LSM6 [The Human Chemical-Genetic Interaction Map Project]

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======= LSM6 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: LSM6
  * **<color #00a2e8>Official Name</color>**: LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=11157|11157]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/P62312|P62312]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=LSM6&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20LSM6|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/607286|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity). {ECO:0000250}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|LSM|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|Lsm2-8 complex|
|U6 snRNP|
|small nucleolar ribonucleoprotein complex|
|small nuclear ribonucleoprotein complex|
|exonucleolytic catabolism of deadenylated mRNA|
|U4/U6 x U5 tri-snRNP complex|
|nuclear-transcribed mRNA catabolic process, exonucleolytic|
|maturation of SSU-rRNA|
|U2-type precatalytic spliceosome|
|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay|
|ribosomal small subunit biogenesis|
|P-body|
|tRNA processing|
|tRNA metabolic process|
|nuclear-transcribed mRNA catabolic process|
|rRNA processing|
|mRNA catabolic process|
|rRNA metabolic process|
|RNA catabolic process|
|RNA splicing, via transesterification reactions with bulged adenosine as nucleophile|
|mRNA splicing, via spliceosome|
|ribosome biogenesis|
|RNA splicing, via transesterification reactions|
|nucleobase-containing compound catabolic process|
|ncRNA processing|
|RNA splicing|
|heterocycle catabolic process|
|cellular nitrogen compound catabolic process|
|aromatic compound catabolic process|
|ribonucleoprotein complex biogenesis|
|ncRNA metabolic process|
|mRNA processing|
|organic cyclic compound catabolic process|
|mRNA metabolic process|
|nucleolus|
|RNA processing|
|cellular macromolecule catabolic process|
|macromolecule catabolic process|
|RNA binding|
|RNA metabolic process|
|negative regulation of gene expression|
|organic substance catabolic process|
|cellular catabolic process|
|gene expression|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='default' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp211|AICAR 240μM R05 exp211]]|-2.14|
|[[:results:exp329|Hydroxyurea 100μM R07 exp329]]|-2.08|
|[[:results:exp418|Tunicamycin 0.04μM R07 exp418]]|-1.96|
|[[:results:exp224|CB-839 10μM R05 exp224]]|-1.91|
|[[:results:exp496|Lead acetate 990μM R08 exp496]]|-1.81|
|[[:results:exp430|Rifampicin 30μM R08 exp430]]|-1.81|
|[[:results:exp113|1-Methyl-nicotinamide-chloride 1000μM R03 exp113]]|1.76|
|[[:results:exp142|OICR-9429 10μM R03 exp142]]|1.84|
|[[:results:exp222|Betulinic acid 10 to 15μM on day4 R05 exp222]]|2.01|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
No correlation found to any other genes in chemogenomics.
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 443/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|20/28|
|blood|10/28|
|bone|18/26|
|breast|22/33|
|central nervous system|46/56|
|cervix|4/4|
|colorectal|6/17|
|esophagus|4/13|
|fibroblast|0/1|
|gastric|9/16|
|kidney|10/21|
|liver|12/20|
|lung|37/75|
|lymphocyte|9/16|
|ovary|20/26|
|pancreas|15/24|
|peripheral nervous system|12/16|
|plasma cell|3/15|
|prostate|1/1|
|skin|13/24|
|soft tissue|7/9|
|thyroid|1/2|
|upper aerodigestive|12/22|
|urinary tract|18/29|
|uterus|2/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 2009
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 4.99 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='LSM6 Expression in NALM6 Cells: 4.99'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>