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 LSM3 Gene

Aliases for LSM3 Gene

  • LSM3 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated 2 3 5
  • U6 SnRNA-Associated Sm-Like Protein LSm3 3 4
  • YLR438C 2 3
  • SMX4 2 3
  • USS2 2 3
  • LSM3 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM3 U6 Small Nuclear RNA And MRNA Degradation Associated 3
  • LSM3 Homolog, U6 Small Nuclear RNA Associated 3
  • LSM3 5

External Ids for LSM3 Gene

Previous GeneCards Identifiers for LSM3 Gene

  • GC03P014149
  • GC03P014195
  • GC03P014155
  • GC03P014219

Summaries for LSM3 Gene

Entrez Gene Summary for LSM3 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 LSM3 Gene

LSM3 (LSM3 Homolog, U6 Small Nuclear RNA And MRNA Degradation Associated) is a Protein Coding gene. Diseases associated with LSM3 include Spondylolysis. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot Summary for LSM3 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 LSM3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LSM3 Gene

Genomics for LSM3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LSM3 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
GH03J014177 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 -0.1 -116 3 BRCA1 ARHGAP35 SP1 HNRNPL CREB1 GATAD2A PRDM10 ZNF629 ZNF692 POLR2A XPC LSM3 TMEM43 CHCHD4
GH03J014140 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 12.3 -34.1 -34056 8.5 SP1 CREB1 CTCF ZBTB33 ATF7 TEAD4 PRDM10 ZNF629 RFX1 ZNF692 TMEM43 ENSG00000228242 lnc-XPC-7 XPC VN1R20P LSM3 CHCHD4 RBSN XPC-AS1 ENSG00000268279
GH03J014265 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.5 +88.3 88321 3.9 CREB1 ZNF629 LEF1 ZNF692 ZHX2 JUND FOXA1 PATZ1 REST DPF2 CAPN7 XPC SH3BP5-AS1 ENSG00000228242 CCDC174 NR2C2 SLC6A6 LSM3 RBSN lnc-XPC-8
GH03J014470 Enhancer 1 Ensembl ENCODE dbSUPER 10.3 +293.7 293741 3.5 PRDM1 ZNF341 SP2 JUND RUNX3 ESR1 FOS ZBTB17 RBM22 ZFHX2 SLC6A6 LSM3 XPC FGD5-AS1 lnc-CCDC174-3 lnc-XPC-5 GRIP2
GH03J014473 Enhancer 0.8 ENCODE dbSUPER 10.9 +289.4 289411 0.2 CTCF PATZ1 REST RAD21 TRIM22 ZNF600 RUNX3 MAFF ZNF592 SMC3 SLC6A6 LSM3 XPC lnc-CCDC174-3 lnc-XPC-5 GRIP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LSM3

Top Transcription factor binding sites by QIAGEN in the LSM3 gene promoter:
  • Brachyury
  • LUN-1
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • p300
  • SRF
  • SRF (504 AA)

Genomic Locations for LSM3 Gene

Genomic Locations for LSM3 Gene
chr3:14,178,817-14,201,122
(GRCh38/hg38)
Size:
22,306 bases
Orientation:
Plus strand
chr3:14,219,858-14,242,619
(GRCh37/hg19)
Size:
22,762 bases
Orientation:
Plus strand

Genomic View for LSM3 Gene

Genes around LSM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM3 Gene

Proteins for LSM3 Gene

  • Protein details for LSM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P62310-LSM3_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm3
    Protein Accession:
    P62310
    Secondary Accessions:
    • Q6IAH0
    • Q9Y4Z1

    Protein attributes for LSM3 Gene

    Size:
    102 amino acids
    Molecular mass:
    11845 Da
    Quaternary structure:
    • Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:11991638, 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 LSM3 Gene

neXtProt entry for LSM3 Gene

Post-translational modifications for LSM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LSM3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LSM3 Gene

Domains & Families for LSM3 Gene

Gene Families for LSM3 Gene

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

Protein Domains for LSM3 Gene

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

Suggested Antigen Peptide Sequences for LSM3 Gene

GenScript: Design optimal peptide antigens:
  • U6 snRNA-associated Sm-like protein LSm3 (LSM3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P62310

UniProtKB/Swiss-Prot:

LSM3_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 LSM3: view

Function for LSM3 Gene

Molecular function for LSM3 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 LSM3 Gene

Gene Ontology (GO) - Molecular Function for LSM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA 21873635
GO:0005515 protein binding IPI 14667819
GO:0030629 U6 snRNA 3'-end binding IDA 10369684
genes like me logo Genes that share ontologies with LSM3: view
genes like me logo Genes that share phenotypes with LSM3: view

Animal Model Products

CRISPR Products

miRNA for LSM3 Gene

miRTarBase miRNAs that target LSM3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LSM3 Gene

Localization for LSM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM3 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 LSM3 gene
Compartment Confidence
nucleus 5
cytosol 4
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LSM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-body IBA 21873635
GO:0005634 nucleus TAS 10369684
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005688 U6 snRNP IBA 21873635
genes like me logo Genes that share ontologies with LSM3: view

Pathways & Interactions for LSM3 Gene

genes like me logo Genes that share pathways with LSM3: view

Pathways by source for LSM3 Gene

Gene Ontology (GO) - Biological Process for LSM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0000956 nuclear-transcribed mRNA catabolic process IEA --
GO:0006397 mRNA processing TAS 10369684
GO:0008380 RNA splicing IEA --
GO:0033962 cytoplasmic mRNA processing body assembly IBA 21873635
genes like me logo Genes that share ontologies with LSM3: view

No data available for SIGNOR curated interactions for LSM3 Gene

Drugs & Compounds for LSM3 Gene

No Compound Related Data Available

Transcripts for LSM3 Gene

mRNA/cDNA for LSM3 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
1 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 LSM3

Alternative Splicing Database (ASD) splice patterns (SP) for LSM3 Gene

No ASD Table

Relevant External Links for LSM3 Gene

GeneLoc Exon Structure for
LSM3

Expression for LSM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LSM3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for LSM3 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (8.4) and Bone marrow stromal cell (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LSM3 Gene



Protein tissue co-expression partners for LSM3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LSM3

SOURCE GeneReport for Unigene cluster for LSM3 Gene:

Hs.111632

Evidence on tissue expression from TISSUES for LSM3 Gene

  • Kidney(4.5)
  • Spleen(4.4)
  • Nervous system(2.7)
  • Liver(2.6)
  • Heart(2.3)
  • Muscle(2.2)
  • Intestine(2.2)
  • Blood(2)
genes like me logo Genes that share expression patterns with LSM3: 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 LSM3 Gene

Orthologs for LSM3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LSM3 30 31
  • 100 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LSM3 31
  • 99 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LSM3 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LSM3 30 31
  • 94.44 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lsm3 30 17 31
  • 90.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lsm3 30
  • 90.52 (n)
Cow
(Bos Taurus)
Mammalia LSM3 30 31
  • 90.2 (n)
OneToOne
Chicken
(Gallus gallus)
Aves LSM3 30
  • 84.31 (n)
Lizard
(Anolis carolinensis)
Reptilia LSM3 31
  • 99 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lsm3 30
  • 80.39 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6080 30
Zebrafish
(Danio rerio)
Actinopterygii CABZ01028296.1 31
  • 97 (a)
OneToOne
LOC100535720 30
  • 79.08 (n)
cldng 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2463 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013519 30
  • 70.1 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta LSm3 30 31
  • 66.34 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea lsm-3 30 31
  • 62.75 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM3 31 33
  • 39 (a)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT1G76860 30
  • 68.89 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.956 30
Soybean
(Glycine max)
eudicotyledons Gma.12513 30
Rice
(Oryza sativa)
Liliopsida Os01g0866700 30
  • 69.63 (n)
Os.8993 30
Corn
(Zea mays)
Liliopsida Zm.3271 30
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.644 31
  • 83 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.1658 30
Species where no ortholog for LSM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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 LSM3 Gene

ENSEMBL:
Gene Tree for LSM3 (if available)
TreeFam:
Gene Tree for LSM3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LSM3: view image

Paralogs for LSM3 Gene

(1) SIMAP similar genes for LSM3 Gene using alignment to 1 proteins:

  • LSM3_HUMAN
genes like me logo Genes that share paralogs with LSM3: view

No data available for Paralogs for LSM3 Gene

Variants for LSM3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LSM3 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
775193 Benign: not provided 14,181,574(+) C/T SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for LSM3 Gene

Structural Variations from Database of Genomic Variants (DGV) for LSM3 Gene

Variant ID Type Subtype PubMed ID
esv2724945 CNV deletion 23290073
esv3374413 CNV insertion 20981092
esv34163 CNV loss 18971310
nsv1003121 CNV loss 25217958
nsv1011766 CNV gain 25217958
nsv1014571 CNV gain 25217958
nsv963299 CNV duplication 23825009

Variation tolerance for LSM3 Gene

Residual Variation Intolerance Score: 36.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.20; 4.49% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LSM3 Gene

Human Gene Mutation Database (HGMD)
LSM3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM3 Gene

Disorders for LSM3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LSM3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spondylolysis
- elite association - COSMIC cancer census association via MalaCards
Search LSM3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LSM3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LSM3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LSM3 Gene

Publications for LSM3 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 LSM3 Gene

Sources for LSM3 Gene