======= UPF3B =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: UPF3B
  * **<color #00a2e8>Official Name</color>**: UPF3B regulator of nonsense mediated mRNA decay
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=65109|65109]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q9BZI7|Q9BZI7]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=UPF3B&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20UPF3B|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/300298|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome X. Two splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Involved in nonsense-mediated decay (NMD) of mRNAs containing premature stop codons by associating with the nuclear exon junction complex (EJC) and serving as link between the EJC core and NMD machinery. Recruits UPF2 at the cytoplasmic side of the nuclear envelope and the subsequent formation of an UPF1-UPF2- UPF3 surveillance complex (including UPF1 bound to release factors at the stalled ribosome) is believed to activate NMD. In cooperation with UPF2 stimulates both ATPase and RNA helicase activities of UPF1. Binds spliced mRNA upstream of exon-exon junctions. In vitro, stimulates translation; the function is independent of association with UPF2 and components of the EJC core. {ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:12718880, ECO:0000269|PubMed:16209946, ECO:0000269|PubMed:16601204, ECO:0000269|PubMed:18066079}.

<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'>
|Smg4 UPF3|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|exon-exon junction complex|
|structural constituent of nuclear pore|
|mRNA 3-end processing|
|mRNA-containing ribonucleoprotein complex export from nucleus|
|mRNA export from nucleus|
|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|
|ribonucleoprotein complex export from nucleus|
|ribonucleoprotein complex localization|
|positive regulation of translation|
|RNA export from nucleus|
|RNA 3-end processing|
|protein export from nucleus|
|positive regulation of cellular amide metabolic process|
|mRNA transport|
|microtubule organizing center|
|nuclear export|
|mRNA binding|
|RNA transport|
|nucleic acid transport|
|establishment of RNA localization|
|nuclear-transcribed mRNA catabolic process|
|RNA localization|
|mRNA catabolic process|
|nucleobase-containing compound transport|
|RNA catabolic process|
|protein-containing complex localization|
|nucleocytoplasmic transport|
|nuclear transport|
|mRNA splicing, via spliceosome|
|RNA splicing, via transesterification reactions with bulged adenosine as nucleophile|
|RNA splicing, via transesterification reactions|
|regulation of translation|
|nucleobase-containing compound catabolic process|
|RNA splicing|
|regulation of cellular amide metabolic process|
|heterocycle catabolic process|
|cellular nitrogen compound catabolic process|
|aromatic compound catabolic process|
|mRNA processing|
|organic cyclic compound catabolic process|
|posttranscriptional regulation of gene expression|
|mRNA metabolic process|
|nucleolus|
|RNA processing|
|cellular macromolecule catabolic process|
|intracellular protein transport|
|macromolecule catabolic process|
|RNA binding|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|positive regulation of cellular protein metabolic process|
|establishment of protein localization|
|RNA metabolic process|
|positive regulation of protein metabolic process|
|negative regulation of gene expression|
|organic substance catabolic process|
|cellular catabolic process|
|establishment of localization in cell|
|nitrogen compound transport|
|positive regulation of macromolecule biosynthetic process|
|positive regulation of cellular biosynthetic process|
|positive regulation of gene expression|
|gene expression|
|positive regulation of biosynthetic process|
</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:exp450|Artemisinin 50μM R08 exp450]]|-2.43|
|[[:results:exp436|Dynasore 7μM R08 exp436]]|-2.3|
|[[:results:exp409|THZ531 0.11μM R07 exp409]]|-2.29|
|[[:results:exp227|Cryptotanshinone 12μM R05 exp227]]|-2.26|
|[[:results:exp489|Hippuristanol 0.12μM R08 exp489 no dilution day6]]|-2.21|
|[[:results:exp180|Dynasore 10μM R04 exp180]]|-2.09|
|[[:results:exp458|Bisphenol S 100μM R08 exp458]]|-1.97|
|[[:results:exp122|Golgicide-A 4μM R03 exp122]]|-1.89|
|[[:results:exp25|Oligomycin-A 2μM R00 exp25]]|-1.87|
|[[:results:exp7|Bortezomib 0.05μM R00 exp7]]|-1.81|
|[[:results:exp382|Palbociclib 1μM R07 exp382]]|-1.75|
|[[:results:exp259|6-Thio-2-deoxyguanosine 2μM R06 exp259]]|-1.74|
|[[:results:exp492|iCRT14 30μM R08 exp492]]|-1.74|
|[[:results:exp472|CI-1040 9.5μM R08 exp472]]|1.74|
|[[:results:exp36|TRAIL 50ng/ml R00 exp36]]|1.95|
</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: 0/683
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/26|
|bone|0/25|
|breast|0/30|
|central nervous system|0/49|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/11|
|fibroblast|0/1|
|gastric|0/14|
|kidney|0/18|
|liver|0/19|
|lung|0/72|
|lymphocyte|0/14|
|ovary|0/25|
|pancreas|0/22|
|peripheral nervous system|0/15|
|plasma cell|0/12|
|prostate|0/1|
|skin|0/20|
|soft tissue|0/7|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/28|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 13651
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.96 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='UPF3B Expression in NALM6 Cells: 5.96'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>