Snd1 staphylococcal nuclease and tudor domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Snd1provided by RGD
Official Full Name: staphylococcal nuclease and tudor domain containing 1provided by RGD
Primary source: RGD:631340
See related: Ensembl:ENSRNOG00000031173 AllianceGenome:RGD:631340
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: SND p102
Summary: Predicted to enable RISC complex binding activity; RNA binding activity; and endoribonuclease activity. Predicted to be involved in mRNA catabolic process; miRNA catabolic process; and regulation of cell cycle process. Predicted to be located in dense body. Predicted to be part of RISC complex. Predicted to be active in cytosol and nucleus. Orthologous to human SND1 (staphylococcal nuclease and tudor domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 306.9), Spleen (RPKM 290.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q22

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (58060689..58459926)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (57095205..57494501)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (55772377..56171669)

Chromosome 4 - NC_086022.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SND1 aggravates mitochondrial damage, apoptosis and extracellular matrix degradation in IL-1beta-stimulated chondrocytes via PINK1/BECN1 pathway.
Title: SND1 aggravates mitochondrial damage, apoptosis and extracellular matrix degradation in IL-1β-stimulated chondrocytes via PINK1/BECN1 pathway.
Circular RNA METTL9 contributes to neuroinflammation following traumatic brain injury by complexing with astrocytic SND1.
Title: Circular RNA METTL9 contributes to neuroinflammation following traumatic brain injury by complexing with astrocytic SND1.
The RNA-binding protein SND1 promotes the degradation of GPX4 by destabilizing the HSPA5 mRNA and suppressing HSPA5 expression, promoting ferroptosis in osteoarthritis chondrocytes.
Title: The RNA-binding protein SND1 promotes the degradation of GPX4 by destabilizing the HSPA5 mRNA and suppressing HSPA5 expression, promoting ferroptosis in osteoarthritis chondrocytes.
Overproduction of reactive oxygen species at the early stage of high glucose incubation stimulates p102 synthesis, which in turn up-regulates AT1 receptor expression.
Title: Elevated transcriptional co-activator p102 mediates angiotensin II type 1 receptor up-regulation and extracellular matrix overproduction in the high glucose-treated rat glomerular mesangial cells and isolated glomeruli.
cells overexpressing SND p102 secreted phospholipid-rich lipoproteins
Title: Overexpression of SND p102, a rat homologue of p100 coactivator, promotes the secretion of lipoprotein phospholipids in primary hepatocytes.
Absence of TATA box and location and reverse orientation of the CCAAT boxes in the promoter region strongly suggest a role for NF-Y in the regulation of transcription of SND p102 gene.
Title: Isolation and characterization of the rat SND p102 gene promoter: putative role for nuclear factor-Y in regulation of transcription.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI176053 (e-PCR)
- UniSTS:250120

GDB:4585141 (e-PCR)
- UniSTS:4885

RH144306 (e-PCR)
- UniSTS:233551

STS-H23117 (e-PCR)
- UniSTS:9556

AU049569 (e-PCR)
- UniSTS:146016

NoName (e-PCR)
- UniSTS:235393

AW528121 (e-PCR)
- UniSTS:260806

D4Mit2 (e-PCR), detects polymorphism
- UniSTS:240107

Lrrc4 (e-PCR), detects polymorphism
- UniSTS:525557

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RISC complex binding	IEA Inferred from Electronic Annotation more info
enables RISC complex binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA endonuclease activity	IEA Inferred from Electronic Annotation more info
enables RNA endonuclease activity	ISO Inferred from Sequence Orthology more info
enables endonuclease activity	ISO Inferred from Sequence Orthology more info
enables endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters	IEA Inferred from Electronic Annotation more info
enables nuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in miRNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in miRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle process	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle process	ISO Inferred from Sequence Orthology more info
involved_in regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of RISC complex	IEA Inferred from Electronic Annotation more info
part_of RNAi effector complex	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dense body	IEA Inferred from Electronic Annotation more info
located_in dense body	ISO Inferred from Sequence Orthology more info
located_in melanosome	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: staphylococcal nuclease domain-containing protein 1

Names: 100 kDa coactivator; p100 co-activator; p105 coactivator; staphylococcal nuclease domain containing 1

NP_073185.2

EC 3.1.31.1

XP_038964252.1

EC 3.1.31.1

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_022694.2 → NP_073185.2 staphylococcal nuclease domain-containing protein 1

See identical proteins and their annotated locations for NP_073185.2

Status: VALIDATED

Source sequence(s)

BC072471

UniProtKB/Swiss-Prot

P97693, Q66X93, Q6IN40

UniProtKB/TrEMBL

A0A8L2QK81, A6IEB2

Related

ENSRNOP00000041531.4, ENSRNOT00000047698.6

Conserved Domains (5) summary

smart00333
Location:727 → 783

TUDOR; Tudor domain

smart00318
Location:20 → 165

SNc; Staphylococcal nuclease homologues

cd00175
Location:25 → 165

SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.

pfam00567
Location:676 → 798

TUDOR; Tudor domain

cl00140
Location:843 → 894

SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.

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

NC_086022.1 Reference GRCr8

Range

58060689..58459926

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108324.2 → XP_038964252.1 staphylococcal nuclease domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A8L2QK81

Conserved Domains (5) summary

smart00318
Location:20 → 165

SNc; Staphylococcal nuclease homologues

cd00175
Location:349 → 495

SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.

cl29560
Location:524 → 598

SNc; Staphylococcal nuclease homologues

cd20433
Location:639 → 721

Tudor_TDRD11; Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins

cl00140
Location:786 → 829

SNc; Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds.