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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
  • U6 SnRNA-Associated Sm-Like Protein LSm4 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 mRNA Splicing - Major Pathway and Deadenylation-dependent mRNA decay.

UniProtKB/Swiss-Prot for LSM4 Gene

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

Gene Wiki entry for LSM4 Gene

Additional gene information for LSM4 Gene

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

Genomics for LSM4 Gene

GeneHancer (GH) Regulatory Elements for LSM4 Gene

Promoters and enhancers for LSM4 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
GH19J018315 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 666.9 +3.3 3273 9.4 MLX DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 LSM4 IQCN UPF1 ELL ENSG00000268030 ENSG00000268938 COLGALT1 ENSG00000269439 ENSG00000269191 PGPEP1
GH19J018300 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 17 +18.8 18769 8.2 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC PPARGC1A GLIS1 RCOR2 ENSG00000268030 UPF1 ENSG00000268938 IQCN NR2C2AP ENSG00000269191 COLGALT1 MEF2B MVB12A ELL
GH19J018328 Promoter/Enhancer 1.9 EPDnew FANTOM5 Ensembl ENCODE 14.8 -5.6 -5596 1.7 HDGF PKNOX1 ATF1 ARNT SIN3A ZBTB7B ZNF48 NCOA2 YY1 ZNF766 PGPEP1 LSM4 LRRC25 MPV17L2 ENSG00000268030 RN7SL513P
GH19J018203 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 11.5 +117.3 117327 6.3 HDGF PKNOX1 CLOCK ARID4B SIN3A ZNF2 YY1 ZNF207 ZNF143 FOS LOC102725254 RAB3A IQCN UPF1 ENSG00000268030 PDE4C ENSG00000268938 NR2C2AP ENSG00000269191 COLGALT1
GH19J018277 Promoter/Enhancer 2 Ensembl ENCODE dbSUPER 12.9 +42.6 42646 6.4 MLX FEZF1 DMAP1 YBX1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC JUND MIR3188 GC19P020561 PIR55689 IQCN ENSG00000268030 UPF1 ENSG00000268938 NR2C2AP ENSG00000269191
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LSM4 gene promoter:
  • GATA-1
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • NF-YB
  • NF-YA
  • NF-Y
  • CP1A
  • CBF-B
  • CBF-A

Genomic Locations for LSM4 Gene

Genomic Locations for LSM4 Gene
chr19:18,306,230-18,323,274
(GRCh38/hg38)
Size:
17,045 bases
Orientation:
Minus strand
chr19:18,417,040-18,434,084
(GRCh37/hg19)
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.

    Three dimensional structures from OCA and Proteopedia for LSM4 Gene

neXtProt entry for LSM4 Gene

Post-translational modifications for LSM4 Gene

  • Ubiquitination at posLast=8080
  • Modification sites at PhosphoSitePlus

Other Protein References for LSM4 Gene

No data available for DME Specific Peptides for LSM4 Gene

Domains & Families for LSM4 Gene

Gene Families for LSM4 Gene

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

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

Function for LSM4 Gene

Molecular function for LSM4 Gene

UniProtKB/Swiss-Prot Function:
Binds specifically to the 3-terminal U-tract of U6 snRNA.

Phenotypes From GWAS Catalog for LSM4 Gene

Gene Ontology (GO) - Molecular Function for LSM4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,IBA --
GO:0005515 protein binding IPI 15231747
GO:0017070 U6 snRNA binding IBA --
GO:0042731 PH domain binding IDA 15905169
genes like me logo Genes that share ontologies with LSM4: view
genes like me logo Genes that share phenotypes with LSM4: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
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 LSM4 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LSM4 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 TAS 10369684
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:0000387 spliceosomal snRNP assembly IBA --
GO:0000398 mRNA splicing, via spliceosome TAS,IEA --
GO:0000956 nuclear-transcribed mRNA catabolic process IEA,IBA --
GO:0006396 RNA processing IEA --
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

mRNA/cDNA for LSM4 Gene

Unigene Clusters for LSM4 Gene

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

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for LSM4 Gene



Protein tissue co-expression partners for LSM4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LSM4 Gene:

LSM4

SOURCE GeneReport for Unigene cluster for LSM4 Gene:

Hs.515255

Evidence on tissue expression from TISSUES for LSM4 Gene

  • Lung(4.8)
  • Nervous system(4.8)
  • Liver(4.3)
  • Pancreas(3.1)
  • Intestine(2.4)
genes like me logo Genes that share expression patterns with LSM4: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia LSM4 34
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia LSM4 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LSM4 34 33
  • 92.57 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LSM4 34 33
  • 91.85 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM4 34
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm4 33
  • 88.89 (n)
mouse
(Mus musculus)
Mammalia Lsm4 16 34 33
  • 88.41 (n)
chicken
(Gallus gallus)
Aves LSM4 34 33
  • 79.23 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm4 33
  • 71.5 (n)
MGC76085 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.3329 33
zebrafish
(Danio rerio)
Actinopterygii lsm4 34 33
  • 79.17 (n)
OneToOne
zgc73057 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4425 33
fruit fly
(Drosophila melanogaster)
Insecta CG17768 34
  • 62 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea lsm-4 34
  • 68 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM4 34
  • 24 (a)
OneToOne
corn
(Zea mays)
Liliopsida Zm.3350 33
wheat
(Triticum aestivum)
Liliopsida Ta.3949 33
barley
(Hordeum vulgare)
Liliopsida Hv.3996 33
rice
(Oryza sativa)
Liliopsida Os.197 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 84 (a)
OneToOne
Species where no ortholog for LSM4 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for LSM4: view image

Paralogs for LSM4 Gene

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

  • LSM4_HUMAN
  • M0QXB0_HUMAN
  • U3KQK1_HUMAN
  • U3KQS7_HUMAN
  • V9GZ56_HUMAN
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 Variation AA Info Type
rs1000029179 -- 18,308,693(-) G/A intron_variant
rs1000201773 -- 18,306,632(-) A/G 3_prime_UTR_variant
rs1000260355 -- 18,324,369(-) T/C upstream_transcript_variant
rs1000365262 -- 18,315,878(-) G/A intron_variant
rs1000378967 -- 18,317,970(-) G/A/T intron_variant

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

Variant ID Type Subtype PubMed ID
esv3643836 CNV loss 21293372
nsv952420 CNV deletion 24416366

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)

Additional Variant Information for LSM4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM4

SNP Genotyping and Copy Number Assay Products

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

Disorders for LSM4 Gene

Additional Disease Information for LSM4

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

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. 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
  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 58
  3. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 44 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. 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

Products for LSM4 Gene

Sources for LSM4 Gene

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