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Aliases for LSM10 Gene

Aliases for LSM10 Gene

  • LSM10, U7 Small Nuclear RNA Associated 2 3 5
  • U7 SnRNA-Associated Sm-Like Protein LSm10 3
  • U7 SnRNP-Specific Sm-Like Protein LSM10 3
  • MSTP074 3
  • MST074 3

External Ids for LSM10 Gene

Previous GeneCards Identifiers for LSM10 Gene

  • GC01P036417
  • GC01M035913
  • GC01M036285
  • GC01M036286
  • GC01M036528
  • GC01M036631
  • GC01M036856
  • GC01M034975

Summaries for LSM10 Gene

GeneCards Summary for LSM10 Gene

LSM10 (LSM10, U7 Small Nuclear RNA Associated) is a Protein Coding gene. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Cleavage of Growing Transcript in the Termination Region. Gene Ontology (GO) annotations related to this gene include histone pre-mRNA DCP binding.

UniProtKB/Swiss-Prot for LSM10 Gene

  • Appears to function in the U7 snRNP complex that is involved in histone 3-end processing. Increases U7 snRNA levels but not histone 3-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Gene Wiki entry for LSM10 Gene

Additional gene information for LSM10 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM10 Gene

Genomics for LSM10 Gene

GeneHancer (GH) Regulatory Elements for LSM10 Gene

Promoters and enhancers for LSM10 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
GH01J036396 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 656.6 +0.4 448 2.5 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B LSM10 AGO3 EVA1B LOC105378647 OSCP1 COL8A2 STK40
GH01J036222 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.2 +173.6 173567 4.7 CLOCK MLX FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF263 SP3 THRAP3 AGO3 MAP7D1 TRAPPC3 COL8A2 ADPRHL2 LOC100128093 TEKT2 LSM10 RNU4-27P
GH01J036370 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 13 +21.9 21879 10.6 HDGF PKNOX1 FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A YBX1 FEZF1 CSF3R STK40 AGO3 LSM10 RNU4-27P SNORA63C OSCP1 ENSG00000223944 EVA1B LOC105378647
GH01J036299 Promoter/Enhancer 2 Ensembl ENCODE dbSUPER 10.9 +94.2 94176 8.8 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 SH3D21 AGO3 STK40 SNORA63C OSCP1 MAP7D1 TRAPPC3 LSM10 RNU4-27P LOC100128093
GH01J036449 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10 -52.7 -52723 1.8 HDGF PKNOX1 ARID4B NEUROD1 SIN3A ZNF48 YY1 GLIS2 ZNF207 ZNF143 OSCP1 SNORA63C LSM10 AGO3 GC01P036455
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM10 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LSM10 gene promoter:
  • LCR-F1
  • GR-alpha
  • GR
  • YY1
  • PPAR-gamma1
  • PPAR-gamma2
  • GATA-1
  • RORalpha1

Genomic Locations for LSM10 Gene

Genomic Locations for LSM10 Gene
chr1:36,391,238-36,397,959
(GRCh38/hg38)
Size:
6,722 bases
Orientation:
Minus strand
chr1:36,856,839-36,863,493
(GRCh37/hg19)
Size:
6,655 bases
Orientation:
Minus strand

Genomic View for LSM10 Gene

Genes around LSM10 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM10 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM10 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM10 Gene

Proteins for LSM10 Gene

  • Protein details for LSM10 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q969L4-LSM10_HUMAN
    Recommended name:
    U7 snRNA-associated Sm-like protein LSm10
    Protein Accession:
    Q969L4

    Protein attributes for LSM10 Gene

    Size:
    123 amino acids
    Molecular mass:
    14080 Da
    Quaternary structure:
    • Component of the heptameric ring U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Formation of the U7 snRNP is an ATP-dependent process mediated by a specialized SMN complex containing at least the Sm protein core complex and additionally, the U7-specific LSM10 and LSM11 proteins. Interacts with CLNS1A and SMN.

neXtProt entry for LSM10 Gene

Post-translational modifications for LSM10 Gene

  • Not methylated. Methylation is not necessary for interaction with SMN.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LSM10 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LSM10 Gene

Domains & Families for LSM10 Gene

Gene Families for LSM10 Gene

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

Suggested Antigen Peptide Sequences for LSM10 Gene

Graphical View of Domain Structure for InterPro Entry

Q969L4

UniProtKB/Swiss-Prot:

LSM10_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 LSM10: view

Function for LSM10 Gene

Molecular function for LSM10 Gene

UniProtKB/Swiss-Prot Function:
Appears to function in the U7 snRNP complex that is involved in histone 3-end processing. Increases U7 snRNA levels but not histone 3-end pre-mRNA processing activity, when overexpressed. Required for cell cycle progression from G1 to S phases. Binds specifically to U7 snRNA. Binds to the downstream cleavage product (DCP) of histone pre-mRNA in a U7 snRNP dependent manner.

Gene Ontology (GO) - Molecular Function for LSM10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12975319
GO:0071208 histone pre-mRNA DCP binding IEA,ISS --
GO:0071209 U7 snRNA binding IPI 18082603
genes like me logo Genes that share ontologies with LSM10: view
genes like me logo Genes that share phenotypes with LSM10: view

Animal Model Products

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 LSM10 Gene

Localization for LSM10 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM10 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 LSM10 gene
Compartment Confidence
nucleus 5
extracellular 1
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LSM10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005683 U7 snRNP IDA 11574479
GO:0015030 Cajal body IDA 11574479
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with LSM10: view

Pathways & Interactions for LSM10 Gene

genes like me logo Genes that share pathways with LSM10: view

Gene Ontology (GO) - Biological Process for LSM10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0008334 histone mRNA metabolic process TAS --
GO:0008380 RNA splicing IEA --
GO:1900087 positive regulation of G1/S transition of mitotic cell cycle IMP 16914750
genes like me logo Genes that share ontologies with LSM10: view

No data available for SIGNOR curated interactions for LSM10 Gene

Drugs & Compounds for LSM10 Gene

No Compound Related Data Available

Transcripts for LSM10 Gene

mRNA/cDNA for LSM10 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(161) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LSM10 Gene

LSM10, U7 small nuclear RNA associated:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LSM10 Gene

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

Relevant External Links for LSM10 Gene

GeneLoc Exon Structure for
LSM10
ECgene alternative splicing isoforms for
LSM10

Expression for LSM10 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LSM10 Gene

Protein differential expression in normal tissues from HIPED for LSM10 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LSM10 Gene



Protein tissue co-expression partners for LSM10 Gene

NURSA nuclear receptor signaling pathways regulating expression of LSM10 Gene:

LSM10

SOURCE GeneReport for Unigene cluster for LSM10 Gene:

Hs.603131

Evidence on tissue expression from TISSUES for LSM10 Gene

  • Eye(4.1)
genes like me logo Genes that share expression patterns with LSM10: 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 LSM10 Gene

Orthologs for LSM10 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LSM10 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LSM10 34 33
  • 99.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LSM10 34 33
  • 90.71 (n)
OneToOne
dog
(Canis familiaris)
Mammalia LSM10 34 33
  • 86.72 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Lsm10 16 34 33
  • 84.44 (n)
rat
(Rattus norvegicus)
Mammalia Lsm10 33
  • 84.44 (n)
oppossum
(Monodelphis domestica)
Mammalia LSM10 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM10 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM10 34 33
  • 73.44 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LSM10 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm10 33
  • 68.32 (n)
Str.905 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.6554 33
zebrafish
(Danio rerio)
Actinopterygii lsm10 34
  • 70 (a)
OneToOne
LOC101884591 33
  • 67.51 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4129 34
  • 28 (a)
OneToOne
Species where no ortholog for LSM10 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • 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 (Oryza sativa)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for LSM10 Gene

ENSEMBL:
Gene Tree for LSM10 (if available)
TreeFam:
Gene Tree for LSM10 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LSM10: view image

Paralogs for LSM10 Gene

(2) SIMAP similar genes for LSM10 Gene using alignment to 1 proteins:

  • LSM10_HUMAN
genes like me logo Genes that share paralogs with LSM10: view

No data available for Paralogs for LSM10 Gene

Variants for LSM10 Gene

Sequence variations from dbSNP and Humsavar for LSM10 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000103786 -- 36,397,878(-) C/T 5_prime_UTR_variant
rs1000966588 -- 36,397,649(-) A/G intron_variant
rs1001250204 -- 36,397,896(-) G/C 5_prime_UTR_variant
rs1002101570 -- 36,397,061(-) C/G/T intron_variant
rs1002153929 -- 36,397,378(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LSM10 Gene

Variant ID Type Subtype PubMed ID
esv2758931 CNV loss 17122850
esv3577808 CNV loss 25503493
nsv545998 CNV loss 21841781
nsv545999 CNV loss 21841781

Variation tolerance for LSM10 Gene

Residual Variation Intolerance Score: 39.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.91; 18.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LSM10 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM10

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM10 Gene

Disorders for LSM10 Gene

Additional Disease Information for LSM10

No disorders were found for LSM10 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSM10 Gene

Publications for LSM10 Gene

  1. ZFP100, a component of the active U7 snRNP limiting for histone pre-mRNA processing, is required for entry into S phase. (PMID: 16914750) Wagner EJ … Marzluff WF (Molecular and cellular biology 2006) 3 4 22 58
  2. Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein. (PMID: 11574479) Pillai RS … Müller B (The EMBO journal 2001) 2 3 4 58
  3. Toward an assembly line for U7 snRNPs: interactions of U7-specific Lsm proteins with PRMT5 and SMN complexes. (PMID: 16087681) Azzouz TN … Schümperli D (The Journal of biological chemistry 2005) 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for LSM10 Gene

Sources for LSM10 Gene

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