Exosc3 exosome component 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Exosc3provided by RGD
Official Full Name: exosome component 3provided by RGD
Primary source: RGD:1304739
See related: EnsemblRapid:ENSRNOG00000012409 AllianceGenome:RGD:1304739
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
Summary: Predicted to enable RNA binding activity. Predicted to be involved in DNA metabolic process and RNA metabolic process. Predicted to act upstream of or within positive regulation of isotype switching. Predicted to be located in cytosol; euchromatin; and nuclear lumen. Predicted to be part of cytoplasmic exosome (RNase complex) and nuclear exosome (RNase complex). Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 1B. Orthologous to human EXOSC3 (exosome component 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 95.2), Spleen (RPKM 73.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q22

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (64369495..64374711, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (59573849..59579065, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (60866498..60871734, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
NOT enables RNA exonuclease activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in CUT catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in CUT catabolic process	ISO Inferred from Sequence Orthology more info
involved_in DNA deamination	ISO Inferred from Sequence Orthology more info
involved_in RNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in RNA processing	ISO Inferred from Sequence Orthology more info
involved_in TRAMP-dependent tRNA surveillance pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in U4 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA Inferred from Biological aspect of Ancestor more info
involved_in isotype switching	ISO Inferred from Sequence Orthology more info
involved_in mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in poly(A)-dependent snoRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of isotype switching	ISO Inferred from Sequence Orthology more info
involved_in rRNA processing	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
part_of cytoplasmic exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of cytoplasmic exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in euchromatin	ISO Inferred from Sequence Orthology more info
part_of exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
part_of nuclear exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear exosome (RNase complex)	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: exosome complex component RRP40

Names: exosome complex exonuclease RRP40

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_001107936.2 → NP_001101406.2 exosome complex component RRP40

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

D3ZT51

Related

ENSRNOP00000016582.7, ENSRNOT00000016582.8

Conserved Domains (2) summary

cd05790
Location:115 → 200

S1_Rrp40; Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...

cd22526
Location:203 → 280

KH-I_Rrp40; type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins