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Aliases for LSM5 Gene

Aliases for LSM5 Gene

  • LSM5 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • LSM5 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM5 U6 Small Nuclear RNA And MRNA Degradation Associated 3
  • LSM5 Homolog, U6 Small Nuclear RNA Associated 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 And MRNA Degradation Associated) is a Protein Coding gene. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. 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

Promoters for LSM5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LSM5 on UCSC Golden Path with GeneCards custom track

Genomic Location for LSM5 Gene

Chromosome:
7
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

Genes around LSM5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

    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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LSM5 Gene

Domains & Families 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 :
  • Belongs to the snRNP Sm proteins family.
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.
genes like me logo Genes that share phenotypes with LSM5: view

Animal Model Products

miRNA for LSM5 Gene

miRTarBase miRNAs that target LSM5

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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 5
nucleus 5
extracellular 1

Gene Ontology (GO) - Cellular Components for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005688 U6 snRNP IBA --
GO:0005829 cytosol TAS --
GO:0046540 U4/U6 x U5 tri-snRNP complex IBA --
GO:1990726 Lsm1-7-Pat1 complex IBA --
genes like me logo Genes that share ontologies with LSM5: view

Pathways & Interactions for LSM5 Gene

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

Gene Ontology (GO) - Biological Process for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IBA,TAS --
genes like me logo Genes that share ontologies with LSM5: view

No data available for SIGNOR curated interactions for LSM5 Gene

Drugs & Compounds for LSM5 Gene

No Compound Related Data Available

Transcripts for LSM5 Gene

Unigene Clusters for LSM5 Gene

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

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LSM5 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.2), Bone marrow stromal cell (8.6), Fetal ovary (8.6), and Fetal heart (6.6).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with LSM5: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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 36
  • 100 (a)
OneToOne
LSM5 35
  • 99.63 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia LSM5 35
  • 93.77 (n)
  • 100 (a)
LSM5 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LSM5 35
  • 93.41 (n)
  • 100 (a)
-- 36
  • 60 (a)
OneToMany
LSM5 36
  • 99 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Lsm5 16
Lsm5 35
  • 90.11 (n)
  • 100 (a)
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 zgc:171959 35
  • 79.12 (n)
  • 94.51 (a)
LSM5 36
  • 95 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006604 35
  • 66.29 (n)
  • 84.09 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6610 37
  • 85 (a)
CG6610 35
  • 70.16 (n)
  • 81.4 (a)
CG6610 36
  • 78 (a)
OneToOne
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

(1) 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
rs921407 -- 32,490,586(+) CCCAT(A/T)ATGCC intron-variant, nc-transcript-variant, upstream-variant-2KB
rs921408 -- 32,490,587(+) CCATA(A/C)TGCCC intron-variant, nc-transcript-variant, upstream-variant-2KB
rs1584614 -- 32,490,324(-) CTGCC(C/G)TTAGG intron-variant, nc-transcript-variant, reference, synonymous-codon
rs2167274 -- 32,485,232(-) ACTGA(C/T)TTGTA downstream-variant-500B
rs3750087 -- 32,487,596(-) GCTTG(A/G)CTAAA intron-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

Variation tolerance for LSM5 Gene

Residual Variation Intolerance Score: 58.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.19; 4.34% of all genes are more intolerant (likely to be disease-causing)

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

Relevant External Links for LSM5

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LSM5

No disorders were found for LSM5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSM5 Gene

Publications for LSM5 Gene

  1. 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 67
  2. 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
  3. 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. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3

Products for LSM5 Gene

Sources for LSM5 Gene

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