Lsm4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lsm4provided by RGD
Official Full Name: LSM4 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
Primary source: RGD:1306808
See related: AllianceGenome:RGD:1306808
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 PH domain binding activity and U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to be located in cytosol; membrane; and nucleus. Predicted to be part of Lsm2-8 complex; U2-type precatalytic spliceosome; and spliceosomal snRNP complex. Predicted to be active in P-body. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 244.3), Spleen (RPKM 155.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16p14

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (18789466..18795164, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (18755481..18761106, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (20506399..20511818, complement)

Chromosome 16 - NC_086034.1 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

What's a GeneRIF?

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General gene information

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Markers

LSM4 (e-PCR)
- UniSTS:505728

RH141667 (e-PCR)
- UniSTS:223660

RH133230 (e-PCR)
- UniSTS:216513

RH129410 (e-PCR)
- UniSTS:212717

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables PH domain binding	ISO Inferred from Sequence Orthology more info
enables U6 snRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in P-body assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in biological_process	ND No biological Data available more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in nuclear-transcribed mRNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal snRNP assembly	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of Lsm2-8 complex	ISO Inferred from Sequence Orthology more info
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor 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 U6 snRNP	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of spliceosomal tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: U6 snRNA-associated Sm-like protein LSm4

Names: LSM4 U6 small nuclear RNA and mRNA degradation associated; LSM4 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_001106073.1 → NP_001099543.1 U6 snRNA-associated Sm-like protein LSm4

See identical proteins and their annotated locations for NP_001099543.1

Status: PROVISIONAL

Source sequence(s)

CH474031

UniProtKB/TrEMBL

A6KA13, D4A2C6

Conserved Domains (1) summary

cd01723
Location:2 → 77

LSm4; Like-Sm protein 4

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_086034.1 Reference GRCr8

Range

18789466..18795164 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063275158.1 → XP_063131228.1 U6 snRNA-associated Sm-like protein LSm4 isoform X1

UniProtKB/TrEMBL

A6KA13, D4A2C6
XM_039094317.1 → XP_038950245.1 U6 snRNA-associated Sm-like protein LSm4 isoform X2

UniProtKB/TrEMBL

A0A8I5ZZ77, A6KA14

Conserved Domains (1) summary

cd01723
Location:1 → 42

LSm4; Like-Sm protein 4
XM_039094318.2 → XP_038950246.1 U6 snRNA-associated Sm-like protein LSm4 isoform X3