Ssc5d scavenger receptor cysteine rich family, 5 domains [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ssc5dprovided by MGI
Official Full Name: scavenger receptor cysteine rich family, 5 domainsprovided by MGI
Primary source: MGI:MGI:3606211
See related: Ensembl:ENSMUSG00000035279 AllianceGenome:MGI:3606211
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: S5D-SRCRB; A430110N23Rik
Summary: Enables fibronectin binding activity; laminin binding activity; and scavenger receptor activity. Involved in negative regulation of interleukin-8 production and response to bacterium. Acts upstream of or within defense response and regulation of interleukin-8 production. Located in collagen-containing extracellular matrix and extracellular space. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; immune system; and limb mesenchyme. Orthologous to human SSC5D (scavenger receptor cysteine rich family member with 5 domains). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in limb E14.5 (RPKM 11.6), subcutaneous fat pad adult (RPKM 7.8) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A1; 7 2.85 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (4928820..4947827)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (4925129..4944828)

Chromosome 7 - NC_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

the results indicate that S5D-SRCRB is an integral component of the urogenital tract involved in innate immune functions.
Title: Expression of the innate defense receptor S5D-SRCRB in the urogenital tract.
Group B scavenger receptor protein S5D-SRCRB might play a role in innate defense and homeostasis of certain specialized epithelial surfaces.
Title: Molecular and functional characterization of mouse S5D-SRCRB: a new group B member of the scavenger receptor cysteine-rich superfamily.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)

General gene information

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Markers

RH135111 (e-PCR)
- UniSTS:218388

A430110N23Rik (e-PCR), detects polymorphism
- UniSTS:532530

A430110N23Rik (e-PCR), detects polymorphism
- UniSTS:532531

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix binding	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix binding	IDA Inferred from Direct Assay more info	PubMed
enables fibronectin binding	IDA Inferred from Direct Assay more info	PubMed
enables laminin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables scavenger receptor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in defense response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within defense response	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to Gram-negative bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in defense response to Gram-positive bacterium	IDA Inferred from Direct Assay more info	PubMed
involved_in detection of bacterial lipoprotein	IBA Inferred from Biological aspect of Ancestor more info
involved_in detection of bacterial lipoprotein	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of interleukin-8 production	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of interleukin-8 production	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
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: group B scavenger receptor cysteine-rich domain-containing; scavenger receptor cysteine rich domain containing (5 domains); scavenger receptor cysteine-rich domain-containing protein LOC284297 homolog

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)

NM_173008.3 → NP_766596.1 soluble scavenger receptor cysteine-rich domain-containing protein SSC5D precursor

See identical proteins and their annotated locations for NP_766596.1

Status: VALIDATED

Source sequence(s)

AC157563, AK079906, BX637081

Consensus CDS

CCDS20750.1

UniProtKB/Swiss-Prot

B2RUB0, C6ZFQ2, Q3TMW2, Q8BV57

Related

ENSMUSP00000052126.8, ENSMUST00000057612.9

Conserved Domains (4) summary

smart00202
Location:464 → 565

SR; Scavenger receptor Cys-rich

COG3266
Location:594 → 757

DamX; Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning]

pfam00530
Location:469 → 565

SRCR; Scavenger receptor cysteine-rich domain

pfam10846
Location:1011 → 1187

DUF2722; Protein of unknown function (DUF2722)