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Aliases for LSM5 Gene

Aliases for LSM5 Gene

  • LSM5 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2 3
  • U6 SnRNA-Associated Sm-Like Protein LSm5 3
  • YER146W 3

External Ids for LSM5 Gene

Previous GeneCards Identifiers for LSM5 Gene

  • GC07M032167
  • GC07M032233
  • GC07M032267
  • GC07M032298
  • GC07M032491
  • GC07M032402

Summaries for LSM5 Gene

Entrez Gene Summary for LSM5 Gene

  • Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.[supplied by OMIM, Apr 2004]

GeneCards Summary for LSM5 Gene

LSM5 (LSM5 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae)) is a Protein Coding gene. Among its related pathways are Gene Expression and Spliceosome. GO annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot for LSM5 Gene

  • Plays a role in U6 snRNP assembly and function. Binds to the 3 end of U6 snRNA, thereby facilitating formation of the spliceosomal U4/U6 duplex formation in vitro

Gene Wiki entry for LSM5 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM5 Gene

Genomics for LSM5 Gene

Regulatory Elements for LSM5 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for LSM5 Gene

Start:
32,485,332 bp from pter
End:
32,495,283 bp from pter
Size:
9,952 bases
Orientation:
Minus strand

Genomic View for LSM5 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LSM5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM5 Gene

Proteins for LSM5 Gene

  • Protein details for LSM5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4Y9-LSM5_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm5
    Protein Accession:
    Q9Y4Y9
    Secondary Accessions:

    Protein attributes for LSM5 Gene

    Size:
    91 amino acids
    Molecular mass:
    9937 Da
    Quaternary structure:
    • LSm subunits form a heteromer with a doughnut shape.

    Alternative splice isoforms for LSM5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LSM5 Gene

Proteomics data for LSM5 Gene at MOPED

Post-translational modifications for LSM5 Gene

  • Ubiquitination at Lys20
  • Modification sites at PhosphoSitePlus

Other Protein References for LSM5 Gene

No data available for DME Specific Peptides for LSM5 Gene

Domains for LSM5 Gene

Suggested Antigen Peptide Sequences for LSM5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y4Y9

UniProtKB/Swiss-Prot:

LSM5_HUMAN :
  • Q9Y4Y9
Family:
  • Belongs to the snRNP Sm proteins family.
genes like me logo Genes that share domains with LSM5: view

No data available for Gene Families for LSM5 Gene

Function for LSM5 Gene

Molecular function for LSM5 Gene

UniProtKB/Swiss-Prot Function: Plays a role in U6 snRNP assembly and function. Binds to the 3 end of U6 snRNA, thereby facilitating formation of the spliceosomal U4/U6 duplex formation in vitro

Gene Ontology (GO) - Molecular Function for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 15231747
genes like me logo Genes that share ontologies with LSM5: view
genes like me logo Genes that share phenotypes with LSM5: view

Animal Model Products

CRISPR Products

miRNA for LSM5 Gene

miRTarBase miRNAs that target LSM5

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for LSM5 Gene

Localization for LSM5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM5 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LSM5 Gene COMPARTMENTS Subcellular localization image for LSM5 gene
Compartment Confidence
cytosol 4
nucleus 4
extracellular 1

Gene Ontology (GO) - Cellular Components for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10369684
GO:0005681 spliceosomal complex IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with LSM5: view

Pathways for LSM5 Gene

genes like me logo Genes that share pathways with LSM5: view

Pathways by source for LSM5 Gene

Gene Ontology (GO) - Biological Process for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0010467 gene expression TAS --
GO:0016070 RNA metabolic process --
genes like me logo Genes that share ontologies with LSM5: view

Transcripts for LSM5 Gene

Unigene Clusters for LSM5 Gene

LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LSM5

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LSM5 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5
SP1: -
SP2:

Relevant External Links for LSM5 Gene

GeneLoc Exon Structure for
LSM5
ECgene alternative splicing isoforms for
LSM5

Expression for LSM5 Gene

mRNA expression in normal human tissues for LSM5 Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for LSM5 Gene

SOURCE GeneReport for Unigene cluster for LSM5 Gene Hs.424908

genes like me logo Genes that share expressions with LSM5: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for LSM5 Gene

Orthologs for LSM5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LSM5 35
  • 99.63 (n)
  • 100 (a)
LSM5 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LSM5 35
  • 93.77 (n)
  • 100 (a)
LSM5 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 60 (a)
OneToMany
LSM5 35
  • 93.41 (n)
  • 100 (a)
LSM5 36
  • 99 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Lsm5 35
  • 90.11 (n)
  • 100 (a)
Lsm5 16
Lsm5 36
  • 100 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSM5 36
  • 58 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM5 36
  • 61 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm5 35
  • 90.84 (n)
  • 100 (a)
chicken
(Gallus gallus)
Aves LSM5 35
  • 86.45 (n)
  • 98.9 (a)
LSM5 36
  • 99 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LSM5 36
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm5 35
  • 82.78 (n)
  • 96.7 (a)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7249 35
zebrafish
(Danio rerio)
Actinopterygii LSM5 36
  • 95 (a)
OneToOne
zgc:171959 35
  • 79.12 (n)
  • 94.51 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006604 35
  • 66.29 (n)
  • 84.09 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6610 35
  • 70.16 (n)
  • 81.4 (a)
CG6610 36
  • 78 (a)
OneToOne
CG6610 37
  • 85 (a)
worm
(Caenorhabditis elegans)
Secernentea lsm-5 35
  • 64.47 (n)
  • 73.63 (a)
lsm-5 36
  • 74 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM5 36
  • 42 (a)
OneToOne
LSM5 38
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2381 35
soybean
(Glycine max)
eudicotyledons Gma.18055 35
thale cress
(Arabidopsis thaliana)
eudicotyledons SAD1 35
  • 70.37 (n)
  • 75.31 (a)
corn
(Zea mays)
Liliopsida Zm.4938 35
rice
(Oryza sativa)
Liliopsida Os.26574 35
Os05g0389300 35
  • 66.28 (n)
  • 73.56 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU03766 35
  • 65.38 (n)
  • 75 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm5 35
  • 60.53 (n)
  • 59.21 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4402 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2293 36
  • 86 (a)
OneToOne
Species with no ortholog for LSM5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LSM5 Gene

ENSEMBL:
Gene Tree for LSM5 (if available)
TreeFam:
Gene Tree for LSM5 (if available)

Paralogs for LSM5 Gene

Selected SIMAP similar genes for LSM5 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for LSM5 Gene

genes like me logo Genes that share paralogs with LSM5: view

No data available for Paralogs for LSM5 Gene

Variants for LSM5 Gene

Sequence variations from dbSNP and Humsavar for LSM5 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type MAF
rs10736 -- 32,487,075(-) AAAGA(A/G)CTTCT utr-variant-3-prime, nc-transcript-variant
rs921407 -- 32,490,586(+) CCCAT(A/T)ATGCC intron-variant, upstream-variant-2KB, nc-transcript-variant
rs921408 -- 32,490,587(+) CCATA(A/C)TGCCC intron-variant, upstream-variant-2KB, nc-transcript-variant
rs1065207 -- 32,486,256(-) TAATA(A/T)GTACA utr-variant-3-prime, nc-transcript-variant
rs1584613 -- 32,490,493(-) CGACC(A/C/G)ACGCA intron-variant, upstream-variant-2KB, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for LSM5 Gene

Variant ID Type Subtype PubMed ID
nsv436557 CNV Deletion 17901297
nsv887921 CNV Gain 21882294
nsv887922 CNV Gain 21882294

Relevant External Links for LSM5 Gene

HapMap Linkage Disequilibrium report
LSM5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM5 Gene

Disorders for LSM5 Gene

No disorders were found for LSM5 Gene.

No data available for UniProtKB/Swiss-Prot for LSM5 Gene

Publications for LSM5 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) 3 4
  3. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. (PMID: 12515382) Ingelfinger D. … Achsel T. (RNA 2002) 2 3
  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. Transcriptome analysis of human gastric cancer. (PMID: 16341674) Oh J.H. … Kim N.S. (Mamm. Genome 2005) 3

Products for LSM5 Gene

Sources for LSM5 Gene

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