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 LSM6 Gene

Aliases for LSM6 Gene

  • LSM6 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • U6 SnRNA-Associated Sm-Like Protein LSm6 3 4
  • YDR378C 2 3
  • LSM6 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM6 U6 Small Nuclear RNA And MRNA Degradation Associated 3
  • LSM6 Homolog, U6 Small Nuclear RNA Associated 3
  • Sm Protein F 3
  • LSM6 5

External Ids for LSM6 Gene

Previous GeneCards Identifiers for LSM6 Gene

  • GC04P147896
  • GC04P147468
  • GC04P147563
  • GC04P147674
  • GC04P147454
  • GC04P147316
  • GC04P147097
  • GC04P142817

Summaries for LSM6 Gene

Entrez Gene Summary for LSM6 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 LSM6 Gene

LSM6 (LSM6 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. An important paralog of this gene is SNRPF.

UniProtKB/Swiss-Prot Summary for LSM6 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). Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway (Probable).

Gene Wiki entry for LSM6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LSM6 Gene

Genomics for LSM6 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LSM6 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
GH04J146175 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.8 798 3 PRDM10 RFX1 IKZF1 KDM1A ZNF692 POLR2A BACH1 LARP7 ZNF143 ZIC2 LSM6 lnc-REELD1-3 REELD1 ENSG00000279845
GH04J145934 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 22 -238.3 -238309 6.2 SP1 GATAD2A PRDM10 ZNF629 TFE3 SOX13 ZNF692 POLR2A ZNF7 BACH1 ZNF827 lnc-ZNF827-8 LSM6 SLC10A7 piR-49535 C4orf51
GH04J145617 Promoter/Enhancer 1.9 Ensembl ENCODE CraniofacialAtlas 9.8 -556.2 -556248 3.6 SP1 CTCF HNRNPL ZNF629 REST TFE3 POLR2A ZNF692 RCOR2 BACH1 MMAA ENSG00000248356 SLC10A7 OTUD4 LSM6 NCOA4P3 LINC02491 C4orf51
GH04J146095 Enhancer 0.7 Ensembl ENCODE 11 -79.5 -79543 2 CTCF ZNF143 RAD21 TRIM22 RUNX3 SMC3 ZNF654 ZNF2 LINC01095 LSM6 LOC105377469 LOC105377468 ZNF827
GH04J146146 Enhancer 0.5 ENCODE 10.8 -27.9 -27940 2.2 CEBPA CEBPB FOXA2 NFIL3 HLF FOXA3 CEBPG REELD1 LSM6 piR-37663-041 RF01061-131 ZNF827
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM6 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LSM6

Top Transcription factor binding sites by QIAGEN in the LSM6 gene promoter:
  • AML1a
  • c-Myb
  • FOXJ2
  • FOXJ2 (long isoform)
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • RFX1

Genomic Locations for LSM6 Gene

Genomic Locations for LSM6 Gene
chr4:146,175,703-146,204,436
(GRCh38/hg38)
Size:
28,734 bases
Orientation:
Plus strand
chr4:147,096,835-147,121,152
(GRCh37/hg19)
Size:
24,318 bases
Orientation:
Plus strand

Genomic View for LSM6 Gene

Genes around LSM6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM6 Gene

Proteins for LSM6 Gene

  • Protein details for LSM6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62312-LSM6_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm6
    Protein Accession:
    P62312
    Secondary Accessions:
    • Q4W5J5
    • Q9Y4Y8

    Protein attributes for LSM6 Gene

    Size:
    80 amino acids
    Molecular mass:
    9128 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). Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7 (PubMed:12515382).

    Three dimensional structures from OCA and Proteopedia for LSM6 Gene

neXtProt entry for LSM6 Gene

Post-translational modifications for LSM6 Gene

  • Ubiquitination at Lys13 and Lys23
  • Modification sites at PhosphoSitePlus

Other Protein References for LSM6 Gene

No data available for DME Specific Peptides for LSM6 Gene

Domains & Families for LSM6 Gene

Gene Families for LSM6 Gene

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

Protein Domains for LSM6 Gene

InterPro:
Blocks:
  • Like-Sm ribonucleoprotein-related, core
ProtoNet:

Suggested Antigen Peptide Sequences for LSM6 Gene

GenScript: Design optimal peptide antigens:
  • U6 snRNA-associated Sm-like protein LSm6 (LSM6_HUMAN)
  • cDNA, FLJ92408, Homo sapiens LSM6 homolog, U6 small nuclear RNA associated (S.cerevisiae) (LSM6), mRNA (Q4W5J5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P62312

UniProtKB/Swiss-Prot:

LSM6_HUMAN :
  • Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.
Family:
  • Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.
genes like me logo Genes that share domains with LSM6: view

Function for LSM6 Gene

Molecular function for LSM6 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). Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway (Probable).

Phenotypes From GWAS Catalog for LSM6 Gene

Gene Ontology (GO) - Molecular Function for LSM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 15231747
GO:0046982 protein heterodimerization activity IDA 12515382
genes like me logo Genes that share ontologies with LSM6: view
genes like me logo Genes that share phenotypes with LSM6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM6

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LSM6 Gene

Localization for LSM6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM6 Gene

Cytoplasm. Nucleus.

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 LSM6 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LSM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA 21873635
GO:0005634 nucleus IEA,IDA 26912367
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA 21873635
genes like me logo Genes that share ontologies with LSM6: view

Pathways & Interactions for LSM6 Gene

genes like me logo Genes that share pathways with LSM6: view

Pathways by source for LSM6 Gene

Gene Ontology (GO) - Biological Process for LSM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006364 rRNA processing IEA --
GO:0006397 mRNA processing IEA --
GO:0006402 mRNA catabolic process IDA 12515382
GO:0008033 tRNA processing IEA --
genes like me logo Genes that share ontologies with LSM6: view

No data available for SIGNOR curated interactions for LSM6 Gene

Drugs & Compounds for LSM6 Gene

(3) Drugs for LSM6 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Citric acid Approved, Vet_approved Nutra Activator, Agonist, Target 1509
Uridine Experimental, Investigational Pharma Target 0
Uridine monophosphate Experimental Pharma Target 0
genes like me logo Genes that share compounds with LSM6: view

Transcripts for LSM6 Gene

mRNA/cDNA for LSM6 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
8 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 LSM6

Alternative Splicing Database (ASD) splice patterns (SP) for LSM6 Gene

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

Relevant External Links for LSM6 Gene

GeneLoc Exon Structure for
LSM6

Expression for LSM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LSM6 Gene

Protein differential expression in normal tissues from HIPED for LSM6 Gene

This gene is overexpressed in Tlymphocyte (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LSM6 Gene



Protein tissue co-expression partners for LSM6 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LSM6

SOURCE GeneReport for Unigene cluster for LSM6 Gene:

Hs.190520

Evidence on tissue expression from TISSUES for LSM6 Gene

  • Nervous system(2.2)
genes like me logo Genes that share expression patterns with LSM6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LSM6 Gene

Orthologs for LSM6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM6 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LSM6 30 31
  • 100 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LSM6 31
  • 100 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LSM6 30 31
  • 95 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lsm6 30 17 31
  • 92.08 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LSM6 30 31
  • 91.67 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lsm6 30
  • 90.42 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 71 (a)
OneToMany
-- 31
  • 71 (a)
OneToMany
Chicken
(Gallus gallus)
Aves LSM6 30 31
  • 87.5 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LSM6 31
  • 100 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lsm6 30
  • 82.92 (n)
Zebrafish
(Danio rerio)
Actinopterygii lsm6 30 31
  • 81.67 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005314 30
  • 71.86 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG9344 30 31 32
  • 69.7 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea lsm-6 30 31
  • 68 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMX3 31
  • 35 (a)
OneToMany
LSM6 33
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT3G59810 30
  • 70.22 (n)
Soybean
(Glycine max)
eudicotyledons Gma.2690 30
Rice
(Oryza sativa)
Liliopsida Os04g0388900 30
  • 71.56 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1789 31
  • 88 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm6 30
  • 66.67 (n)
Species where no ortholog for LSM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 LSM6 Gene

ENSEMBL:
Gene Tree for LSM6 (if available)
TreeFam:
Gene Tree for LSM6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LSM6: view image

Paralogs for LSM6 Gene

Paralogs for LSM6 Gene

(2) SIMAP similar genes for LSM6 Gene using alignment to 1 proteins:

  • LSM6_HUMAN

Pseudogenes.org Pseudogenes for LSM6 Gene

genes like me logo Genes that share paralogs with LSM6: view

Variants for LSM6 Gene

Additional dbSNP identifiers (rs#s) for LSM6 Gene

Structural Variations from Database of Genomic Variants (DGV) for LSM6 Gene

Variant ID Type Subtype PubMed ID
nsv1018859 CNV gain 25217958
nsv461674 CNV gain 19166990
nsv595650 CNV gain 21841781

Variation tolerance for LSM6 Gene

Residual Variation Intolerance Score: 59.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.23; 5.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LSM6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM6

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 LSM6 Gene

Disorders for LSM6 Gene

No disorders were found for LSM6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSM6 Gene

Publications for LSM6 Gene

  1. 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 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 … Lührmann R (The EMBO journal 1999) 2 3 4
  3. 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
  4. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  5. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4

Products for LSM6 Gene

Sources for LSM6 Gene