Lsm5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lsm5provided by RGD
Official Full Name: LSM5 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
Primary source: RGD:1308655
See related: Ensembl:ENSRNOG00000042126 AllianceGenome:RGD:1308655
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable protein heterodimerization activity. Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA catabolic process and response to bacterium. Predicted to be located in cytoplasm and nucleus. Predicted to be part of several cellular components, including Lsm1-7-Pat1 complex; Lsm2-8 complex; and spliceosomal snRNP complex. Orthologous to human LSM5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 125.7), Spleen (RPKM 91.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q24

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (87281260..87284476, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (85951073..85954289, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (87016003..87019219, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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

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General gene information

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Markers

NoName (e-PCR)
- UniSTS:237643

RH137282 (e-PCR)
- UniSTS:219370

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
contributes_to RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within mRNA catabolic process	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to bacterium	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of Lsm1-7-Pat1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Lsm2-8 complex	ISO Inferred from Sequence Orthology more info
part_of U2-type precatalytic spliceosome	ISO Inferred from Sequence Orthology more info
part_of U4/U6 x U5 tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U4/U6 x U5 tri-snRNP complex	ISO Inferred from Sequence Orthology more info
part_of U6 snRNP	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in membrane	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: U6 snRNA-associated Sm-like protein LSm5

Names: LSM5 U6 small nuclear RNA and mRNA degradation associated; LSM5 homolog, U6 small nuclear RNA associated

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.