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 ... See more...

Aliases for LSM5 Gene

Aliases for LSM5 Gene

  • LSM5 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • U6 SnRNA-Associated Sm-Like Protein LSm5 3 4
  • YER146W 2 3
  • 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
  • LSM5 5

External Ids for LSM5 Gene

Previous GeneCards Identifiers for LSM5 Gene

  • GC07M032167
  • GC07M032233
  • GC07M032267
  • GC07M032298
  • GC07M032491
  • GC07M032402
  • GC07M032524

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. Diseases associated with LSM5 include Retinitis Pigmentosa. 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 Summary for LSM5 Gene

  • Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).

Gene Wiki entry for LSM5 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LSM5 Gene

Genomics for LSM5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LSM5 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LSM5

Top Transcription factor binding sites by QIAGEN in the LSM5 gene promoter:
  • AML1a
  • FOXF2
  • FOXJ2 (long isoform)
  • HSF2

Genomic Locations for LSM5 Gene

Genomic Locations for LSM5 Gene
chr7:32,485,338-32,495,283
(GRCh38/hg38)
Size:
9,946 bases
Orientation:
Minus strand
chr7:32,524,945-32,534,895
(GRCh37/hg19)
Size:
9,951 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:
    • Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:10523320, PubMed:28781166, PubMed:26912367). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome (PubMed:10523320, PubMed:26912367, PubMed:28781166).

    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

  • Ubiquitination at Lys20
  • Modification sites at PhosphoSitePlus

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

Protein Domains for LSM5 Gene

InterPro:
Blocks:
  • Small nuclear ribonucleoprotein (Sm protein)
  • Like-Sm ribonucleoprotein-related, core
ProtoNet:

Suggested Antigen Peptide Sequences for LSM5 Gene

GenScript: Design optimal peptide antigens:
  • U6 snRNA-associated Sm-like protein LSm5 (LSM5_HUMAN)

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 role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).

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 RNA binding TAS,IEA --
GO:0005515 protein binding IPI 15231747
GO:0046982 protein heterodimerization activity IDA 12515382
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM5

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 3
plasma membrane 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
endosome 2
lysosome 2
golgi apparatus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for LSM5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 26912367
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA 21873635
GO:0005737 cytoplasm IDA 12515382
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:0006397 mRNA processing TAS 10369684
GO:0006402 mRNA catabolic process IDA 12515382
GO:0008380 RNA splicing IEA --
GO:0009617 response to bacterium IEA --
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

mRNA/cDNA for LSM5 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM5

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

Expression for LSM5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for LSM5 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LSM5

SOURCE GeneReport for Unigene cluster for LSM5 Gene:

Hs.424908

Evidence on tissue expression from TISSUES for LSM5 Gene

  • Nervous system(4.6)
  • Bone marrow(4.5)
  • Skin(3.1)
  • Muscle(2.9)
  • Kidney(2.9)
  • Heart(2.8)
  • Intestine(2.7)
  • Liver(2.6)
  • Lung(2.5)
  • Lymph node(2.5)
  • Blood(2.4)
  • Spleen(2.3)
  • Thyroid gland(2.3)
  • Adrenal gland(2.3)
  • Eye(2.3)
  • Stomach(2.3)
  • Pancreas(2.2)
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 30 31
  • 99.63 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LSM5 30 31
  • 93.77 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LSM5 30 31
  • 93.41 (n)
OneToMany
-- 31
  • 60 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Lsm5 30
  • 90.84 (n)
Mouse
(Mus musculus)
Mammalia Lsm5 30 17 31
  • 90.11 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LSM5 31
  • 61 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LSM5 31
  • 58 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LSM5 30 31
  • 86.45 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LSM5 31
  • 93 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lsm5 30
  • 82.78 (n)
Zebrafish
(Danio rerio)
Actinopterygii LSM5 31
  • 95 (a)
OneToOne
zgc:171959 30
  • 79.12 (n)
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7249 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG6610 30 31 32
  • 70.16 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006604 30
  • 66.29 (n)
Worm
(Caenorhabditis elegans)
Secernentea lsm-5 30 31
  • 64.47 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM5 31 33
  • 42 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons SAD1 30
  • 70.37 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.2381 30
Soybean
(Glycine max)
eudicotyledons Gma.18055 30
Rice
(Oryza sativa)
Liliopsida Os05g0389300 30
  • 66.28 (n)
Os.26574 30
Corn
(Zea mays)
Liliopsida Zm.4938 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2293 31
  • 86 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU03766 30
  • 65.38 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm5 30
  • 60.53 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4402 30
Species where no ortholog for LSM5 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for LSM5: view image

Paralogs for LSM5 Gene

(1) SIMAP similar genes for LSM5 Gene using alignment to 3 proteins:

  • LSM5_HUMAN
  • B8ZZF8_HUMAN
  • F8W8Y8_HUMAN

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

Additional dbSNP identifiers (rs#s) for LSM5 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LSM5 Gene

Disorders for LSM5 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LSM5 Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search LSM5 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with LSM5: view

No data available for 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
  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
  3. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  4. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4
  5. 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

Products for LSM5 Gene

Sources for LSM5 Gene