SMG6 [The Human Chemical-Genetic Interaction Map Project]

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======= SMG6 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: SMG6
  * **<color #00a2e8>Official Name</color>**: SMG6 nonsense mediated mRNA decay factor
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=23293|23293]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q86US8|Q86US8]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=SMG6&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20SMG6|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/610963|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a component of the telomerase ribonucleoprotein complex responsible for the replication and maintenance of chromosome ends. The encoded protein also plays a role in the nonsense-mediated mRNA decay (NMD) pathway, providing the endonuclease activity near the premature translation termination codon that is needed to initiate NMD. Alternatively spliced transcript variants encoding distinct protein isoforms have been described. [provided by RefSeq, Feb 2014]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Component of the telomerase ribonucleoprotein (RNP) complex that is essential for the replication of chromosome termini. May have a general role in telomere regulation. Promotes in vitro the ability of TERT to elongate telomeres. Overexpression induces telomere uncapping, chromosomal end-to-end fusions (telomeric DNA persists at the fusion points) and did not perturb TRF2 telomeric localization. Binds to the single-stranded 5'- (GTGTGG)(4)GTGT-3' telomeric DNA, but not to a telomerase RNA template component (TER).

<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'>
|EST1|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|negative regulation of telomere capping|
|DNA polymerase binding|
|telomerase holoenzyme complex|
|exon-exon junction complex|
|telomere maintenance via telomerase|
|telomerase RNA binding|
|regulation of telomere capping|
|telomeric DNA binding|
|endoribonuclease activity|
|telomere maintenance via telomere lengthening|
|ribonucleoprotein complex binding|
|RNA-dependent DNA biosynthetic process|
|negative regulation of telomere maintenance|
|chromosome, telomeric region|
|regulation of telomerase activity|
|regulation of telomere maintenance via telomerase|
|regulation of telomere maintenance via telomere lengthening|
|RNA phosphodiester bond hydrolysis, endonucleolytic|
|regulation of telomere maintenance|
|telomere maintenance|
|telomere organization|
|mRNA-containing ribonucleoprotein complex export from nucleus|
|mRNA export from nucleus|
|DNA biosynthetic process|
|regulation of DNA biosynthetic process|
|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|
|negative regulation of DNA metabolic process|
|ribonucleoprotein complex export from nucleus|
|ribonucleoprotein complex localization|
|RNA export from nucleus|
|negative regulation of chromosome organization|
|protein export from nucleus|
|mRNA transport|
|nuclear export|
|RNA phosphodiester bond hydrolysis|
|regulation of RNA stability|
|RNA transport|
|nucleic acid transport|
|establishment of RNA localization|
|nuclear-transcribed mRNA catabolic process|
|regulation of dephosphorylation|
|RNA localization|
|mRNA catabolic process|
|nucleobase-containing compound transport|
|RNA catabolic process|
|protein-containing complex localization|
|nucleocytoplasmic transport|
|nuclear transport|
|nucleic acid phosphodiester bond hydrolysis|
|anatomical structure homeostasis|
|regulation of chromosome organization|
|regulation of DNA metabolic process|
|negative regulation of organelle organization|
|nucleobase-containing compound catabolic process|
|heterocycle catabolic process|
|cellular nitrogen compound catabolic process|
|aromatic compound catabolic process|
|organic cyclic compound catabolic process|
|posttranscriptional regulation of gene expression|
|mRNA metabolic process|
|negative regulation of cellular component organization|
|DNA metabolic process|
|regulation of cellular catabolic process|
|nucleolus|
|cellular macromolecule catabolic process|
|regulation of transferase activity|
|regulation of catabolic process|
|intracellular protein transport|
|macromolecule catabolic process|
|chromosome organization|
|nucleobase-containing compound biosynthetic process|
|heterocycle biosynthetic process|
|aromatic compound biosynthetic process|
|regulation of organelle organization|
|organic cyclic compound biosynthetic process|
|RNA binding|
|negative regulation of nucleobase-containing compound metabolic process|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|cellular nitrogen compound biosynthetic process|
|homeostatic process|
|RNA metabolic process|
|cellular macromolecule biosynthetic process|
|negative regulation of gene expression|
|macromolecule biosynthetic process|
|organic substance catabolic process|
|regulation of phosphate metabolic process|
|regulation of phosphorus metabolic process|
|cellular catabolic process|
|establishment of localization in cell|
|nitrogen compound transport|
|gene expression|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' 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:exp111|R-DABN 8μM R03 exp111]]|-1.86|
|[[:results:exp72|LB-100 4.1μM R02 exp72]]|-1.72|
|[[:results:exp27|Pimelic-diphenylamide-106 0.5μM R00 exp27]]|1.83|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:b:bcl2l1|BCL2L1]]|0.484|
|[[:human genes:s:smg7|SMG7]]|0.455|
|[[:human genes:s:smg1|SMG1]]|0.43|
|[[:human genes:z:zfand5|ZFAND5]]|0.418|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 494/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|1/1|
|bile duct|19/28|
|blood|13/28|
|bone|16/26|
|breast|22/33|
|central nervous system|39/56|
|cervix|0/4|
|colorectal|10/17|
|esophagus|9/13|
|fibroblast|1/1|
|gastric|8/16|
|kidney|11/21|
|liver|14/20|
|lung|47/75|
|lymphocyte|13/16|
|ovary|21/26|
|pancreas|13/24|
|peripheral nervous system|15/16|
|plasma cell|14/15|
|prostate|1/1|
|skin|15/24|
|soft tissue|6/9|
|thyroid|1/2|
|upper aerodigestive|16/22|
|urinary tract|17/29|
|uterus|5/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 534
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.89 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='SMG6 Expression in NALM6 Cells: 5.89'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>