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Entry version 172 (16 Oct 2019)
Sequence version 2 (01 Nov 1997)
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Protein

RNA polymerase-associated protein RTF1

Gene

RTF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of RAD6 ubiquitin conjugate and the BRE1 ubiquitin ligase which ubiquitinate 'Lys-126' histone H2B. Activates the SET1 histone methyltransferase complex for methylation of 'Lys-4' of histone H3 and for methylation of 'Lys-73' of histone H3 by DOT1 and 'Lys-36' of histone H3 by SET2. Important for TATA site selection by TBP. Directly or indirectly regulates the DNA-binding properties of SPT15, the TATA box-binding protein, and the relative activities of different TATA elements.2 Publications

Miscellaneous

Present with 6510 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionActivator
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-30715-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-75955 RNA Polymerase II Transcription Elongation

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
RNA polymerase-associated protein RTF1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:RTF1
Synonyms:CSL3
Ordered Locus Names:YGL244W
ORF Names:HRA458
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome VII

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YGL244W

Saccharomyces Genome Database

More...
SGDi
S000003213 RTF1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000975121 – 558RNA polymerase-associated protein RTF1Add BLAST558

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei17PhosphoserineCombined sources1
Modified residuei69PhosphotyrosineCombined sources1
Modified residuei71PhosphoserineCombined sources1
Modified residuei477PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P53064

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P53064

PRoteomics IDEntifications database

More...
PRIDEi
P53064

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P53064

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1.

1 Publication

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
32996, 724 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-1726 PAF1 complex

Database of interacting proteins

More...
DIPi
DIP-4065N

Protein interaction database and analysis system

More...
IntActi
P53064, 18 interactors

Molecular INTeraction database

More...
MINTi
P53064

STRING: functional protein association networks

More...
STRINGi
4932.YGL244W

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1558
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P53064

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini238 – 370Plus3PROSITE-ProRule annotationAdd BLAST133

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi72 – 76Poly-Glu5

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000065976

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P53064

KEGG Orthology (KO)

More...
KOi
K15178

Identification of Orthologs from Complete Genome Data

More...
OMAi
SGCKSAV

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.170.260.30, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR004343 Plus-3_dom
IPR036128 Plus3-like_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03126 Plus-3, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00719 Plus3, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF159042 SSF159042, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51360 PLUS3, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P53064-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV
60 70 80 90 100
EDDDEEDDYN PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE
110 120 130 140 150
MERETLLFER SQIMQKYQER KLFRARGRDM KEQQQRAKND EDSRKTRAST
160 170 180 190 200
RSTHATGHSD IKASKLSQLK KQRARKNRHY SDNEDEDDEE DYREEDYKDD
210 220 230 240 250
EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE ISDFNKLRIG
260 270 280 290 300
RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP
310 320 330 340 350
YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM
360 370 380 390 400
IKPSLHSLSN KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE
410 420 430 440 450
KTVLREKLQY AKETNNEKDI AKYSAQLRNF EKRMSVYEKH HENDQSDIKK
460 470 480 490 500
LGELTSKNRK LNMSNIRNAE HVKKEDSNNF DSKSDPFSRL KTRTKVYYQE
510 520 530 540 550
IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL GGLERMVGEL

DIKFDLKF
Length:558
Mass (Da):65,869
Last modified:November 1, 1997 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i13AECCEC6D63CED4
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence CAA89011 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U86702 Genomic DNA Translation: AAB47535.1
Z49149 Genomic DNA Translation: CAA89011.1 Different initiation.
Z72766 Genomic DNA Translation: CAA96963.1
Z72767 Genomic DNA Translation: CAA96965.1
BK006941 Genomic DNA Translation: DAA07875.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S53936

NCBI Reference Sequences

More...
RefSeqi
NP_011270.1, NM_001181110.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YGL244W_mRNA; YGL244W; YGL244W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
852607

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YGL244W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U86702 Genomic DNA Translation: AAB47535.1
Z49149 Genomic DNA Translation: CAA89011.1 Different initiation.
Z72766 Genomic DNA Translation: CAA96963.1
Z72767 Genomic DNA Translation: CAA96965.1
BK006941 Genomic DNA Translation: DAA07875.1
PIRiS53936
RefSeqiNP_011270.1, NM_001181110.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5E8BX-ray1.62A/B74-139[»]
5EMXX-ray1.40A/B74-139[»]
SMRiP53064
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi32996, 724 interactors
ComplexPortaliCPX-1726 PAF1 complex
DIPiDIP-4065N
IntActiP53064, 18 interactors
MINTiP53064
STRINGi4932.YGL244W

PTM databases

iPTMnetiP53064

Proteomic databases

MaxQBiP53064
PaxDbiP53064
PRIDEiP53064

Genome annotation databases

EnsemblFungiiYGL244W_mRNA; YGL244W; YGL244W
GeneIDi852607
KEGGisce:YGL244W

Organism-specific databases

EuPathDBiFungiDB:YGL244W
SGDiS000003213 RTF1

Phylogenomic databases

HOGENOMiHOG000065976
InParanoidiP53064
KOiK15178
OMAiSGCKSAV

Enzyme and pathway databases

BioCyciYEAST:G3O-30715-MONOMER
ReactomeiR-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-75955 RNA Polymerase II Transcription Elongation

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P53064

Family and domain databases

Gene3Di2.170.260.30, 1 hit
InterProiView protein in InterPro
IPR004343 Plus-3_dom
IPR036128 Plus3-like_sf
PfamiView protein in Pfam
PF03126 Plus-3, 1 hit
SMARTiView protein in SMART
SM00719 Plus3, 1 hit
SUPFAMiSSF159042 SSF159042, 1 hit
PROSITEiView protein in PROSITE
PS51360 PLUS3, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRTF1_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P53064
Secondary accession number(s): D6VV91, P89115
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: October 16, 2019
This is version 172 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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