RTF1 [The Human Chemical-Genetic Interaction Map Project]

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======= RTF1 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: RTF1
  * **<color #00a2e8>Official Name</color>**: RTF1 homolog, Paf1/RNA polymerase II complex component
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=23168|23168]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q92541|Q92541]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=RTF1&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20RTF1|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/611633|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity). {ECO:0000250, ECO:0000269|PubMed:19345177, ECO:0000269|PubMed:20178742}.

<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'>
|Plus-3|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|RNA polymerase II C-terminal domain phosphoserine binding|
|Cdc73/Paf1 complex|
|endodermal cell fate commitment|
|histone H3-K4 trimethylation|
|positive regulation of histone H3-K4 methylation|
|positive regulation of transcription elongation from RNA polymerase II promoter|
|blastocyst growth|
|regulation of histone H3-K4 methylation|
|cell fate commitment involved in formation of primary germ layer|
|peptidyl-lysine trimethylation|
|regulation of transcription elongation from RNA polymerase II promoter|
|positive regulation of DNA-templated transcription, elongation|
|histone H3-K4 methylation|
|positive regulation of histone methylation|
|endodermal cell differentiation|
|endoderm formation|
|regulation of DNA-templated transcription, elongation|
|regulation of histone methylation|
|histone lysine methylation|
|endoderm development|
|transcription elongation from RNA polymerase II promoter|
|peptidyl-lysine methylation|
|DNA-templated transcription, elongation|
|positive regulation of histone modification|
|histone methylation|
|blastocyst development|
|positive regulation of chromatin organization|
|single-stranded DNA binding|
|formation of primary germ layer|
|protein alkylation|
|protein methylation|
|stem cell population maintenance|
|maintenance of cell number|
|regulation of histone modification|
|gastrulation|
|positive regulation of chromosome organization|
|regulation of chromatin organization|
|cell fate commitment|
|macromolecule methylation|
|methylation|
|peptidyl-lysine modification|
|regulation of chromosome organization|
|Wnt signaling pathway|
|cell-cell signaling by wnt|
|histone modification|
|covalent chromatin modification|
|in utero embryonic development|
|developmental growth|
|growth|
|cell surface receptor signaling pathway involved in cell-cell signaling|
|transcription by RNA polymerase II|
|embryonic morphogenesis|
|positive regulation of organelle organization|
|chordate embryonic development|
|transcription, DNA-templated|
|nucleic acid-templated transcription|
|embryo development ending in birth or egg hatching|
|RNA biosynthetic process|
|protein ubiquitination|
|chromatin organization|
|protein modification by small protein conjugation|
|nucleolus|
|negative regulation of transcription by RNA polymerase II|
|peptidyl-amino acid modification|
|anatomical structure formation involved in morphogenesis|
|embryo development|
|protein modification by small protein conjugation or removal|
|chromosome organization|
|nucleobase-containing compound biosynthetic process|
|cell-cell signaling|
|heterocycle biosynthetic process|
|aromatic compound biosynthetic process|
|negative regulation of transcription, DNA-templated|
|positive regulation of cellular component organization|
|positive regulation of transcription by RNA polymerase II|
|positive regulation of protein modification process|
|negative regulation of nucleic acid-templated transcription|
|negative regulation of RNA biosynthetic process|
|regulation of organelle organization|
|organic cyclic compound biosynthetic process|
|negative regulation of RNA metabolic process|
|negative regulation of cellular macromolecule biosynthetic process|
|RNA binding|
|negative regulation of nucleobase-containing compound metabolic process|
|negative regulation of macromolecule biosynthetic process|
|negative regulation of cellular biosynthetic process|
|positive regulation of transcription, DNA-templated|
|negative regulation of biosynthetic process|
|positive regulation of cellular protein metabolic process|
|cellular nitrogen compound biosynthetic process|
|positive regulation of nucleic acid-templated transcription|
|positive regulation of RNA biosynthetic process|
|RNA metabolic process|
|positive regulation of protein metabolic process|
|cellular macromolecule biosynthetic process|
|negative regulation of gene expression|
|positive regulation of RNA metabolic process|
|tissue development|
|macromolecule biosynthetic process|
|regulation of protein modification process|
|positive regulation of nucleobase-containing compound metabolic process|
|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:exp430|Rifampicin 30μM R08 exp430]]|-2.06|
|[[:results:exp346|CoCl2 18μM R07 exp346]]|-2.02|
|[[:results:exp292|Menadione 5μM R06 exp292]]|-1.98|
|[[:results:exp293|Myriocin 25μM R06 exp293]]|-1.94|
|[[:results:exp67|BVD-523 15μM R02 exp67]]|-1.9|
|[[:results:exp320|ABT-702 5μM plus CoCl2 18μM R07 exp320]]|-1.88|
|[[:results:exp6|Bortezomib 0.005μM R00 exp6]]|-1.88|
|[[:results:exp165|RO-3306 3 to 4μM on day4 R04 exp165]]|-1.87|
|[[:results:exp72|LB-100 4.1μM R02 exp72]]|-1.82|
|[[:results:exp341|BRD2 inhibitor II 20μM R07 exp341]]|-1.8|
|[[:results:exp389|PF-06409577 20μM R07 exp389]]|-1.74|
|[[:results:exp175|3-Bromopyruvate 7μM R04 exp175]]|-1.7|
|[[:results:exp536|Vitamin-D3 40μM R08 exp536]]|2.17|
</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: 24/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|2/28|
|bone|0/26|
|breast|0/33|
|central nervous system|1/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|1/16|
|kidney|0/21|
|liver|1/20|
|lung|4/75|
|lymphocyte|1/16|
|ovary|2/26|
|pancreas|1/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/9|
|thyroid|0/2|
|upper aerodigestive|1/22|
|urinary tract|1/29|
|uterus|1/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 2604
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.87 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='RTF1 Expression in NALM6 Cells: 6.87'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>