Protein Overview: RTF1

General Information:
Name(s) found:	RTF1 / YGL244W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|6321193\|ref\|NP_011270.1\| Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance; Rtf1p [Saccharomy [NCBI NR] gi\|2506764\|sp\|P53064.2\|RTF1_YEAST RecName: Full=RNA polymerase-associated protein RTF1 [NCBI NR] gi\|1945310\|emb\|CAA96963.1\| RTF1 [Saccharomyces cerevisiae] [NCBI NR] gi\|1841839\|gb\|AAB47535.1\| Rtf1p [Saccharomyces cerevisiae] [NCBI NR] RNA polymerase-associated protein RTF1 OS=Saccharomyces cerevisiae GN=RTF1 PE=1 SV=2 [Swiss-Prot] RTF1 Regulates DNA binding properties of TBP [mips] Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance [SGD] RTF1, Chr VII from 41498-43174 [yeast_orfs2] Chr VII from 41498-43174 [yeastorf3.fasta] (P53064) RTF1 protein [4932.FASTACCERV.txt] RTF1 SGDID:S0003213, Chr VII from 41498-43174, Verified ORF [yeastflysequest.fasta] Rtf1p [Saccharomyces cerevisiae]gi\|1841839\|gb\|AAB47535.1\| Rtf1p [Saccharomyces cerevisiae]gi\|1945310\|emb\|CAA96963.1\| RTF1 [Saccharomyces cerevisiae]gi\|2506764\|sp\|P53064\|RTF1_YEAST RTF1 protein [nrdb_11152004_Chlamydomonas] RTF1 SGDID:S000003213, Chr VII from 41498-43174, Verified ORF, "Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p (TATA box-binding protein) and relative activities of different TAT [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] RTF1 SGDID:S000003213, Chr VII from 41498-43174, Verified ORF, "Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in tel [yeast-contam.fasta] RNA polymerase-associated protein RTF1 [nr-271106-contam.fasta] RTF1 [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Rtf1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance; Rtf1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] RTF1 SGDID:S000003213, Chr VII from 41498-43174, Verified ORF, "Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance" [yeast-bovrabprots.fasta] [chemostatdb.fasta] RNA polymerase-associated protein RTF1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RTF1 PE=1 SV=2 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] RTF1 SGDID:S000003213, Chr VII from 41498-43174, Genome Release 64-1-1, Verified ORF, "Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay" [yeast-030211-contam.fasta] RTF1 SGDID:S000003213, Chr VII from 41498-43174, Genome Release 64-2-1, Verified ORF, "Subunit of RNAPII-associated chromatin remodeling Paf1 complex; regulates gene expression by directing cotranscriptional histone modification, influences transcription and chromatin structure through several independent functional domains; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay" [20141208_orf_trans.fasta] TR4116\|c0_g1_i1\|g.2950 ORF TR4116\|c0_g1_i1\|g.2950 TR4116\|c0_g1_i1\|m.2950 type:complete len:559 (+) TR4116\|c0_g1_i1:58-1734(+) [Y12_S_cerevisiae-Sep2015-contam.fasta] YGL244W SGDID:S000003213, Chr VII from 41498-43174, Genome Release 64-1-1, Verified ORF, "Subunit of the RNA polymerase II-associated Paf1 complex; directly or indirectly regulates DNA-binding properties of Spt15p and relative activities of different TATA elements; involved in telomere maintenance; involved in transcription elongation as demonstrated by the G-less-based run-on (GLRO) assay" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta] asmbl_1642\|g.1466 ORF asmbl_1642\|g.1466 asmbl_1642\|m.1466 type:complete len:559 (+) asmbl_1642:57-1733(+) [Y12_Trinity_v2_2_0_PASA_6May2016-contam.fasta] ID=asmbl_1652\|g.1304 ORF ID=asmbl_1652\|g.1304 ID=asmbl_1652\|m.1304 type:complete len:559 (+) ID=asmbl_1652:57-1733(+) [Y12_quiver_Trinity_v2_2_0_PASA_2June2016-contam.fasta]
Organism:	Saccharomyces cerevisiae
Length:	558 amino acids
Gene Ontology:
Cellular Component:	nucleus [IDA] transcription elongation factor complex [IPI] Cdc73/Paf1 complex [IPI][TAS]
Biological Process:	histone methylation [IMP] telomere maintenance [IMP ] transcription from RNA polymerase II promoter [IMP] RNA elongation from RNA polymerase II promoter [IPI]
Molecular Function:	RNA polymerase II transcription elongation factor activity [IPI]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV EDDDEEDDYN  60
   61 PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE MERETLLFER SQIMQKYQER 120
  121 KLFRARGRDM KEQQQRAKND EDSRKTRAST RSTHATGHSD IKASKLSQLK KQRARKNRHY 180
  181 SDNEDEDDEE DYREEDYKDD EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE 240
  241 ISDFNKLRIG RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP 300
  301 YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM IKPSLHSLSN 360
  361 KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE KTVLREKLQY AKETNNEKDI 420
  421 AKYSAQLRNF EKRMSVYEKH HENDQSDIKK LGELTSKNRK LNMSNIRNAE HVKKEDSNNF 480
  481 DSKSDPFSRL KTRTKVYYQE IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL 540
  541 GGLERMVGEL DIKFDLKF

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Riffle et al. (2010) (Unpublished Data)		CDC73 CHD1 CKA1 CKA2 CKB1 CKB2 CTR9 LEO1 PAF1 POB3 RTF1 SPT16
View Details	Krogan NJ, et al. (2006)		ARA2 AYT1 BRO1 CDC73 CTR9 GLO4 HHT1, HHT2 LEO1 PAF1 PML39 POB3 PSH1 RTF1 SEN1 SPT16 YHR035W
View Details	Gavin AC, et al. (2002)		CDC73 CKA1 CKA2 CKB1 CKB2 CTR9 IML1 LEO1 LYS12 PAF1 POB3 RTF1 SPT16
View Details	Ho Y, et al. (2002)		RTF1 SPT7 TDA3
View Details	Qiu et al. (2008)		CDC73 ELA1 ELC1 ELP2 IKI3 LEO1 PAF1 RTF1 SPN1 SPT16 SPT4 SPT5 SPT6 TFB5

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	SPT23	RTF1	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	RTF1	Huh WK, et al. (2003)

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..230]	MSA	2.050994	View MSA. No confident structure predictions are available.
2	View Details	[231..350]	Pfam	48.537602	Plus-3 domain No confident structure predictions are available.
3	View Details	[351..558]	deduced	N/A	No confident structure predictions are available.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.99

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2