Lsm2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lsm2provided by RGD
Official Full Name: LSM2 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
Primary source: RGD:1598536
See related: EnsemblRapid:ENSRNOG00000048725 AllianceGenome:RGD:1598536
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: G7b
Summary: Predicted to enable protein kinase binding activity and small GTPase binding 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 spliceosomal tri-snRNP complex assembly. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of Lsm1-7-Pat1 complex; Lsm2-8 complex; and nucleus. Predicted to be active in P-body. Orthologous to human LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 59.7), Testes (RPKM 57.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (3848120..3853298, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (3843467..3847217, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (4966817..4970567)

Chromosome 20 - NC_086038.1 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 protein kinase binding	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology 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: U6 snRNA-associated Sm-like protein LSm2

Names: LSM2 U6 small nuclear RNA and mRNA degradation associated; LSM2 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.

mRNA and Protein(s)

NM_001004073.1 → NP_001004073.1 U6 snRNA-associated Sm-like protein LSm2 isoform 1

See identical proteins and their annotated locations for NP_001004073.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BX883045

UniProtKB/TrEMBL

A6KTP7, M0R7N1, Q6MG66

Related

ENSRNOP00000065463.1, ENSRNOT00000070846.5

Conserved Domains (1) summary

cd01725
Location:38 → 126

LSm2; Like-Sm protein 2
NM_001165922.1 → NP_001159394.1 U6 snRNA-associated Sm-like protein LSm2 isoform 2

See identical proteins and their annotated locations for NP_001159394.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

BX883045

UniProtKB/TrEMBL

A0A0G2K8Q7, A6KTP6

Conserved Domains (1) summary

cd01725
Location:2 → 90

LSm2; Like-Sm protein 2