Description: Homo sapiens Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) (PAF1), transcript variant 1, mRNA. RefSeq Summary (NM_019088): This gene encodes a subunit of the polymerase associated factor (PAF1) complex. The PAF1 complex interacts with RNA polymerase II and plays a role in transcription elongation as well as histone modifications including ubiquitylation and methylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]. Transcript (Including UTRs) Position: hg19 chr19:39,876,270-39,881,835 Size: 5,566 Total Exon Count: 14 Strand: - Coding Region Position: hg19 chr19:39,876,631-39,881,504 Size: 4,874 Coding Exon Count: 14
ID:PAF1_HUMAN DESCRIPTION: RecName: Full=RNA polymerase II-associated factor 1 homolog; Short=hPAF1; AltName: Full=Pancreatic differentiation protein 2; FUNCTION: 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 MLL1; it promotes leukemogenesis though association with MLL-rearranged oncoproteins, such as MLL-MLLT3/AF9 and MLL-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. Connects PAF1C with the RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors. Has oncogenic activity in vivo and in vitro. SUBUNIT: Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Interacts with POLR2A, TCEA1, TTC37, MLL, SUPT5H, RNF20 and RNF40. Interacts with UBE2E1. Interacts with influenza A strain H3N2 NS1 protein; the interaction interferes with host cell gene transcription, specifically with that of antiviral genes. INTERACTION: Q6P1J9:CDC73; NbExp=25; IntAct=EBI-2607770, EBI-930143; Q6PD62:CTR9; NbExp=22; IntAct=EBI-2607770, EBI-1019583; Q8WVC0:LEO1; NbExp=17; IntAct=EBI-2607770, EBI-932432; Q03164:MLL; NbExp=4; IntAct=EBI-2607770, EBI-591370; B2BUF1:NS1 (xeno); NbExp=6; IntAct=EBI-2607770, EBI-4291940; P24928:POLR2A; NbExp=5; IntAct=EBI-2607770, EBI-295301; Q92541:RTF1; NbExp=16; IntAct=EBI-2607770, EBI-1055239; P23193:TCEA1; NbExp=4; IntAct=EBI-2607770, EBI-2608271; Q6PGP7:TTC37; NbExp=2; IntAct=EBI-2607770, EBI-6083436; P51965:UBE2E1; NbExp=2; IntAct=EBI-2607770, EBI-348546; SUBCELLULAR LOCATION: Nucleus. Note=Punctuate distribution throughout the nucleus except in nucleoli and the perinuclear chromatin. SIMILARITY: Belongs to the PAF1 family. SEQUENCE CAUTION: Sequence=AAC25503.1; Type=Erroneous gene model prediction; Sequence=EAW56880.1; Type=Erroneous gene model prediction; Sequence=EAW56881.1; Type=Erroneous gene model prediction; WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PAF1ID44202ch19q13.html";
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on Q8N7H5
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
BC000017 - Homo sapiens Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae), mRNA (cDNA clone MGC:898 IMAGE:3504227), complete cds. AF086555 - Homo sapiens full length insert cDNA clone ZE14E04. AJ401156 - Homo sapiens mRNA for PD2 protein. AK001985 - Homo sapiens cDNA FLJ11123 fis, clone PLACE1006167. BC013402 - Homo sapiens Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae), mRNA (cDNA clone MGC:4224 IMAGE:2960015), complete cds. AK098423 - Homo sapiens cDNA FLJ25557 fis, clone JTH02756. JD273296 - Sequence 254320 from Patent EP1572962. KJ894050 - Synthetic construct Homo sapiens clone ccsbBroadEn_03444 PAF1 gene, encodes complete protein. DQ891839 - Synthetic construct clone IMAGE:100004469; FLH180482.01X; RZPDo839C09134D Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) (PAF1) gene, encodes complete protein. DQ895026 - Synthetic construct Homo sapiens clone IMAGE:100009486; FLH180478.01L; RZPDo839C09133D Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) (PAF1) gene, encodes complete protein. AK294625 - Homo sapiens cDNA FLJ52855 complete cds, highly similar to Rattus norvegicus Paf1, RNA polymerase II associated factor, mRNA. CU673992 - Synthetic construct Homo sapiens gateway clone IMAGE:100017690 5' read PAF1 mRNA. JD409736 - Sequence 390760 from Patent EP1572962. JD226913 - Sequence 207937 from Patent EP1572962. JD180628 - Sequence 161652 from Patent EP1572962.
Biochemical and Signaling Pathways
Reactome (by CSHL, EBI, and GO)
Protein Q8N7H5 (Reactome details) participates in the following event(s):
R-HSA-112379 Recruitment of elongation factors to form elongation complex R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B R-HSA-113429 Elongating transcript encounters a lesion in the template R-HSA-112385 Addition of nucleotides leads to transcript elongation R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest R-HSA-112392 Resumption of elongation after recovery from pausing R-HSA-113413 TFIIS-mediated recovery of elongation from arrest R-HSA-112395 Abortive termination of elongation after arrest R-HSA-112396 Separation of elongating transcript from template R-HSA-112382 Formation of RNA Pol II elongation complex R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins R-HSA-674695 RNA Polymerase II Pre-transcription Events R-HSA-75955 RNA Polymerase II Transcription Elongation R-HSA-8852135 Protein ubiquitination R-HSA-73857 RNA Polymerase II Transcription R-HSA-597592 Post-translational protein modification R-HSA-74160 Gene expression (Transcription) R-HSA-392499 Metabolism of proteins
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