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

    Gene ID: 6748, updated on 3-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
    mouse all
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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 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 Variation Viewer (GRCh37.p13)

    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

    Gene LinkOut

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

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