Prot
    A8K378, P51571, Q53XY1
    UniProtKB/TrEMBL
    A6NLM8
    Related
    ENSP00000359103.3, ENST00000370086.8
    Conserved Domains (1) summary
    pfam05404
    Location:24 → 172
    TRAP-delta; Translocon-associated protein, delta subunit precursor (TRAP-delta)

RNA

  1. NR_037927.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC032351, BE791319, CD672615, U52111
    Related
    ENST00000471880.5

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    153794159..153798512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442389.1 → XP_047298345.1  translocon-associated protein subunit delta isoform X1

  2. XM_047442390.1 → XP_047298346.1  translocon-associated protein subunit delta isoform X2

    UniProtKB/Swiss-Prot
    A8K378, P51571, Q53XY1
    Related
    ENSP00000317331.3, ENST00000320857.7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    152067822..152072175
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327622.1 → XP_054183597.1  translocon-associated protein subunit delta isoform X1

  2. XM_054327623.1 → XP_054183598.1  translocon-associated protein subunit delta isoform X2

    UniProtKB/Swiss-Prot
    A8K378, P51571, Q53XY1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51571.1 GenPept UniProtKB/Swiss-Prot:P51571

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