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

Gene ID: 284297, updated on 23-Nov-2021

Summary

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
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
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

See SSC5D in Genome Data Viewer
Location:
19q13.42
Exon count:
15
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (55488436..55519099)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55999803..56030466)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 628 Neighboring gene N-acetyltransferase 14 (putative) Neighboring gene SH3 domain binding kinase family member 2 Neighboring gene SH3 domain binding kinase family member 3

Genomic regions, transcripts, and products

Expression

  • 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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables extracellular matrix binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
involved_in detection of bacterial lipoprotein ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in endocytosis IEA
Inferred from Electronic Annotation
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
 
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
PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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

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_001144950.2NP_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
    Related
    ENSP00000374274.4, ENST00000389623.11
    Conserved Domains (3) summary
    smart00202
    Location:772872
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:472568
    SRCR; Scavenger receptor cysteine-rich domain
    pfam15279
    Location:13311479
    SOBP; Sine oculis-binding protein
  2. NM_001195267.2NP_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:602729
    PHA03255; BDLF3; Provisional
    smart00202
    Location:772872
    SR; Scavenger receptor Cys-rich
    pfam00530
    Location:472568
    SRCR; Scavenger receptor cysteine-rich domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    55488436..55519099
    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.
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