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Ssc5d scavenger receptor cysteine rich family member with 5 domains [ Rattus norvegicus (Norway rat) ]

Gene ID: 308341, updated on 2-Nov-2024

Summary

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Official Symbol
Ssc5dprovided by RGD
Official Full Name
scavenger receptor cysteine rich family member with 5 domainsprovided by RGD
Primary source
RGD:1565772
See related
EnsemblRapid:ENSRNOG00000016687 AllianceGenome:RGD:1565772
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1565772
Summary
Predicted to enable fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Predicted to be involved in negative regulation of interleukin-8 production and response to bacterium. 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. Orthologous to human SSC5D (scavenger receptor cysteine rich family member with 5 domains). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Uterus (RPKM 35.2), Muscle (RPKM 30.1) and 8 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ssc5d in Genome Data Viewer
Location:
1q12
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (77920781..77939284, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (68891942..68910462, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (72443750..72462293, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene SH3 domain binding kinase family, member 3 Neighboring gene SH3 domain binding kinase family, member 2 Neighboring gene N-acetyltransferase 14 Neighboring gene zinc finger protein 628

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Molecular and functional characterization of mouse S5D-SRCRB: a new group B member of the scavenger receptor cysteine-rich superfamily. Miró-Julià C, et al. J Immunol, 2011 Feb 15. PMID 21217009
  2. Extracellular matrix secretion by cardiac fibroblasts: role of microRNA-29b and microRNA-30c. Abonnenc M, et al. Circ Res, 2013 Oct 25. PMID 24006456
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables extracellular matrix binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix binding ISO
Inferred from Sequence Orthology
more info
  
enables fibronectin binding ISO
Inferred from Sequence Orthology
more info
  
enables laminin binding ISO
Inferred from Sequence Orthology
more info
  
enables scavenger receptor activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in defense response IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within defense response ISO
Inferred from Sequence Orthology
more info
  
involved_in defense response to Gram-negative bacterium ISO
Inferred from Sequence Orthology
more info
  
involved_in defense response to Gram-positive bacterium ISO
Inferred from Sequence Orthology
more info
  
involved_in detection of bacterial lipoprotein IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in detection of bacterial lipoprotein ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of interleukin-8 production ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of interleukin-8 production ISO
Inferred from Sequence Orthology
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in collagen-containing extracellular matrix ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
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

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)

  1. NM_001134545.1 → NP_001128017.1  soluble scavenger receptor cysteine-rich domain-containing protein SSC5D precursor

    See identical proteins and their annotated locations for NP_001128017.1

    Status: PROVISIONAL

    Source sequence(s)
    CH474075
    UniProtKB/TrEMBL
    A6KNQ6, D3ZPK4
    Related
    ENSRNOP00000022480.5, ENSRNOT00000022480.7
    Conserved Domains (3) summary
    smart00202
    Location:465 → 566
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:470 → 566
    SRCR; Scavenger receptor cysteine-rich domain
    pfam06752
    Location:1158 → 1299
    E_Pc_C; Enhancer of Polycomb C-terminus

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    77920781..77939284 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063288690.1 → XP_063144760.1  soluble scavenger receptor cysteine-rich domain-containing protein SSC5D isoform X2

  2. XM_006228257.4 → XP_006228319.1  soluble scavenger receptor cysteine-rich domain-containing protein SSC5D isoform X1

    Related
    ENSRNOP00000100469.1, ENSRNOT00000132939.1
    Conserved Domains (2) summary
    smart00202
    Location:465 → 566
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:470 → 566
    SRCR; Scavenger receptor cysteine-rich domain
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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