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RNA polymerase II-associated factor 1 homolog

 PAF1_MOUSE              Reviewed;         535 AA.
Q8K2T8; Q3UY97; Q9CS63; Q9JJ99;
08-APR-2008, integrated into UniProtKB/Swiss-Prot.
01-OCT-2002, sequence version 1.
07-NOV-2018, entry version 122.
RecName: Full=RNA polymerase II-associated factor 1 homolog;
Name=Paf1;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Brain;
Osada N., Kusuda J., Tanuma R., Ito A., Hirata M., Sugano S.,
Hashimoto K.;
"Isolation of full-length cDNA clones from mouse brain cDNA library
made by oligo-capping method.";
Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J; TISSUE=Embryo;
PubMed=16141072; DOI=10.1126/science.1112014;
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
Hayashizaki Y.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=C57BL/6J, and Czech II; TISSUE=Brain, and Mammary tumor;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
FUNCTION.
PubMed=19345177; DOI=10.1016/j.stem.2009.03.009;
Ding L., Paszkowski-Rogacz M., Nitzsche A., Slabicki M.M.,
Heninger A.K., de Vries I., Kittler R., Junqueira M., Shevchenko A.,
Schulz H., Hubner N., Doss M.X., Sachinidis A., Hescheler J.,
Iacone R., Anastassiadis K., Stewart A.F., Pisabarro M.T.,
Caldarelli A., Poser I., Theis M., Buchholz F.;
"A genome-scale RNAi screen for Oct4 modulators defines a role of the
Paf1 complex for embryonic stem cell identity.";
Cell Stem Cell 4:403-415(2009).
[5]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-456, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
[6]
IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
PubMed=27749823; DOI=10.1038/ncb3424;
Strikoudis A., Lazaris C., Trimarchi T., Galvao Neto A.L., Yang Y.,
Ntziachristos P., Rothbart S., Buckley S., Dolgalev I., Stadtfeld M.,
Strahl B.D., Dynlacht B.D., Tsirigos A., Aifantis I.;
"Regulation of transcriptional elongation in pluripotency and cell
differentiation by the PHD-finger protein Phf5a.";
Nat. Cell Biol. 18:1127-1138(2016).
-!- 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
KMT2A/MLL1. 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. Connects PAF1C with the RNF20/40 E3 ubiquitin-protein
ligase complex. Involved in polyadenylation of mRNA precursors (By
similarity). {ECO:0000250, ECO:0000269|PubMed:19345177}.
-!- SUBUNIT: Component of the PAF1 complex, which consists of CDC73,
PAF1, LEO1, CTR9, RTF1 and WDR61. The PAF1 complex interacts with
PHF5A (PubMed:27749823). Interacts with POLR2A, TCEA1, TTC37,
KMT2A/MLL1, SUPT5H, RNF20 and RNF40. Interacts with UBE2E1 (By
similarity). {ECO:0000250|UniProtKB:Q8N7H5,
ECO:0000269|PubMed:27749823}.
-!- SUBCELLULAR LOCATION: Nucleus. Note=Punctuate distribution
throughout the nucleus except in nucleoli and the perinuclear
chromatin. {ECO:0000250}.
-!- SIMILARITY: Belongs to the PAF1 family. {ECO:0000305}.
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EMBL; AB041615; BAA95098.1; -; mRNA.
EMBL; AK017762; BAB30913.1; -; mRNA.
EMBL; AK134857; BAE22315.1; -; mRNA.
EMBL; AK148538; BAE28608.1; -; mRNA.
EMBL; BC029843; AAH29843.1; -; mRNA.
EMBL; BC083337; AAH83337.1; -; mRNA.
CCDS; CCDS21043.1; -.
RefSeq; NP_062331.2; NM_019458.3.
UniGene; Mm.7916; -.
ProteinModelPortal; Q8K2T8; -.
SMR; Q8K2T8; -.
BioGrid; 207692; 5.
IntAct; Q8K2T8; 8.
MINT; Q8K2T8; -.
STRING; 10090.ENSMUSP00000003529; -.
iPTMnet; Q8K2T8; -.
PhosphoSitePlus; Q8K2T8; -.
EPD; Q8K2T8; -.
MaxQB; Q8K2T8; -.
PaxDb; Q8K2T8; -.
PeptideAtlas; Q8K2T8; -.
PRIDE; Q8K2T8; -.
Ensembl; ENSMUST00000003529; ENSMUSP00000003529; ENSMUSG00000003437.
GeneID; 54624; -.
KEGG; mmu:54624; -.
UCSC; uc009fyu.1; mouse.
CTD; 54623; -.
MGI; MGI:1923988; Paf1.
eggNOG; KOG2478; Eukaryota.
eggNOG; ENOG410YZXE; LUCA.
GeneTree; ENSGT00390000001474; -.
HOGENOM; HOG000115425; -.
HOVERGEN; HBG053131; -.
InParanoid; Q8K2T8; -.
KO; K15174; -.
OMA; DPRLDCA; -.
OrthoDB; EOG091G0C3Y; -.
PhylomeDB; Q8K2T8; -.
TreeFam; TF313642; -.
Reactome; R-MMU-112382; Formation of RNA Pol II elongation complex.
Reactome; R-MMU-674695; RNA Polymerase II Pre-transcription Events.
Reactome; R-MMU-75955; RNA Polymerase II Transcription Elongation.
Reactome; R-MMU-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
PRO; PR:Q8K2T8; -.
Proteomes; UP000000589; Chromosome 7.
Bgee; ENSMUSG00000003437; Expressed in 274 organ(s), highest expression level in vestibular organ.
Genevisible; Q8K2T8; MM.
GO; GO:0016593; C:Cdc73/Paf1 complex; ISS:UniProtKB.
GO; GO:0030054; C:cell junction; ISO:MGI.
GO; GO:0005737; C:cytoplasm; ISO:MGI.
GO; GO:0016020; C:membrane; ISO:MGI.
GO; GO:0005654; C:nucleoplasm; ISO:MGI.
GO; GO:0035327; C:transcriptionally active chromatin; IBA:GO_Central.
GO; GO:0003682; F:chromatin binding; IDA:MGI.
GO; GO:0000993; F:RNA polymerase II complex binding; ISS:UniProtKB.
GO; GO:0071222; P:cellular response to lipopolysaccharide; IDA:UniProtKB.
GO; GO:0001711; P:endodermal cell fate commitment; IMP:UniProtKB.
GO; GO:0033523; P:histone H2B ubiquitination; ISO:MGI.
GO; GO:0010390; P:histone monoubiquitination; ISO:MGI.
GO; GO:0006378; P:mRNA polyadenylation; ISS:UniProtKB.
GO; GO:0045638; P:negative regulation of myeloid cell differentiation; ISS:UniProtKB.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:UniProtKB.
GO; GO:0016584; P:nucleosome positioning; ISO:MGI.
GO; GO:1902808; P:positive regulation of cell cycle G1/S phase transition; ISS:UniProtKB.
GO; GO:0031062; P:positive regulation of histone methylation; ISO:MGI.
GO; GO:0031442; P:positive regulation of mRNA 3'-end processing; ISS:UniProtKB.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISS:UniProtKB.
GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; ISS:UniProtKB.
GO; GO:0034504; P:protein localization to nucleus; ISO:MGI.
GO; GO:0019827; P:stem cell population maintenance; IMP:UniProtKB.
GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:InterPro.
GO; GO:0016055; P:Wnt signaling pathway; IEA:UniProtKB-KW.
InterPro; IPR007133; RNA_pol_II-assoc_Paf1.
PANTHER; PTHR23188; PTHR23188; 1.
Pfam; PF03985; Paf1; 1.
1: Evidence at protein level;
Coiled coil; Complete proteome; Isopeptide bond; Nucleus;
Phosphoprotein; Reference proteome; Transcription;
Transcription regulation; Ubl conjugation; Wnt signaling pathway.
CHAIN 1 535 RNA polymerase II-associated factor 1
homolog.
/FTId=PRO_0000326401.
COILED 352 400 {ECO:0000255}.
COMPBIAS 358 452 Glu-rich.
COMPBIAS 478 534 Ser-rich.
MOD_RES 117 117 Phosphoserine.
{ECO:0000250|UniProtKB:Q8N7H5}.
MOD_RES 456 456 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
CROSSLNK 133 133 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000250|UniProtKB:Q8N7H5}.
CROSSLNK 154 154 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000250|UniProtKB:Q8N7H5}.
CONFLICT 227 227 P -> L (in Ref. 1; BAA95098).
{ECO:0000305}.
CONFLICT 336 336 R -> Q (in Ref. 1; BAE22315).
{ECO:0000305}.
CONFLICT 505 505 Missing (in Ref. 1; BAE22315).
{ECO:0000305}.
SEQUENCE 535 AA; 60518 MW; 7A5EAB1284988070 CRC64;
MAPTIQTQAQ REDGHRPNSH RTLPERSGVV CRVKYCNSLP DIPFDPKFIT YPFDQNRFVQ
YKATSLEKQH KHDLLTEPDL GVTIDLINPD TYRIDPNVLL DPADEKLLEE EIQAPTSSKR
SQQHAKVVPW MRKTEYISTE FNRYGISNEK PEVKIGVSVK QQFTEEEIYK DRDSQITAIE
KTFEDAQKSI SQHYSKPRVT PVEVMPVFPD FKMWINPCAQ VIFDSDPAPK DTSGAAALEM
MSQAMIRGMM DEEGNQFVAY FLPVEETLKK RKRDQEEEMD YAPDDVYDYK IAREYNWNVK
NKASKGYEEN YFFIFREGDG VYYNELETRV RLSKRRAKAG VQSGTNALLV VKHRDMNEKE
LEAQEARKAQ LENHEPEEEE EEEMEAEEKE AGGSDEEQEK GSSSEKEGSE DEHSGSESDR
EEGDRDEASD KSGSGEDESS EDEARAARDK EEIFGSDADS EDDADSDDED RGQAHRGSDN
DSDSGSDGGG QRSRSQSRSR SRSASPFPSG SEHSAQEDGS EAAASDSSEA DSDSD


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