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

Gene ID: 284297, updated on 11-Apr-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, Apr 2022]
Expression
Broad expression in gall bladder (RPKM 7.3), endometrium (RPKM 6.2) and 21 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.42
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55488436..55519099)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58584709..58615450)
105.20220307 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. 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
  3. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
  4. 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
  5. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article

See all (10) 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)

Genotypes

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
  

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_2023_10

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

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Chemical Information
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