======= UPF1 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: UPF1
  * **<color #00a2e8>Official Name</color>**: UPF1 RNA helicase and ATPase
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=5976|5976]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q92900|Q92900]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=UPF1&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20UPF1|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/601430|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  RNA-dependent helicase and ATPase required for nonsense- mediated decay (NMD) of mRNAs containing premature stop codons. Is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. Recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1- eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) (located 50-55 or more nucleotides downstream from the termination codon) through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Phosphorylated UPF1 is recognized by EST1B/SMG5, SMG6 and SMG7 which are thought to provide a link to the mRNA degradation machinery involving exonucleolytic and endonucleolytic pathways, and to serve as adapters to protein phosphatase 2A (PP2A), thereby triggering UPF1 dephosphorylation and allowing the recycling of NMD factors. UPF1 can also activate NMD without UPF2 or UPF3, and in the absence of the NMD-enhancing downstream EJC indicative for alternative NMD pathways. Plays a role in replication-dependent histone mRNA degradation at the end of phase S; the function is independent of UPF2. For the recognition of premature termination codons (PTC) and initiation of NMD a competitive interaction between UPF1 and PABPC1 with the ribosome-bound release factors is proposed. The ATPase activity of UPF1 is required for disassembly of mRNPs undergoing NMD. Essential for embryonic viability. {ECO:0000269|PubMed:11163187, ECO:0000269|PubMed:16086026, ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:21145460, ECO:0000269|PubMed:21419344}.

<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'>
|ResIII|
|UPF1 Zn bind|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay|
|supraspliceosomal complex|
|regulation of translational termination|
|histone mRNA catabolic process|
|3-UTR-mediated mRNA destabilization|
|dosage compensation by inactivation of X chromosome|
|dosage compensation|
|exon-exon junction complex|
|telomere maintenance via semi-conservative replication|
|telomeric DNA binding|
|histone mRNA metabolic process|
|mRNA destabilization|
|RNA destabilization|
|helicase activity|
|nuclear DNA replication|
|cell cycle DNA replication|
|positive regulation of mRNA catabolic process|
|RNA helicase activity|
|positive regulation of mRNA metabolic process|
|regulation of telomere maintenance|
|P-body|
|telomere maintenance|
|telomere organization|
|mRNA-containing ribonucleoprotein complex export from nucleus|
|mRNA export from nucleus|
|nuclear chromosome, telomeric region|
|regulation of protein complex disassembly|
|chromatin|
|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|
|DNA-dependent DNA replication|
|ribonucleoprotein complex export from nucleus|
|ribonucleoprotein complex localization|
|RNA export from nucleus|
|negative regulation of translation|
|negative regulation of cellular amide metabolic process|
|protein export from nucleus|
|mRNA transport|
|nuclear export|
|cellular response to interleukin-1|
|regulation of mRNA stability|
|cellular response to lipopolysaccharide|
|regulation of RNA stability|
|nucleic acid transport|
|cellular response to molecule of bacterial origin|
|RNA transport|
|establishment of RNA localization|
|nuclear-transcribed mRNA catabolic process|
|response to interleukin-1|
|regulation of mRNA catabolic process|
|DNA replication|
|cellular response to biotic stimulus|
|mRNA catabolic process|
|RNA localization|
|regulation of gene expression, epigenetic|
|nucleobase-containing compound transport|
|RNA catabolic process|
|protein-containing complex localization|
|nucleocytoplasmic transport|
|nuclear transport|
|cell cycle phase transition|
|response to lipopolysaccharide|
|response to molecule of bacterial origin|
|regulation of mRNA metabolic process|
|anatomical structure homeostasis|
|regulation of chromosome organization|
|regulation of translation|
|regulation of DNA metabolic process|
|positive regulation of cellular catabolic process|
|nucleobase-containing compound catabolic process|
|chromatin binding|
|regulation of cellular amide metabolic process|
|positive regulation of catabolic process|
|heterocycle catabolic process|
|cellular nitrogen compound catabolic process|
|aromatic compound catabolic process|
|organic cyclic compound catabolic process|
|DNA repair|
|cellular response to lipid|
|posttranscriptional regulation of gene expression|
|response to bacterium|
|mRNA metabolic process|
|viral process|
|DNA metabolic process|
|cellular response to DNA damage stimulus|
|symbiotic process|
|interspecies interaction between organisms|
|regulation of cellular catabolic process|
|zinc ion binding|
|response to lipid|
|cellular homeostasis|
|cellular macromolecule catabolic process|
|intracellular protein transport|
|regulation of catabolic process|
|cell cycle process|
|cellular response to cytokine stimulus|
|negative regulation of cellular protein metabolic process|
|macromolecule catabolic process|
|cellular response to oxygen-containing compound|
|chromosome organization|
|response to cytokine|
|negative regulation of protein metabolic process|
|regulation of organelle organization|
|response to other organism|
|response to external biotic stimulus|
|response to biotic stimulus|
|cell cycle|
|negative regulation of cellular macromolecule biosynthetic process|
|RNA binding|
|negative regulation of macromolecule biosynthetic process|
|ATP binding|
|protein transport|
|negative regulation of cellular biosynthetic process|
|intracellular transport|
|peptide transport|
|negative regulation of biosynthetic process|
|response to oxygen-containing compound|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|homeostatic process|
|RNA metabolic process|
|cellular response to stress|
|cellular macromolecule biosynthetic process|
|negative regulation of gene expression|
|positive regulation of RNA metabolic process|
|macromolecule biosynthetic process|
|organic substance catabolic process|
|cellular catabolic process|
|establishment of localization in cell|
|nitrogen compound transport|
|positive regulation of nucleobase-containing compound metabolic process|
|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:exp28|Pimelic-diphenylamide-106 5μM R00 exp28]]|-2.38|
|[[:results:exp17|DABN 20μM R00 exp17]]|-2.06|
|[[:results:exp93|DABN racemic mixture R03 exp93]]|-1.74|
|[[:results:exp525|Sulforaphane 9μM R08 exp525]]|-1.71|
|[[:results:exp40|2-Methoxyestradiol 0.2μM R01 exp40]]|1.72|
|[[:results:exp61|YM155 0.0002μM R01 exp61]]|1.74|
|[[:results:exp159|Docetaxel 0.001 to 0.002μM on day4 R04 exp159]]|1.77|
|[[:results:exp372|Ibrutinib 1μM R07 exp372]]|1.78|
|[[:results:exp83|Trametinib 10μM R02 exp83]]|1.82|
|[[:results:exp50|Nicotinamide 2000μM R01 exp50]]|1.84|
|[[:results:exp48|Mubritinib 0.2μM R01 exp48]]|1.85|
|[[:results:exp51|Nifuroxazide 1μM R01 exp51]]|1.9|
|[[:results:exp391|Pomalidomide 20μM R07 exp391]]|1.91|
|[[:results:exp52|Ribavirin 10μM R01 exp52]]|1.98|
|[[:results:exp516|Pyrazinamide 100μM R08 exp516]]|2.01|
|[[:results:exp496|Lead acetate 990μM R08 exp496]]|2.03|
|[[:results:exp46|HMS-I1 1μM R01 exp46]]|2.08|
|[[:results:exp58|UM131593 0.1μM R01 exp58]]|2.29|
|[[:results:exp331|A-769662 20μM R07 exp331]]|2.44|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:t:tceb3cl2|TCEB3CL2]]|0.592|
|[[:human genes:p:prim1|PRIM1]]|0.588|
|[[:human genes:t:tceb3c|TCEB3C]]|0.586|
|[[:human genes:t:tceb3cl|TCEB3CL]]|0.577|
|[[:human genes:p:psmb4|PSMB4]]|0.574|
|[[:human genes:r:rad21|RAD21]]|0.541|
|[[:human genes:p:psma6|PSMA6]]|0.538|
|[[:human genes:c:ccna2|CCNA2]]|0.538|
|[[:human genes:p:psmc2|PSMC2]]|0.532|
|[[:human genes:x:xab2|XAB2]]|0.529|
|[[:human genes:s:smg1|SMG1]]|0.527|
|[[:human genes:c:col2a1|COL2A1]]|0.527|
|[[:human genes:t:tbc1d3h|TBC1D3H]]|0.525|
|[[:human genes:p:psmd3|PSMD3]]|0.522|
|[[:human genes:p:polr2j3|POLR2J3]]|0.522|
|[[:human genes:p:psmd2|PSMD2]]|0.521|
|[[:human genes:t:tbc1d3g|TBC1D3G]]|0.521|
|[[:human genes:c:cdc45|CDC45]]|0.52|
|[[:human genes:n:npipb8|NPIPB8]]|0.519|
|[[:human genes:t:tbc1d3f|TBC1D3F]]|0.518|
|[[:human genes:a:atp6v1c1|ATP6V1C1]]|0.515|
|[[:human genes:a:atp6v0c|ATP6V0C]]|0.513|
|[[:human genes:p:psmd1|PSMD1]]|0.513|
|[[:human genes:n:npipb5|NPIPB5]]|0.513|
|[[:human genes:p:pola1|POLA1]]|0.51|
|[[:human genes:c:c1qtnf9b|C1QTNF9B]]|0.504|
|[[:human genes:m:mt1e|MT1E]]|0.503|
|[[:human genes:c:cbwd3|CBWD3]]|0.503|
|[[:human genes:c:cope|COPE]]|0.502|
|[[:human genes:h:hist2h3a|HIST2H3A]]|0.5|
|[[:human genes:h:hist2h3c|HIST2H3C]]|0.5|
|[[:human genes:a:atp6v0b|ATP6V0B]]|0.5|
|[[:human genes:c:chd4|CHD4]]|0.499|
|[[:human genes:p:psmd14|PSMD14]]|0.498|
|[[:human genes:s:slc6a17|SLC6A17]]|0.498|
|[[:human genes:p:psmb2|PSMB2]]|0.497|
|[[:human genes:s:snrpa1|SNRPA1]]|0.495|
|[[:human genes:l:lrr1|LRR1]]|0.495|
|[[:human genes:r:rrp7a|RRP7A]]|0.494|
|[[:human genes:t:twistnb|TWISTNB]]|0.492|
|[[:human genes:p:psmc1|PSMC1]]|0.489|
|[[:human genes:p:pan2|PAN2]]|0.489|
|[[:human genes:c:copb1|COPB1]]|0.489|
|[[:human genes:c:chaf1a|CHAF1A]]|0.487|
|[[:human genes:t:tbc1d3c|TBC1D3C]]|0.486|
|[[:human genes:d:ddtl|DDTL]]|0.485|
|[[:human genes:r:rps2|RPS2]]|0.485|
|[[:human genes:w:wdr75|WDR75]]|0.484|
|[[:human genes:s:slc4a1|SLC4A1]]|0.483|
|[[:human genes:z:zfand5|ZFAND5]]|0.483|
|[[:human genes:a:atp6v1a|ATP6V1A]]|0.482|
|[[:human genes:s:supt6h|SUPT6H]]|0.481|
|[[:human genes:m:med17|MED17]]|0.479|
|[[:human genes:p:pole|POLE]]|0.479|
|[[:human genes:p:pola2|POLA2]]|0.479|
|[[:human genes:s:scaf1|SCAF1]]|0.478|
|[[:human genes:c:copg1|COPG1]]|0.477|
|[[:human genes:o:ogfr|OGFR]]|0.476|
|[[:human genes:p:psmb1|PSMB1]]|0.476|
|[[:human genes:c:cbwd5|CBWD5]]|0.475|
|[[:human genes:t:tbc1d3|TBC1D3]]|0.474|
|[[:human genes:m:myb|MYB]]|0.474|
|[[:human genes:t:traip|TRAIP]]|0.472|
|[[:human genes:t:tspy1|TSPY1]]|0.472|
|[[:human genes:p:pan3|PAN3]]|0.472|
|[[:human genes:c:ccdc116|CCDC116]]|0.47|
|[[:human genes:h:hap1|HAP1]]|0.469|
|[[:human genes:g:golga6l1|GOLGA6L1]]|0.469|
|[[:human genes:a:arcn1|ARCN1]]|0.468|
|[[:human genes:p:pwp2|PWP2]]|0.468|
|[[:human genes:p:polr2d|POLR2D]]|0.467|
|[[:human genes:d:ddt|DDT]]|0.466|
|[[:human genes:r:rad51|RAD51]]|0.464|
|[[:human genes:n:nup160|NUP160]]|0.464|
|[[:human genes:e:exosc5|EXOSC5]]|0.463|
|[[:human genes:r:rps19bp1|RPS19BP1]]|0.463|
|[[:human genes:t:ticrr|TICRR]]|0.462|
|[[:human genes:h:hist2h2bf|HIST2H2BF]]|0.462|
|[[:human genes:f:fam160a1|FAM160A1]]|0.462|
|[[:human genes:f:fcn2|FCN2]]|0.461|
|[[:human genes:m:myo1h|MYO1H]]|0.459|
|[[:human genes:p:psmd6|PSMD6]]|0.457|
|[[:human genes:o:orc6|ORC6]]|0.457|
|[[:human genes:t:tbc1d3k|TBC1D3K]]|0.457|
|[[:human genes:t:tbc1d3i|TBC1D3I]]|0.457|
|[[:human genes:a:acsf2|ACSF2]]|0.457|
|[[:human genes:t:tbc1d3l|TBC1D3L]]|0.457|
|[[:human genes:t:tbc1d3e|TBC1D3E]]|0.457|
|[[:human genes:k:krt78|KRT78]]|0.456|
|[[:human genes:s:ssh2|SSH2]]|0.454|
|[[:human genes:t:tp53tg3b|TP53TG3B]]|0.453|
|[[:human genes:t:tp53tg3|TP53TG3]]|0.452|
|[[:human genes:t:tp53tg3c|TP53TG3C]]|0.451|
|[[:human genes:r:rps9|RPS9]]|0.451|
|[[:human genes:z:znf830|ZNF830]]|0.451|
|[[:human genes:a:atp13a1|ATP13A1]]|0.451|
|[[:human genes:p:paf1|PAF1]]|0.451|
|[[:human genes:i:igfn1|IGFN1]]|0.45|
|[[:human genes:p:psmc6|PSMC6]]|0.448|
|[[:human genes:n:nfatc4|NFATC4]]|0.447|
|[[:human genes:s:srgap2c|SRGAP2C]]|0.447|
|[[:human genes:n:nupl1|NUPL1]]|0.446|
|[[:human genes:p:psmd11|PSMD11]]|0.446|
|[[:human genes:p:pde4dip|PDE4DIP]]|0.445|
|[[:human genes:a:aatf|AATF]]|0.444|
|[[:human genes:n:nbpf10|NBPF10]]|0.442|
|[[:human genes:o:orc1|ORC1]]|0.441|
|[[:human genes:k:kif3c|KIF3C]]|0.441|
|[[:human genes:t:tsg101|TSG101]]|0.441|
|[[:human genes:s:slc38a7|SLC38A7]]|0.44|
|[[:human genes:n:nup205|NUP205]]|0.44|
|[[:human genes:t:tspy8|TSPY8]]|0.44|
|[[:human genes:c:copz1|COPZ1]]|0.44|
|[[:human genes:i:ik|IK]]|0.438|
|[[:human genes:a:ankle2|ANKLE2]]|0.438|
|[[:human genes:c:cbwd6|CBWD6]]|0.438|
|[[:human genes:p:psma7|PSMA7]]|0.437|
|[[:human genes:c:copb2|COPB2]]|0.437|
|[[:human genes:c:c14orf93|C14orf93]]|0.435|
|[[:human genes:u:utp3|UTP3]]|0.433|
|[[:human genes:r:rpl35|RPL35]]|0.432|
|[[:human genes:c:cdca3|CDCA3]]|0.432|
|[[:human genes:z:znf106|ZNF106]]|0.432|
|[[:human genes:k:kpnb1|KPNB1]]|0.431|
|[[:human genes:g:golga6l6|GOLGA6L6]]|0.431|
|[[:human genes:h:hist1h2be|HIST1H2BE]]|0.43|
|[[:human genes:k:kctd17|KCTD17]]|0.429|
|[[:human genes:h:hivep3|HIVEP3]]|0.429|
|[[:human genes:t:tyms|TYMS]]|0.428|
|[[:human genes:m:med14|MED14]]|0.428|
|[[:human genes:z:znf655|ZNF655]]|0.428|
|[[:human genes:m:mcoln1|MCOLN1]]|0.426|
|[[:human genes:v:vasn|VASN]]|0.426|
|[[:human genes:l:lad1|LAD1]]|0.426|
|[[:human genes:s:smg7|SMG7]]|0.426|
|[[:human genes:p:psmc3|PSMC3]]|0.425|
|[[:human genes:r:rps12|RPS12]]|0.424|
|[[:human genes:s:stil|STIL]]|0.424|
|[[:human genes:k:krt2|KRT2]]|0.423|
|[[:human genes:r:rrn3|RRN3]]|0.423|
|[[:human genes:l:lrrc56|LRRC56]]|0.422|
|[[:human genes:n:nol12|NOL12]]|0.422|
|[[:human genes:t:tfip11|TFIP11]]|0.422|
|[[:human genes:r:rps7|RPS7]]|0.421|
|[[:human genes:a:ankle1|ANKLE1]]|0.421|
|[[:human genes:c:ctage4|CTAGE4]]|0.42|
|[[:human genes:v:vps52|VPS52]]|0.419|
|[[:human genes:d:dnm2|DNM2]]|0.419|
|[[:human genes:s:s1pr4|S1PR4]]|0.419|
|[[:human genes:g:golga6l3|GOLGA6L3]]|0.417|
|[[:human genes:p:psma1|PSMA1]]|0.417|
|[[:human genes:t:timeless|TIMELESS]]|0.417|
|[[:human genes:p:psmc5|PSMC5]]|0.416|
|[[:human genes:s:supt5h|SUPT5H]]|0.416|
|[[:human genes:s:sult1a4|SULT1A4]]|0.414|
|[[:human genes:m:mphosph10|MPHOSPH10]]|0.414|
|[[:human genes:w:wdr43|WDR43]]|0.414|
|[[:human genes:f:fbxo5|FBXO5]]|0.414|
|[[:human genes:s:sult1a3|SULT1A3]]|0.414|
|[[:human genes:t:top1mt|TOP1MT]]|0.414|
|[[:human genes:o:osbp|OSBP]]|0.414|
|[[:human genes:d:dnttip2|DNTTIP2]]|0.413|
|[[:human genes:m:med29|MED29]]|0.413|
|[[:human genes:s:sprr2b|SPRR2B]]|0.413|
|[[:human genes:p:psap|PSAP]]|0.413|
|[[:human genes:r:rnpc3|RNPC3]]|0.413|
|[[:human genes:t:tpx2|TPX2]]|0.413|
|[[:human genes:p:pbxip1|PBXIP1]]|0.412|
|[[:human genes:r:rbbp5|RBBP5]]|0.412|
|[[:human genes:r:rhbdd3|RHBDD3]]|0.409|
|[[:human genes:e:exosc9|EXOSC9]]|0.409|
|[[:human genes:b:bcl2l1|BCL2L1]]|0.408|
|[[:human genes:c:ctage9|CTAGE9]]|0.408|
|[[:human genes:b:brix1|BRIX1]]|0.408|
|[[:human genes:d:dtl|DTL]]|0.408|
|[[:human genes:r:rrp15|RRP15]]|0.407|
|[[:human genes:r:riok2|RIOK2]]|0.407|
|[[:human genes:a:atp6v1b2|ATP6V1B2]]|0.407|
|[[:human genes:e:exosc6|EXOSC6]]|0.407|
|[[:human genes:n:numa1|NUMA1]]|0.406|
|[[:human genes:d:dock6|DOCK6]]|0.405|
|[[:human genes:t:tuba8|TUBA8]]|0.405|
|[[:human genes:c:cgb2|CGB2]]|0.405|
|[[:human genes:p:psmd7|PSMD7]]|0.404|
|[[:human genes:c:chchd3|CHCHD3]]|0.404|
|[[:human genes:d:dido1|DIDO1]]|0.404|
|[[:human genes:s:smc3|SMC3]]|0.404|
|[[:human genes:g:golga8j|GOLGA8J]]|0.404|
|[[:human genes:n:nelfcd|NELFCD]]|0.404|
|[[:human genes:s:sema6b|SEMA6B]]|0.403|
|[[:human genes:r:rpp40|RPP40]]|0.402|
|[[:human genes:p:psmb3|PSMB3]]|0.401|
|[[:human genes:u:uqcrh|UQCRH]]|0.401|
|[[:human genes:f:fam231a|FAM231A]]|0.4|
|[[:human genes:n:nop16|NOP16]]|0.4|
|[[:human genes:g:golga8o|GOLGA8O]]|0.4|
|[[:human genes:f:fam231c|FAM231C]]|0.4|
|[[:human genes:c:cebpz|CEBPZ]]|0.4|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 420/726
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|1/1|
|bile duct|19/28|
|blood|10/28|
|bone|10/25|
|breast|20/33|
|central nervous system|15/56|
|cervix|3/4|
|colorectal|13/17|
|esophagus|9/13|
|fibroblast|0/1|
|gastric|8/15|
|kidney|11/21|
|liver|9/20|
|lung|51/75|
|lymphocyte|11/14|
|ovary|19/26|
|pancreas|17/24|
|peripheral nervous system|11/16|
|plasma cell|11/15|
|prostate|1/1|
|skin|11/24|
|soft tissue|0/7|
|thyroid|1/2|
|upper aerodigestive|17/22|
|urinary tract|18/29|
|uterus|3/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 489
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.67 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='UPF1 Expression in NALM6 Cells: 7.67'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>