RNF40 [The Human Chemical-Genetic Interaction Map Project]

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======= RNF40 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: RNF40
  * **<color #00a2e8>Official Name</color>**: ring finger protein 40
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=9810|9810]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/O75150|O75150]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=RNF40&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20RNF40|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/607700|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. {ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:19410543}.

<button type='default' 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'>
No Pfam Domain information is available for this gene.
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|positive regulation of histone H2B ubiquitination|
|positive regulation of histone ubiquitination|
|HULC complex|
|regulation of histone H2B ubiquitination|
|negative regulation of mRNA polyadenylation|
|negative regulation of mRNA 3-end processing|
|regulation of histone ubiquitination|
|histone H2B ubiquitination|
|positive regulation of protein polyubiquitination|
|regulation of mRNA polyadenylation|
|regulation of protein polyubiquitination|
|syntaxin-1 binding|
|regulation of mRNA 3-end processing|
|negative regulation of mRNA processing|
|histone monoubiquitination|
|ubiquitin conjugating enzyme binding|
|histone ubiquitination|
|axon terminus|
|protein monoubiquitination|
|extrinsic component of membrane|
|mRNA 3-UTR binding|
|negative regulation of mRNA metabolic process|
|positive regulation of histone modification|
|positive regulation of chromatin organization|
|positive regulation of proteasomal protein catabolic process|
|ubiquitin ligase complex|
|positive regulation of protein ubiquitination|
|positive regulation of proteolysis involved in cellular protein catabolic process|
|positive regulation of protein modification by small protein conjugation or removal|
|regulation of mRNA processing|
|positive regulation of cellular protein catabolic process|
|regulation of histone modification|
|positive regulation of chromosome organization|
|regulation of proteasomal protein catabolic process|
|regulation of chromatin organization|
|regulation of protein ubiquitination|
|positive regulation of protein catabolic process|
|regulation of proteolysis involved in cellular protein catabolic process|
|regulation of protein modification by small protein conjugation or removal|
|ubiquitin-protein transferase activity|
|regulation of cellular protein catabolic process|
|protein-containing complex binding|
|ubiquitin protein ligase binding|
|neuron projection|
|regulation of mRNA metabolic process|
|regulation of chromosome organization|
|positive regulation of proteolysis|
|positive regulation of cellular catabolic process|
|histone modification|
|covalent chromatin modification|
|regulation of protein catabolic process|
|response to peptide hormone|
|positive regulation of catabolic process|
|response to peptide|
|ubiquitin-dependent protein catabolic process|
|modification-dependent protein catabolic process|
|modification-dependent macromolecule catabolic process|
|proteolysis involved in cellular protein catabolic process|
|cellular protein catabolic process|
|positive regulation of organelle organization|
|regulation of mitotic cell cycle|
|protein catabolic process|
|protein ubiquitination|
|chromatin organization|
|regulation of proteolysis|
|protein modification by small protein conjugation|
|regulation of cellular catabolic process|
|protein homodimerization activity|
|cellular macromolecule catabolic process|
|response to hormone|
|protein modification by small protein conjugation or removal|
|regulation of catabolic process|
|response to organonitrogen compound|
|macromolecule catabolic process|
|organonitrogen compound catabolic process|
|chromosome organization|
|response to nitrogen compound|
|regulation of cell cycle|
|positive regulation of cellular component organization|
|positive regulation of protein modification process|
|proteolysis|
|regulation of organelle organization|
|negative regulation of RNA metabolic process|
|negative regulation of nucleobase-containing compound metabolic process|
|response to endogenous stimulus|
|response to oxygen-containing compound|
|positive regulation of cellular protein metabolic process|
|positive regulation of protein metabolic process|
|negative regulation of gene expression|
|organic substance catabolic process|
|cellular catabolic process|
|regulation of protein modification process|
|membrane|
</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:exp134|MS023 2μM R03 exp134]]|-2.26|
|[[:results:exp529|Thimerosal 0.85μM R08 exp529]]|-1.86|
|[[:results:exp390|Pifithrin-alpha 20μM R07 exp390]]|-1.82|
|[[:results:exp502|Milciclib 2μM R08 exp502]]|-1.71|
|[[:results:exp477|DKK1 89ng/ml R08 exp477]]|1.88|
|[[:results:exp107|UMK57 0.6μM R03 exp107]]|2.07|
|[[:results:exp231|Epothilone-B 0.0015μM R05 exp231]]|2.08|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:r:ruvbl2|RUVBL2]]|0.479|
|[[:human genes:r:rnf20|RNF20]]|0.43|
</modal>

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

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 1307
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.9 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='RNF40 Expression in NALM6 Cells: 6.9'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>