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Aliases for LSM4 Gene

Aliases for LSM4 Gene

  • LSM4 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • Glycine-Rich Protein 3 4
  • GRP 3 4
  • LSM4 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM4 U6 Small Nuclear RNA And MRNA Degradation Associated 3
  • LSM4 Homolog, U6 Small Nuclear RNA Associated 3
  • YER112W 3

External Ids for LSM4 Gene

Previous GeneCards Identifiers for LSM4 Gene

  • GC19M018911
  • GC19M018809
  • GC19M018262
  • GC19M018278
  • GC19M018417
  • GC19M017981

Summaries for LSM4 Gene

Entrez Gene Summary for LSM4 Gene

  • This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

GeneCards Summary for LSM4 Gene

LSM4 (LSM4 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated) is a Protein Coding gene. Among its related pathways are Deadenylation-dependent mRNA decay and mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding.

UniProtKB/Swiss-Prot for LSM4 Gene

  • Binds specifically to the 3-terminal U-tract of U6 snRNA.

Gene Wiki entry for LSM4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM4 Gene

Genomics for LSM4 Gene

Regulatory Elements for LSM4 Gene

Enhancers for LSM4 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LSM4 on UCSC Golden Path with GeneCards custom track

Promoters for LSM4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around LSM4 on UCSC Golden Path with GeneCards custom track

Genomic Location for LSM4 Gene

Chromosome:
19
Start:
18,306,230 bp from pter
End:
18,323,274 bp from pter
Size:
17,045 bases
Orientation:
Minus strand

Genomic View for LSM4 Gene

Genes around LSM4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM4 Gene

Proteins for LSM4 Gene

  • Protein details for LSM4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y4Z0-LSM4_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm4
    Protein Accession:
    Q9Y4Z0

    Protein attributes for LSM4 Gene

    Size:
    139 amino acids
    Molecular mass:
    15350 Da
    Quaternary structure:
    • LSm subunits form a heteromer with a doughnut shape.

neXtProt entry for LSM4 Gene

Proteomics data for LSM4 Gene at MOPED

Post-translational modifications for LSM4 Gene

  • Ubiquitination at Lys 80
  • Modification sites at PhosphoSitePlus

Other Protein References for LSM4 Gene

Antibody Products

No data available for DME Specific Peptides for LSM4 Gene

Domains & Families for LSM4 Gene

Suggested Antigen Peptide Sequences for LSM4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y4Z0

UniProtKB/Swiss-Prot:

LSM4_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 LSM4: view

No data available for Gene Families for LSM4 Gene

Function for LSM4 Gene

Molecular function for LSM4 Gene

UniProtKB/Swiss-Prot Function:
Binds specifically to the 3-terminal U-tract of U6 snRNA.
genes like me logo Genes that share phenotypes with LSM4: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LSM4 Gene

Localization for LSM4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LSM4 Gene COMPARTMENTS Subcellular localization image for LSM4 gene
Compartment Confidence
cytosol 5
nucleus 5
plasma membrane 2
chloroplast 1

Gene Ontology (GO) - Cellular Components for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with LSM4: view

Pathways & Interactions for LSM4 Gene

genes like me logo Genes that share pathways with LSM4: view

Pathways by source for LSM4 Gene

Gene Ontology (GO) - Biological Process for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IBA --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006396 RNA processing IEA --
GO:0033962 cytoplasmic mRNA processing body assembly IBA --
genes like me logo Genes that share ontologies with LSM4: view

No data available for SIGNOR curated interactions for LSM4 Gene

Drugs & Compounds for LSM4 Gene

(2) Drugs for LSM4 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with LSM4: view

Transcripts for LSM4 Gene

Unigene Clusters for LSM4 Gene

LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for LSM4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - -
SP2: - - -
SP3: - -
SP4: - - - -
SP5:

Relevant External Links for LSM4 Gene

GeneLoc Exon Structure for
LSM4
ECgene alternative splicing isoforms for
LSM4

Expression for LSM4 Gene

mRNA expression in normal human tissues for LSM4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LSM4 Gene

This gene is overexpressed in Saliva (8.5) and Peripheral blood mononuclear cells (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LSM4 Gene



SOURCE GeneReport for Unigene cluster for LSM4 Gene Hs.515255

genes like me logo Genes that share expression patterns with LSM4: view

Protein tissue co-expression partners for LSM4 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for LSM4 Gene

Orthologs for LSM4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LSM4 35
  • 91.85 (n)
  • 100 (a)
LSM4 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LSM4 35
  • 92.57 (n)
  • 100 (a)
LSM4 36
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lsm4 35
  • 88.41 (n)
  • 97.1 (a)
Lsm4 16
Lsm4 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm4 35
  • 88.89 (n)
  • 97.1 (a)
oppossum
(Monodelphis domestica)
Mammalia LSM4 36
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM4 36
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LSM4 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM4 35
  • 79.23 (n)
  • 90.58 (a)
LSM4 36
  • 88 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm4 35
  • 71.5 (n)
  • 89.86 (a)
MGC76085 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.3329 35
zebrafish
(Danio rerio)
Actinopterygii lsm4 35
  • 79.17 (n)
  • 98.86 (a)
zgc73057 35
lsm4 36
  • 85 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4425 35
fruit fly
(Drosophila melanogaster)
Insecta CG17768 36
  • 62 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea lsm-4 36
  • 68 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM4 36
  • 24 (a)
OneToOne
barley
(Hordeum vulgare)
Liliopsida Hv.3996 35
rice
(Oryza sativa)
Liliopsida Os.197 35
wheat
(Triticum aestivum)
Liliopsida Ta.3949 35
corn
(Zea mays)
Liliopsida Zm.3350 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 84 (a)
OneToOne
Species with no ortholog for LSM4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for LSM4 Gene

ENSEMBL:
Gene Tree for LSM4 (if available)
TreeFam:
Gene Tree for LSM4 (if available)

Paralogs for LSM4 Gene

(3) SIMAP similar genes for LSM4 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with LSM4: view

No data available for Paralogs for LSM4 Gene

Variants for LSM4 Gene

Sequence variations from dbSNP and Humsavar for LSM4 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs7258697 -- 18,306,344(+) TCAGG(A/C/G)CTTCC utr-variant-3-prime
rs7259046 -- 18,306,568(+) TGGAG(C/T)CCAGG utr-variant-3-prime
rs7260201 -- 18,324,342(+) cccag(C/G)ctgca upstream-variant-2KB
rs12976123 -- 18,312,308(+) CCTGG(A/T)GGGGG intron-variant
rs16982307 -- 18,310,880(+) TTTCC(A/G)GAACA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LSM4 Gene

Variant ID Type Subtype PubMed ID
dgv3774n71 CNV Loss 21882294
dgv3780n71 CNV Loss 21882294
nsv911271 CNV Loss 21882294
dgv3781n71 CNV Loss 21882294

Variation tolerance for LSM4 Gene

Residual Variation Intolerance Score: 34.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.26; 25.11% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LSM4 Gene

HapMap Linkage Disequilibrium report
LSM4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM4 Gene

Disorders for LSM4 Gene

Relevant External Links for LSM4

Genetic Association Database (GAD)
LSM4
Human Genome Epidemiology (HuGE) Navigator
LSM4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LSM4

No disorders were found for LSM4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSM4 Gene

Publications for LSM4 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. 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 W.J. … Dreyfuss G. (J. Biol. Chem. 2000) 3 23
  4. 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
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3

Products for LSM4 Gene

Sources for LSM4 Gene

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