Aliases for LSM11 Gene

Aliases for LSM11 Gene

  • LSM11, U7 Small Nuclear RNA Associated 2 3 5
  • U7 SnRNA-Associated Sm-Like Protein LSm11 3 4
  • LSM11 Homolog, U7 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • FLJ38273 2
  • LSM11 5

External Ids for LSM11 Gene

Previous GeneCards Identifiers for LSM11 Gene

  • GC05P157151
  • GC05P157103
  • GC05P157171
  • GC05P152259

Summaries for LSM11 Gene

GeneCards Summary for LSM11 Gene

LSM11 (LSM11, U7 Small Nuclear RNA Associated) is a Protein Coding gene. Among its related pathways are Processing of Capped Intronless Pre-mRNA and Tat-mediated elongation of the HIV-1 transcript. Gene Ontology (GO) annotations related to this gene include U7 snRNA binding.

UniProtKB/Swiss-Prot Summary for LSM11 Gene

  • Component of the U7 snRNP complex that is involved in the histone 3'-end pre-mRNA processing (By similarity). 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 the Sm-binding site of U7 snRNA.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LSM11 Gene

Genomics for LSM11 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LSM11 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
GH05J157743 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 255.9 +0.5 484 2.4 BCLAF1 SP1 ZNF654 ZNF207 NCOR1 MYC ZNF600 IKZF1 SSRP1 KLF9 LSM11 RF00017-4569 THG1L ENSG00000253630 lnc-CLINT1-3 CLINT1
GH05J158460 Enhancer 1.1 Ensembl ENCODE 10.1 +721.4 721394 8.6 SSRP1 CEBPA ATF3 YY1 MXD4 FOXA1 HOMEZ KMT2B THAP11 FOXA2 ENSG00000272085 LSM11 ENSG00000254135 LINC02227 CLINT1 EBF1
GH05J157747 Enhancer 0.9 Ensembl ENCODE 5 +5.3 5324 3.5 ZNF600 JUND ZNF592 ZIC2 FEZF1 FOXA2 RXRA CTCF RAD21 PRDM6 ENSG00000253630 lnc-CLINT1-3 piR-50444-378 THG1L LSM11 CYFIP2 CLINT1
GH05J157446 Enhancer 0.3 ENCODE 4.3 -296.3 -296316 1.1 POLR2A KLF1 NIPAL4 FNDC9 ENSG00000251405 LSM11 NIPAL4-DT ENSG00000285868 lnc-CYFIP2-2 ADAM19
GH05J157759 Enhancer 0.2 Ensembl 4.9 +16.1 16089 2.8 RNU6-260P CLINT1 RNU2-48P THG1L LSM11 CYFIP2 HSALNG0046142 piR-50444-378
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LSM11 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LSM11

Top Transcription factor binding sites by QIAGEN in the LSM11 gene promoter:
  • CREB
  • deltaCREB
  • FAC1
  • NF-1/L
  • p53
  • RORalpha2
  • RSRFC4
  • S8
  • STAT3
  • TGIF

Genomic Locations for LSM11 Gene

Latest Assembly
chr5:157,743,712-157,760,709
(GRCh38/hg38)
Size:
16,998 bases
Orientation:
Plus strand

Previous Assembly
chr5:157,170,720-157,187,717
(GRCh37/hg19 by Entrez Gene)
Size:
16,998 bases
Orientation:
Plus strand

chr5:157,170,703-157,187,717
(GRCh37/hg19 by Ensembl)
Size:
17,015 bases
Orientation:
Plus strand

Genomic View for LSM11 Gene

Genes around LSM11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LSM11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM11 Gene

Proteins for LSM11 Gene

  • Protein details for LSM11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P83369-LSM11_HUMAN
    Recommended name:
    U7 snRNA-associated Sm-like protein LSm11
    Protein Accession:
    P83369
    Secondary Accessions:
    • A0AVQ1
    • Q7Z7P0
    • Q8N975

    Protein attributes for LSM11 Gene

    Size:
    360 amino acids
    Molecular mass:
    39500 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 LSM10, SMN, SNRPB and ZNF473. Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Interacts (via the Sm domains) with CLNS1A. Interacts with PRMT5 and WDR77 (By similarity).

    Three dimensional structures from OCA and Proteopedia for LSM11 Gene

neXtProt entry for LSM11 Gene

Post-translational modifications for LSM11 Gene

Other Protein References for LSM11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LSM11 Gene

Domains & Families for LSM11 Gene

Gene Families for LSM11 Gene

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

Protein Domains for LSM11 Gene

InterPro:
Blocks:
  • Small nuclear ribonucleoprotein (Sm protein)
  • Like-Sm ribonucleoprotein-related, core

Suggested Antigen Peptide Sequences for LSM11 Gene

GenScript: Design optimal peptide antigens:
  • U7 snRNA-associated Sm-like protein LSm11 (LSM11_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P83369

UniProtKB/Swiss-Prot:

LSM11_HUMAN :
  • The C-terminal SM 1 domain is both necessary for the binding to the Sm-binding site of U7 snRNA and U7 snRNP assembly (By similarity). The N-terminal domain is essential for histone pre-mRNA cleavage. Amino acids 63-82 are sufficient to interact with ZNF473.
  • Belongs to the snRNP Sm proteins family.
Domain:
  • The C-terminal SM 1 domain is both necessary for the binding to the Sm-binding site of U7 snRNA and U7 snRNP assembly (By similarity). The N-terminal domain is essential for histone pre-mRNA cleavage. Amino acids 63-82 are sufficient to interact with ZNF473.
Family:
  • Belongs to the snRNP Sm proteins family.
genes like me logo Genes that share domains with LSM11: view

Function for LSM11 Gene

Molecular function for LSM11 Gene

UniProtKB/Swiss-Prot Function:
Component of the U7 snRNP complex that is involved in the histone 3'-end pre-mRNA processing (By similarity). 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 the Sm-binding site of U7 snRNA.

Phenotypes From GWAS Catalog for LSM11 Gene

Gene Ontology (GO) - Molecular Function for LSM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IPI 12975319
GO:0071209 U7 snRNA binding IBA,IPI 18082603
genes like me logo Genes that share ontologies with LSM11: view
genes like me logo Genes that share phenotypes with LSM11: view

Animal Models for LSM11 Gene

MGI Knock Outs for LSM11:
  • Lsm11 Lsm11<tm1a(KOMP)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM11

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LSM11 Gene

Localization for LSM11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM11 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 LSM11 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for LSM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 12975319
GO:0005654 nucleoplasm TAS --
GO:0005683 U7 snRNP IBA,ISS --
GO:0005697 telomerase holoenzyme complex IDA 18082603
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with LSM11: view

Pathways & Interactions for LSM11 Gene

genes like me logo Genes that share pathways with LSM11: view

Gene Ontology (GO) - Biological Process for LSM11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0006398 mRNA 3'-end processing by stem-loop binding and cleavage IBA,ISS --
GO:0008334 histone mRNA metabolic process TAS --
GO:1900087 positive regulation of G1/S transition of mitotic cell cycle IMP 16914750
genes like me logo Genes that share ontologies with LSM11: view

No data available for SIGNOR curated interactions for LSM11 Gene

Drugs & Compounds for LSM11 Gene

No Compound Related Data Available

Transcripts for LSM11 Gene

mRNA/cDNA for LSM11 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LSM11

Alternative Splicing Database (ASD) splice patterns (SP) for LSM11 Gene

No ASD Table

Relevant External Links for LSM11 Gene

GeneLoc Exon Structure for
LSM11

Expression for LSM11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LSM11 Gene

Protein differential expression in normal tissues from HIPED for LSM11 Gene

This gene is overexpressed in Breast (28.0), Lung (13.4), and Plasma (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LSM11 Gene



Protein tissue co-expression partners for LSM11 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LSM11

SOURCE GeneReport for Unigene cluster for LSM11 Gene:

Hs.631954

Evidence on tissue expression from TISSUES for LSM11 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with LSM11: view

Primer products for research

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 LSM11 Gene

Orthologs for LSM11 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LSM11 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LSM11 29 30
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LSM11 29 30
  • 90.53 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lsm11 29
  • 85.38 (n)
Mouse
(Mus musculus)
Mammalia Lsm11 29 16 30
  • 85.05 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LSM11 30
  • 82 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LSM11 30
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LSM11 29 30
  • 65.91 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LSM11 30
  • 54 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lsm11 29
  • 60 (n)
African clawed frog
(Xenopus laevis)
Amphibia LSM11 29
Zebrafish
(Danio rerio)
Actinopterygii lsm11 30 30
  • 47 (a)
OneToMany
Dr.15509 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13176 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 27 (a)
OneToOne
Species where no ortholog for LSM11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Dog (Canis familiaris)
  • 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 LSM11 Gene

ENSEMBL:
Gene Tree for LSM11 (if available)
TreeFam:
Gene Tree for LSM11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LSM11: view image
Alliance of Genome Resources:
Additional Orthologs for LSM11

Paralogs for LSM11 Gene

No data available for Paralogs for LSM11 Gene

Variants for LSM11 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LSM11 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LSM11 Gene

Variant ID Type Subtype PubMed ID
esv2759389 CNV loss 17122850
nsv5090 CNV insertion 18451855

Variation tolerance for LSM11 Gene

Residual Variation Intolerance Score: 17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.32; 41.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LSM11 Gene

Human Gene Mutation Database (HGMD)
LSM11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM11
Leiden Open Variation Database (LOVD)
LSM11

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LSM11 Gene

Disorders for LSM11 Gene

Additional Disease Information for LSM11

No disorders were found for LSM11 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LSM11 Gene

Publications for LSM11 Gene

  1. Unique Sm core structure of U7 snRNPs: assembly by a specialized SMN complex and the role of a new component, Lsm11, in histone RNA processing. (PMID: 12975319) Pillai RS … Schümperli D (Genes & development 2003) 2 3 4 22
  2. 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
  3. Conserved zinc fingers mediate multiple functions of ZFP100, a U7snRNP associated protein. (PMID: 16714279) Wagner EJ … Marzluff WF (RNA (New York, N.Y.) 2006) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 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 LSM11 Gene

Sources for LSM11 Gene