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Sned1 sushi, nidogen and EGF-like domains 1 [ Mus musculus (house mouse) ]

Gene ID: 208777, updated on 10-Nov-2022

Summary

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Official Symbol
Sned1provided by MGI
Official Full Name
sushi, nidogen and EGF-like domains 1provided by MGI
Primary source
MGI:MGI:3045960
See related
Ensembl:ENSMUSG00000047793 AllianceGenome:MGI:3045960
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
SST3; Snep; 6720455I24Rik; D430044C15Rik
Summary
Predicted to enable Notch binding activity. Predicted to be involved in cell-matrix adhesion. Predicted to be located in extracellular region. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; limb interdigital region; and mesothelium. Orthologous to human SNED1 (sushi, nidogen and EGF like domains 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in ovary adult (RPKM 13.0), limb E14.5 (RPKM 9.8) and 20 other tissues See more
Orthologs
human all
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Genomic context

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See Sned1 in Genome Data Viewer
Location:
1; 1 D
Exon count:
32
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (93163518..93228787)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (93235796..93301065)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene mab-21-like 4 Neighboring gene ciliary rootlet coiled-coil, rootletin family member 2 Neighboring gene microRNA 6901 Neighboring gene mitochondrial transcription termination factor 4 Neighboring gene predicted gene 28535 Neighboring gene 60S ribosomal protein L17 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome. Vallet SD, et al. Biochem J, 2021 Apr 16. PMID 33724335
  2. Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations. Barqué A, et al. Dev Dyn, 2021 Feb. PMID 33012048, Free PMC Article
  3. A stromal cell-derived membrane protein that supports hematopoietic stem cells. Ueno H, et al. Nat Immunol, 2003 May. PMID 12665856
  4. Cloning and expression analysis of the mouse stroma marker Snep encoding a novel nidogen domain protein. Leimeister C, et al. Dev Dyn, 2004 Jun. PMID 15162516
  5. The Type 3 Deiodinase Is a Critical Modulator of Thyroid Hormone Sensitivity in the Fetal Brain. Martinez ME, et al. Front Neurosci, 2021. PMID 34248495, Free PMC Article

See all (19) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations.
    Title: Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations.
  2. comparative expression analysis of kidney stroma markers suggests that Snep is expressed in a specific subpopulation of stromal cells and may provide environmental cues to support regular development
    Title: Cloning and expression analysis of the mouse stroma marker Snep encoding a novel nidogen domain protein.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (3) 

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 MGI

Function Evidence Code Pubs
enables Notch binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in cell-matrix adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular matrix ISO
Inferred from Sequence Orthology
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
sushi, nidogen and EGF-like domain-containing protein 1
Names
secreted nidogen domain protein
secreted protein SST-3
secreted protein SST3
stromal nidogen extracellular matrix protein

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_172463.5 → NP_766051.4  sushi, nidogen and EGF-like domain-containing protein 1 precursor

    See identical proteins and their annotated locations for NP_766051.4

    Status: VALIDATED

    Source sequence(s)
    AC124669
    Consensus CDS
    CCDS35670.1
    UniProtKB/Swiss-Prot
    Q70E20
    UniProtKB/TrEMBL
    A0A0R4J0N0
    Related
    ENSMUSP00000050832.8, ENSMUST00000062202.14
    Conserved Domains (5) summary
    cd00033
    Location:698 → 752
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00060
    Location:1005 → 1084
    FN3; Fibronectin type 3 domain
    smart00539
    Location:104 → 260
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:311 → 347
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam00041
    Location:908 → 988
    fn3; Fibronectin type III domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    93163518..93228787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030252567.1 → XP_030108427.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X3

    Conserved Domains (3) summary
    cd00033
    Location:101 → 155
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    cd00054
    Location:24 → 58
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam00041
    Location:311 → 391
    fn3; Fibronectin type III domain

  2. XM_006529317.3 → XP_006529380.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X1

    Conserved Domains (4) summary
    smart00539
    Location:104 → 260
    NIDO; Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins
    cd00054
    Location:311 → 347
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00063
    Location:1046 → 1138
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:850 → 930
    fn3; Fibronectin type III domain

  3. XM_030252563.2 → XP_030108423.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

    Conserved Domains (4) summary
    cd00033
    Location:239 → 293
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    cd00054
    Location:162 → 196
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00063
    Location:645 → 737
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:449 → 529
    fn3; Fibronectin type III domain

  4. XM_030252564.2 → XP_030108424.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

    Conserved Domains (4) summary
    cd00033
    Location:239 → 293
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    cd00054
    Location:162 → 196
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00063
    Location:645 → 737
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:449 → 529
    fn3; Fibronectin type III domain

  5. XM_030252561.2 → XP_030108421.1  sushi, nidogen and EGF-like domain-containing protein 1 isoform X2

    Conserved Domains (4) summary
    cd00033
    Location:239 → 293
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    cd00054
    Location:162 → 196
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    cd00063
    Location:645 → 737
    FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
    pfam00041
    Location:449 → 529
    fn3; Fibronectin type III domain

RNA

  1. XR_003954306.1 RNA Sequence

  2. XR_003954305.2 RNA Sequence

    Related
    ENSMUST00000172289.8

  3. XR_387153.4 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q70E20.2 GenPept UniProtKB/Swiss-Prot:Q70E20

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