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Aliases for LSM4 Gene

Aliases for LSM4 Gene

  • LSM4 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2 3
  • Glycine-Rich Protein 3 4
  • GRP 3 4
  • U6 SnRNA-Associated Sm-Like Protein LSm4 3
  • YER112W 3

External Ids for LSM4 Gene

Summaries for LSM4 Gene

Entrez Gene Summary for LSM4 Gene

  • This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for LSM4 Gene

LSM4 (LSM4 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae)) is a Protein Coding gene. Among its related pathways are Signaling by GPCR and Signaling by GPCR. GO annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for LSM4 Gene

  • Binds specifically to the 3-terminal U-tract of U6 snRNA

Gene Wiki entry for LSM4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM4 Gene

Genomics for LSM4 Gene

Genomic Location for LSM4 Gene

Start:
18,306,230 bp from pter
End:
18,323,274 bp from pter
Size:
17,045 bases
Orientation:
Minus strand

Genomic View for LSM4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LSM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM4 Gene

Regulatory Elements for LSM4 Gene

Proteins for LSM4 Gene

  • Protein details for LSM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4Z0-LSM4_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm4
    Protein Accession:
    Q9Y4Z0
    Secondary Accessions:

    Protein attributes for LSM4 Gene

    Size:
    139 amino acids
    Molecular mass:
    15350 Da
    Quaternary structure:
    • LSm subunits form a heteromer with a doughnut shape

neXtProt entry for LSM4 Gene

Proteomics data for LSM4 Gene at MOPED

Post-translational modifications for LSM4 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys80

Other Protein References for LSM4 Gene

No data available for DME Specific Peptides for LSM4 Gene

Domains for LSM4 Gene

UniProtKB/Swiss-Prot:

LSM4_HUMAN
Family:
  • Belongs to the snRNP Sm proteins family.:
    • Q9Y4Z0
genes like me logo Genes that share domains with LSM4: view

No data available for Gene Families for LSM4 Gene

Function for LSM4 Gene

Molecular function for LSM4 Gene

UniProtKB/Swiss-Prot Function: Binds specifically to the 3-terminal U-tract of U6 snRNA

Gene Ontology (GO) - Molecular Function for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15231747
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with LSM4: view

Phenotypes for LSM4 Gene

MGI mutant phenotypes for LSM4:
inferred from 1 alleles
GenomeRNAi human phenotypes for LSM4:
genes like me logo Genes that share phenotypes with LSM4: view

miRNA for LSM4 Gene

miRTarBase miRNAs that target LSM4

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for LSM4 Gene

Localization for LSM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LSM4 Gene COMPARTMENTS Subcellular localization image for LSM4 gene
Compartment Confidence
cytosol 4
nucleus 4
plasma membrane 2

Gene Ontology (GO) - Cellular Components for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP TAS 10369684
GO:0005829 cytosol TAS --
GO:0030532 small nuclear ribonucleoprotein complex TAS 10369684
genes like me logo Genes that share ontologies with LSM4: view

Pathways for LSM4 Gene

genes like me logo Genes that share pathways with LSM4: view

Pathways by source for LSM4 Gene

Gene Ontology (GO) - Biological Process for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0010467 gene expression TAS --
genes like me logo Genes that share ontologies with LSM4: view

Compounds for LSM4 Gene

(2) Novoseek inferred chemical compound relationships for LSM4 Gene

Compound -log(P) Hits PubMed IDs
cysteine 6.71 3
calcium 0 3
genes like me logo Genes that share compounds with LSM4: view

Transcripts for LSM4 Gene

Unigene Clusters for LSM4 Gene

LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LSM4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - -
SP2: - - -
SP3: - -
SP4: - - - -
SP5:

Relevant External Links for LSM4 Gene

GeneLoc Exon Structure for
LSM4
ECgene alternative splicing isoforms for
LSM4

Expression for LSM4 Gene

mRNA expression in normal human tissues for LSM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for LSM4 Gene

SOURCE GeneReport for Unigene cluster for LSM4 Gene Hs.515255

genes like me logo Genes that share expressions with LSM4: view

Orthologs for LSM4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LSM4 37
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LSM4 36
  • 91.85 (n)
  • 100 (a)
LSM4 37
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LSM4 36
  • 92.57 (n)
  • 100 (a)
LSM4 37
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lsm4 36
  • 88.41 (n)
  • 97.1 (a)
Lsm4 16
Lsm4 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSM4 37
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM4 37
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm4 36
  • 88.89 (n)
  • 97.1 (a)
chicken
(Gallus gallus)
Aves LSM4 36
  • 79.23 (n)
  • 90.58 (a)
LSM4 37
  • 88 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.3329 36
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm4 36
  • 71.5 (n)
  • 89.86 (a)
MGC76085 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4425 36
zebrafish
(Danio rerio)
Actinopterygii lsm4 36
  • 79.17 (n)
  • 98.86 (a)
lsm4 37
  • 85 (a)
OneToOne
zgc73057 36
fruit fly
(Drosophila melanogaster)
Insecta CG17768 37
  • 62 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea lsm-4 37
  • 68 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM4 37
  • 24 (a)
OneToOne
barley
(Hordeum vulgare)
Liliopsida Hv.3996 36
corn
(Zea mays)
Liliopsida Zm.3350 36
rice
(Oryza sativa)
Liliopsida Os.197 36
wheat
(Triticum aestivum)
Liliopsida Ta.3949 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 84 (a)
OneToOne
Species with no ortholog for LSM4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for LSM4 Gene

ENSEMBL:
Gene Tree for LSM4 (if available)
TreeFam:
Gene Tree for LSM4 (if available)

Paralogs for LSM4 Gene

Selected SIMAP similar genes for LSM4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LSM4: view

No data available for Paralogs for LSM4 Gene

Variants for LSM4 Gene

Sequence variations from dbSNP and Humsavar for LSM4 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs6792 -- 18,307,234(+) GCCAG(C/T)TTTGG utr-variant-3-prime
rs13196 -- 18,307,213(-) GAAGA(G/T)TCTGT utr-variant-3-prime
rs13363 -- 18,307,460(-) GAGCG(C/G)CCACC utr-variant-3-prime
rs14322 -- 18,323,073(+) GCACA(A/C)GCTCC utr-variant-5-prime
rs1035364 -- 18,318,070(+) CCTCA(C/T)GGGAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LSM4 Gene

Variant ID Type Subtype PubMed ID
dgv3774n71 CNV Loss 21882294
dgv3780n71 CNV Loss 21882294
nsv911271 CNV Loss 21882294
dgv3781n71 CNV Loss 21882294

Relevant External Links for LSM4 Gene

HapMap Linkage Disequilibrium report
LSM4

Disorders for LSM4 Gene

(3) Novoseek inferred disease relationships for LSM4 Gene

Disease -log(P) Hits PubMed IDs
shock 7.96 1
autoimmune diseases 0 2
rheumatoid arthritis 0 1

Relevant External Links for LSM4

Genetic Association Database (GAD)
LSM4
Human Genome Epidemiology (HuGE) Navigator
LSM4
genes like me logo Genes that share disorders with LSM4: view

No data available for UniProtKB/Swiss-Prot for LSM4 Gene

Publications for LSM4 Gene

  1. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. (PMID: 10369684) Salgado-Garrido J. … Seraphin B. (EMBO J. 1999) 2 3 4
  2. 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. (PMID: 10523320) Achsel T. … Luehrmann R. (EMBO J. 1999) 2 3 4
  3. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu R.-M. … Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. Specific sequences of the Sm and Sm-like (Lsm) proteins mediate their interaction with the spinal muscular atrophy disease gene product (SMN). (PMID: 10851237) Friesen W.J. … Dreyfuss G. (J. Biol. Chem. 2000) 3 23

Products for LSM4 Gene

Sources for LSM4 Gene

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