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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
  • 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 And MRNA Degradation Associated) is a Protein Coding gene. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. Gene Ontology (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

Additional gene information for LSM5 Gene

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

Genomics for LSM5 Gene

GeneHancer (GH) Regulatory Elements for LSM5 Gene

Promoters and enhancers for LSM5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I032494 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 -0.7 -660 3.2 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZBTB7B POLR2B ZNF207 AVL9 LSM5 ZNRF2P1 LOC100130673 ENSG00000273014 DPY19L1P2 GC07P032460 PIR53283
GH07I032489 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +4.7 4744 2.4 ZFP64 DMAP1 IRF4 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC MEF2D LSM5 LOC100130673 DPY19L1P1 ENSG00000273014 RP9 SLC25A5P5 GC07P032460
GH07I032937 Enhancer 1 Ensembl ENCODE 10.6 -442.6 -442608 1.2 SMAD1 NFIB KLF17 MZF1 FEZF1 ZNF350 ZNF331 ZIK1 ZNF491 NR2F2 ZNRF2P1 DPY19L1P2 ENSG00000272905 DPY19L1P1 ENSG00000273014 LSM5 KBTBD2 RP9P
GH07I032476 Enhancer 0.3 ENCODE 8.2 +18.0 17983 1.8 JUN DPY19L1P1 LSM5 ENSG00000273014 ZNRF2P1 SLC25A5P5 GC07P032460
GH07I032491 Enhancer 0.3 FANTOM5 0.8 +3.4 3365 0.4 ADNP DPY19L1P1 PDE1C LSM5 SLC25A5P5 GC07P032460
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LSM5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LSM5 gene promoter:

Genomic Locations for LSM5 Gene

Genomic Locations for LSM5 Gene
chr7:32,485,332-32,495,283
(GRCh38/hg38)
Size:
9,952 bases
Orientation:
Minus strand
chr7:32,524,945-32,534,895
(GRCh37/hg19)

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.

    Three dimensional structures from OCA and Proteopedia for LSM5 Gene

    Alternative splice isoforms for LSM5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LSM5 Gene

Post-translational modifications for LSM5 Gene

No Post-translational modifications

No data available for DME Specific Peptides for LSM5 Gene

Domains & Families for LSM5 Gene

Gene Families for LSM5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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

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.

Phenotypes From GWAS Catalog for LSM5 Gene

Gene Ontology (GO) - Molecular Function for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 contributes_to RNA binding TAS,IBA --
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

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LSM5 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1

Gene Ontology (GO) - Cellular Components for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10369684
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with LSM5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LSM5 Gene

Pathways & Interactions 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:0000398 mRNA splicing, via spliceosome TAS --
GO:0000956 nuclear-transcribed mRNA catabolic process IBA --
GO:0006397 mRNA processing TAS 10369684
GO:0008380 RNA splicing IEA --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay 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:

CRISPR Products

Inhibitory RNA Products

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for LSM5 Gene



NURSA nuclear receptor signaling pathways regulating expression of LSM5 Gene:

LSM5

SOURCE GeneReport for Unigene cluster for LSM5 Gene:

Hs.424908

Evidence on tissue expression from TISSUES for LSM5 Gene

  • Bone marrow(4.3)
  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LSM5: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 34 33
  • 99.63 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LSM5 34 33
  • 93.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LSM5 34 33
  • 93.41 (n)
OneToMany
-- 34
  • 60 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Lsm5 33
  • 90.84 (n)
mouse
(Mus musculus)
Mammalia Lsm5 16 34 33
  • 90.11 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LSM5 34
  • 61 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSM5 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM5 34 33
  • 86.45 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LSM5 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm5 33
  • 82.78 (n)
zebrafish
(Danio rerio)
Actinopterygii LSM5 34
  • 95 (a)
OneToOne
zgc:171959 33
  • 79.12 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7249 33
fruit fly
(Drosophila melanogaster)
Insecta CG6610 35 33 34
  • 70.16 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006604 33
  • 66.29 (n)
worm
(Caenorhabditis elegans)
Secernentea lsm-5 33 34
  • 64.47 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM5 34 36
  • 42 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons SAD1 33
  • 70.37 (n)
soybean
(Glycine max)
eudicotyledons Gma.18055 33
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2381 33
rice
(Oryza sativa)
Liliopsida Os05g0389300 33
  • 66.28 (n)
Os.26574 33
corn
(Zea mays)
Liliopsida Zm.4938 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2293 34
  • 86 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03766 33
  • 65.38 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm5 33
  • 60.53 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4402 33
Species where no ortholog for LSM5 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1000046709 -- 32,495,555(-) G/T upstream_transcript_variant
rs1000120628 -- 32,496,910(-) A/G upstream_transcript_variant
rs1000913873 -- 32,493,212(-) AA/A genic_upstream_transcript_variant, intron_variant
rs1001164177 -- 32,486,824(-) T/A 3_prime_UTR_variant, non_coding_transcript_variant
rs1001614530 -- 32,488,236(-) C/G intron_variant

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

Variant ID Type Subtype PubMed ID
nsv1068321 OTHER inversion 25765185
nsv1148830 OTHER inversion 26484159
nsv436557 CNV deletion 17901297

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)

Additional Variant Information for LSM5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM5

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

Disorders for LSM5 Gene

Additional Disease Information for 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 … Lührmann R (The EMBO journal 1999) 2 3 4 58
  2. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. (PMID: 10369684) Salgado-Garrido J … Séraphin B (The EMBO journal 1999) 2 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. 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 (New York, N.Y.) 2002) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for LSM5 Gene

Sources for LSM5 Gene

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