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

Gene ID: 290647, updated on 3-Apr-2024

Summary

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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
Ensembl:ENSRNOG00000019572 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. Located in neuron projection and nucleus. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
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

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See Lsm4 in Genome Data Viewer
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_086034.1Genomic Context describing neighboring genes Neighboring gene IQ motif containing N Neighboring gene JunD proto-oncogene, AP-1 transcription factor subunit Neighboring gene uncharacterized LOC134482471 Neighboring gene pyroglutamyl-peptidase I Neighboring gene Mk1 protein Neighboring gene growth differentiation factor 15 Neighboring gene leucine rich repeat containing 25

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Dendritic LSm1/CBP80-mRNPs mark the early steps of transport commitment and translational control. di Penta A, et al. J Cell Biol, 2009 Feb 9. PMID 19188494, Free PMC Article
  2. Aberrantly Methylated-Differentially Expressed Genes Identify Novel Atherosclerosis Risk Subtypes. Xue Y, et al. Front Genet, 2020. PMID 33381146, Free PMC Article
  3. ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4. Fürst J, et al. J Biol Chem, 2005 Sep 2. PMID 15905169
  4. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. Achsel T, et al. EMBO J, 1999 Oct 15. PMID 10523320, Free PMC Article
  5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

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)

  1. 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
    Related
    ENSRNOP00000026567.4, ENSRNOT00000026567.6
    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

  1. NC_086034.1 Reference GRCr8

    Range
    18789466..18795164 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A6KA13, D4A2C6

  2. 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

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

Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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