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

    Gene ID: 308341, updated on 2-May-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
    Ensembl: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, Apr 2022]
    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
    • 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, ENSRNOT00000022480.6
      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

      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

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