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    SSC5D scavenger receptor cysteine rich family member with 5 domains [ Homo sapiens (human) ]

    Gene ID: 284297, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SSC5Dprovided by HGNC
    Official Full Name
    scavenger receptor cysteine rich family member with 5 domainsprovided by HGNC
    Primary source
    HGNC:HGNC:26641
    See related
    Ensembl:ENSG00000179954 MIM:618194; AllianceGenome:HGNC:26641
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    S5D-SRCRB
    Summary
    Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in defense response; detection of bacterial lipoprotein; and negative regulation of interleukin-8 production. Predicted to act upstream of or within regulation of interleukin-8 production. Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in gall bladder (RPKM 7.3), endometrium (RPKM 6.2) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SSC5D in Genome Data Viewer
    Location:
    19q13.42
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55488436..55519099)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58584709..58615450)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55999803..56030466)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11037 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:55988382-55988705 Neighboring gene Sharpr-MPRA regulatory region 3758 Neighboring gene zinc finger protein 628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15097 Neighboring gene N-acetyltransferase 14 (putative) Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11039 Neighboring gene Sharpr-MPRA regulatory region 5021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56028273-56028774 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:56032833-56032983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56037524-56038398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56042573-56043073 Neighboring gene SH3 domain binding kinase family member 2 Neighboring gene Sharpr-MPRA regulatory region 3421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56056311-56057147 Neighboring gene SH3 domain binding kinase family member 3

    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. Molecular cloning and analysis of SSc5D, a new member of the scavenger receptor cysteine-rich superfamily. Gonçalves CM, et al. Mol Immunol, 2009 Aug. PMID 19535143
    2. Assessment of community efforts to advance network-based prediction of protein-protein interactions. Wang XW, et al. Nat Commun, 2023 Mar 22. PMID 36949045, Free PMC Article
    3. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
    4. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
    5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    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

    Function Evidence Code Pubs
    enables extracellular matrix binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables extracellular matrix binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables fibronectin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables laminin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables scavenger receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in defense response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in defense response to Gram-negative bacterium IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in defense response to Gram-positive bacterium IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of bacterial lipoprotein IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in detection of bacterial lipoprotein ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in innate immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of interleukin-8 production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in collagen-containing extracellular matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    soluble scavenger receptor cysteine-rich domain-containing protein SSC5D
    Names
    scavenger receptor cysteine rich domain containing (5 domains)
    scavenger receptor cysteine rich family, 5 domains
    scavenger receptor cysteine-rich glycoprotein
    soluble scavenger protein with 5 SRCR domains
    soluble scavenger with 5 domains

    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_027671.2 RefSeqGene

      Range
      4934..35597
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001144950.2 → NP_001138422.1  soluble scavenger receptor cysteine-rich domain-containing protein SSC5D isoform 1 precursor

      See identical proteins and their annotated locations for NP_001138422.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC008735
      Consensus CDS
      CCDS46196.1
      UniProtKB/Swiss-Prot
      A1L4H1, B5MDQ5, C7S7T9, C7S7U0, K7EP70
      Related
      ENSP00000374274.4, ENST00000389623.11
      Conserved Domains (3) summary
      smart00202
      Location:772 → 872
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:472 → 568
      SRCR; Scavenger receptor cysteine-rich domain
      pfam15279
      Location:1331 → 1479
      SOBP; Sine oculis-binding protein

    2. NM_001195267.2 → NP_001182196.1  soluble scavenger receptor cysteine-rich domain-containing protein SSC5D isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC008735, DA008417, EU699477
      Consensus CDS
      CCDS59424.1
      UniProtKB/Swiss-Prot
      A1L4H1
      Related
      ENSP00000467252.1, ENST00000587166.5
      Conserved Domains (3) summary
      PHA03255
      Location:602 → 729
      PHA03255; BDLF3; Provisional
      smart00202
      Location:772 → 872
      SR; Scavenger receptor Cys-rich
      pfam00530
      Location:472 → 568
      SRCR; Scavenger receptor cysteine-rich domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      55488436..55519099
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      58584709..58615450
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_182571.2: Suppressed sequence

      Description
      NM_182571.2: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1L4H1.3 GenPept UniProtKB/Swiss-Prot:A1L4H1

    Gene LinkOut

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

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