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Aliases for LSM6 Gene

Aliases for LSM6 Gene

  • LSM6 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • 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
  • U6 SnRNA-Associated Sm-Like Protein LSm6 3
  • Sm Protein F 3
  • YDR378C 3

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 mRNA Splicing - Major Pathway and Deadenylation-dependent mRNA decay. An important paralog of this gene is SNRPF.

UniProtKB/Swiss-Prot for LSM6 Gene

  • 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. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity).

Gene Wiki entry for LSM6 Gene

Additional gene information for LSM6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM6 Gene

Genomics for LSM6 Gene

GeneHancer (GH) Regulatory Elements for LSM6 Gene

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 2 EPDnew Ensembl ENCODE 650.7 +0.5 514 2.3 ATF1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 ZNF207 ZNF143 ATF7 LSM6 REELD1 ENSG00000279845
GH04J145175 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 12.9 -996.2 -996169 7.7 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 IRF4 YY1 OTUD4 LSM6 ANAPC10 ABCE1 MMAA GC04M145156
GH04J145934 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10 -238.3 -238289 6.2 HDGF PKNOX1 FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF827 GC04M145938 SLC10A7 ENSG00000248356 LSM6 PIR42534
GH04J145812 Enhancer 1 ENCODE dbSUPER 9.8 -362.6 -362625 1.6 NCOA3 MEIS2 PKNOX1 JUN ZFP64 MAX SIN3A CEBPG BRCA1 ZNF697 OTUD4 ENSG00000248356 SLC10A7 LSM6 ENSG00000279481 GC04M145759 ZNF827
GH04J145769 Enhancer 0.6 Ensembl 9.8 -405.8 -405782 0.6 ZNF654 ZNF680 CEBPB ZNF140 ZC3H11A CEBPG REST ZNF623 ZNF781 ZNF697 OTUD4 ENSG00000248356 SLC10A7 LSM6 GC04M145759 ENSG00000279481 C4orf51 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LSM6 Gene

Genomic Locations for LSM6 Gene
chr4:146,175,683-146,200,000
(GRCh38/hg38)
Size:
24,318 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 heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. The LSm subunits form a seven-membered ring structure with a doughnut shape.

    Three dimensional structures from OCA and Proteopedia for LSM6 Gene

neXtProt entry for LSM6 Gene

Post-translational modifications for LSM6 Gene

  • Ubiquitination at posLast=2323 and posLast=1313
  • 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

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:
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. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity).

Gene Ontology (GO) - Molecular Function for LSM6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA --
GO:0005515 protein binding IPI 15231747
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

miRNA for LSM6 Gene

miRTarBase miRNAs that target LSM6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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
extracellular 5
nucleus 5
cytosol 5
cytoskeleton 2
mitochondrion 1
peroxisome 1

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 --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA --
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:0008033 tRNA processing IEA --
GO:0008380 RNA splicing TAS 10523320
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 Agonist, Activator, Target 1243
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

Unigene Clusters for LSM6 Gene

LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
LSM6

Expression for LSM6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of LSM6 Gene:

LSM6

SOURCE GeneReport for Unigene cluster for LSM6 Gene:

Hs.190520
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 , Evidence on tissue expression from TISSUES 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
oppossum
(Monodelphis domestica)
Mammalia LSM6 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LSM6 34 33
  • 100 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LSM6 34 33
  • 95 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lsm6 16 34 33
  • 92.08 (n)
cow
(Bos Taurus)
Mammalia LSM6 34 33
  • 91.67 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm6 33
  • 90.42 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 71 (a)
OneToMany
-- 34
  • 71 (a)
OneToMany
chicken
(Gallus gallus)
Aves LSM6 34 33
  • 87.5 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LSM6 34
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm6 33
  • 82.92 (n)
zebrafish
(Danio rerio)
Actinopterygii lsm6 34 33
  • 81.67 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005314 33
  • 71.86 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9344 34 35 33
  • 69.7 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea lsm-6 34 33
  • 68 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMX3 34
  • 35 (a)
OneToMany
LSM6 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G59810 33
  • 70.22 (n)
soybean
(Glycine max)
eudicotyledons Gma.2690 33
rice
(Oryza sativa)
Liliopsida Os04g0388900 33
  • 71.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1789 34
  • 88 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm6 33
  • 66.67 (n)
Species where no ortholog for LSM6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

Sequence variations from dbSNP and Humsavar for LSM6 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000093972 -- 146,184,829(+) T/C intron_variant
rs1000181074 -- 146,202,415(+) A/G genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000205899 -- 146,197,093(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000228689 -- 146,191,054(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000260846 -- 146,193,904(+) T/G genic_downstream_transcript_variant, intron_variant

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 for LSM6 Gene

Disorders for LSM6 Gene

Additional Disease Information for LSM6

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 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. 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
  4. 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
  5. Specific sequences of the Sm and Sm-like (Lsm) proteins mediate their interaction with the spinal muscular atrophy disease gene product (SMN). (PMID: 10851237) Friesen WJ … Dreyfuss G (The Journal of biological chemistry 2000) 3 22 58

Products for LSM6 Gene

Sources for LSM6 Gene

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