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Entry version 155 (02 Dec 2020)
Sequence version 2 (29 May 2007)
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Protein

Poly(A) RNA polymerase protein 1

Gene

TRF5

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

Catalytic subunit of the TRAMP5 complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Polyadenylates RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. TRF5 is also required for proper nuclear division in mitosis and sister chromatid cohesion. Involved in the regulation of histone mRNA levels. May mediate mitotic chromosome condensation.8 Publications

Miscellaneous

Present with 2240 molecules/cell in log phase SD medium.1 Publication

Caution

Was originally thought to have DNA polymerase activity.Curated

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi233Magnesium or manganese; catalyticBy similarity1
Metal bindingi235Magnesium or manganese; catalyticBy similarity1

<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 functionNucleotidyltransferase, Transferase
Biological processCell cycle, Cell division, Mitosis
LigandMagnesium, Manganese, Metal-binding

<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%5Fand%5Ftaxonomy%5Fsection">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:
Poly(A) RNA polymerase protein 1 (EC:2.7.7.19By similarity)
Alternative name(s):
Topoisomerase 1-related protein TRF5
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:TRF5
Ordered Locus Names:YNL299W
ORF Names:N0440
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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 XIV

Organism-specific databases

Eukaryotic Pathogen and Host Database Resources

More...
EuPathDBi
FungiDB:YNL299W

Saccharomyces Genome Database

More...
SGDi
S000005243, TRF5

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001203161 – 642Poly(A) RNA polymerase protein 1Add BLAST642

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 residuei596PhosphoserineCombined sources1
Modified residuei602PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P48561

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

More...
PaxDbi
P48561

PRoteomics IDEntifications database

More...
PRIDEi
P48561

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P48561

<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%5Fsection">'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%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the TRAMP5 complex composed of at least AIR1, MTR4 and TFR5.

Interacts with POL2, DPB2 and DPB11.

2 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">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="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
35539, 209 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-1680, TRAMP5 complex

The Eukaryotic Linear Motif resource for Functional Sites in Proteins

More...
ELMi
P48561

Protein interaction database and analysis system

More...
IntActi
P48561, 3 interactors

Molecular INTeraction database

More...
MINTi
P48561

STRING: functional protein association networks

More...
STRINGi
4932.YNL299W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P48561, protein

<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

3D structure databases

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

More...
SMRi
P48561

Database of comparative protein structure models

More...
ModBasei
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%5Fand%5Fdomains%5Fsection">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>Domaini368 – 428PAP-associatedAdd BLAST61

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the DNA polymerase type-B-like family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1906, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000169468

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_013572_5_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P48561

Identification of Orthologs from Complete Genome Data

More...
OMAi
NTESACN

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.460.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR043519, NT_sf
IPR002058, PAP_assoc
IPR002934, Polymerase_NTP_transf_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01909, NTP_transf_2, 1 hit
PF03828, PAP_assoc, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF81301, SSF81301, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P48561-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTRLKAKYSP TKGKRKEDKH TKRMRKSSFT RTQKMLEVFN DNRSHFNKYE
60 70 80 90 100
SLAIDVEDDD TFGNLVLMEN DKSDVDIPVI EEVTSSEDEQ RAESSKRNNS
110 120 130 140 150
LEDNQDFIAF SDSSEDETEQ IKEDDDERSS FLLTDEHEVS KLTSQQSLNT
160 170 180 190 200
ESACNVEYPW IRNHCHSKQR RIADWLTSEI KDFVHYISPS KNEIKCRNRT
210 220 230 240 250
IDKLRRAVKE LWSDADLHVF GSFATDLYLP GSDIDCVVNS RNRDKEDRNY
260 270 280 290 300
IYELARHLKN KGLAIRMEVI VKTRVPIIKF IEPQSQLHID VSFERTNGLE
310 320 330 340 350
AAKLIREWLR DSPGLRELVL IIKQFLHSRR LNNVHTGGLG GFTVICLVYS
360 370 380 390 400
FLNMHPRIKS NDIDVLDNLG VLLIDFFELY GKNFGYDDVA ISISDGYASY
410 420 430 440 450
IPKSCWRTLE PSRSKFSLAI QDPGDPNNNI SRGSFNMKDI KKAFAGAFEL
460 470 480 490 500
LVNKCWELNS ATFKDRVGKS ILGNVIKYRG QKRDFNDERD LVQNKAIIEN
510 520 530 540 550
ERYHKRRTRI VQEDLFINDT EDLPVEEIYK LDEPAKKKQK AKKDKREGEI
560 570 580 590 600
KKSAIPSPPP DFGVSRSKLK RKVKKTDQGS LLHQNNLSID DLMGLSENDQ
610 620 630 640
ESDQDQKGRD TPSGQDEKSP LETKTVDAQT RRDYWLSKGQ AL
Length:642
Mass (Da):74,179
Last modified:May 29, 2007 - 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:i67D4CD75AEBAE1A4
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 AAC49099 differs from that shown. Reason: Frameshift.Curated
The sequence AAC49397 differs from that shown. Reason: Frameshift.Curated
The sequence CAA96217 differs from that shown. Reason: Frameshift.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti354 – 355MH → ID in AAC49397 (PubMed:8710513).Curated2

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U47282 Genomic DNA Translation: AAC49397.1 Frameshift.
U23084 Genomic DNA Translation: AAC49099.1 Frameshift.
Z71575 Genomic DNA Translation: CAA96217.1 Frameshift.
BK006947 Genomic DNA Translation: DAA10261.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S60401

NCBI Reference Sequences

More...
RefSeqi
NP_014100.2, NM_001183137.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YNL299W_mRNA; YNL299W; YNL299W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
855417

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YNL299W

<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
U47282 Genomic DNA Translation: AAC49397.1 Frameshift.
U23084 Genomic DNA Translation: AAC49099.1 Frameshift.
Z71575 Genomic DNA Translation: CAA96217.1 Frameshift.
BK006947 Genomic DNA Translation: DAA10261.1
PIRiS60401
RefSeqiNP_014100.2, NM_001183137.1

3D structure databases

SMRiP48561
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi35539, 209 interactors
ComplexPortaliCPX-1680, TRAMP5 complex
ELMiP48561
IntActiP48561, 3 interactors
MINTiP48561
STRINGi4932.YNL299W

PTM databases

iPTMnetiP48561

Proteomic databases

MaxQBiP48561
PaxDbiP48561
PRIDEiP48561

Genome annotation databases

EnsemblFungiiYNL299W_mRNA; YNL299W; YNL299W
GeneIDi855417
KEGGisce:YNL299W

Organism-specific databases

EuPathDBiFungiDB:YNL299W
SGDiS000005243, TRF5

Phylogenomic databases

eggNOGiKOG1906, Eukaryota
GeneTreeiENSGT00940000169468
HOGENOMiCLU_013572_5_0_1
InParanoidiP48561
OMAiNTESACN

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P48561
RNActiP48561, protein

Family and domain databases

Gene3Di3.30.460.10, 1 hit
InterProiView protein in InterPro
IPR043519, NT_sf
IPR002058, PAP_assoc
IPR002934, Polymerase_NTP_transf_dom
PfamiView protein in Pfam
PF01909, NTP_transf_2, 1 hit
PF03828, PAP_assoc, 1 hit
SUPFAMiSSF81301, SSF81301, 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 nameiTRF5_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: P48561
Secondary accession number(s): D6W0P5
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: May 29, 2007
Last modified: December 2, 2020
This is version 155 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

Reference proteome

Documents

  1. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
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