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Entry version 64 (29 Sep 2021)
Sequence version 1 (14 Dec 2011)
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Protein

RNA polymerase-associated protein RTF1 homolog

Gene

rtfo-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score:

Annotation score:3 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 transcript 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

Component of the PAF1 complex which is a multifunctional complex involved in transcription initiation via genetic interactions with TATA-binding proteins, elongation and transcription-coupled histone modification.

By similarity

<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

<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

Biological processTranscription, Transcription regulation

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-CEL-112382, Formation of RNA Pol II elongation complex
R-CEL-674695, RNA Polymerase II Pre-transcription Events
R-CEL-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 homologBy similarity
<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:rtfo-1Imported
ORF Names:F25B3.6Imported
<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>OrganismiCaenorhabditis elegansImported
<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 identifieri6239 [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 lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditinaRhabditomorphaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
<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
  • UP000001940 <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 V

Organism-specific databases

WormBase

More...
WormBasei
F25B3.6 ; CE09619 ; WBGene00009103 ; rtfo-1

<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

Keywords - Cellular componenti

Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

RNAi-mediated knock-down is mostly embryonic lethal. Embryogenesis proceeds more slowly, with embryos displaying defects in the positioning and shape of epidermal cells.1 Publication

<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_00004315081 – 613RNA polymerase-associated protein RTF1 homologAdd BLAST613

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
G5EBY0

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

More...
PaxDbi
G5EBY0

PeptideAtlas

More...
PeptideAtlasi
G5EBY0

PRoteomics IDEntifications database

More...
PRIDEi
G5EBY0

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section provides information on the expression of the gene product at various stages of a cell, tissue or organism development. By default, the information is derived from experiments at the mRNA level, unless specified 'at the protein level'.<p><a href='/help/developmental_stage' target='_top'>More...</a></p>Developmental stagei

Expressed in somatic cells, but not in germ cells, after the 30 cell stage.1 Publication

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
WBGene00009103, Expressed in multi-cellular organism and 5 other tissues

<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 cdc-73, ctr-9, leo-1, pafo-1 and rtfo-1.

By similarity

GO - Molecular functioni

Protein-protein interaction databases

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-966, PAF1 complex

Protein interaction database and analysis system

More...
IntActi
G5EBY0, 1 interactor

STRING: functional protein association networks

More...
STRINGi
6239.F25B3.6

<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
G5EBY0

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_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>Domaini252 – 383Plus3PROSITE-ProRule annotationAdd BLAST132

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 90DisorderedSequence analysisAdd BLAST90
Regioni121 – 247DisorderedSequence analysisAdd BLAST127
Regioni485 – 549DisorderedSequence analysisAdd BLAST65
Regioni564 – 613DisorderedSequence analysisAdd BLAST50

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili175 – 209Sequence analysisAdd BLAST35
Coiled coili425 – 462Sequence analysisAdd BLAST38

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 type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi8 – 22Basic and acidic residuesSequence analysisAdd BLAST15
Compositional biasi121 – 145Basic and acidic residuesSequence analysisAdd BLAST25
Compositional biasi155 – 203Basic and acidic residuesSequence analysisAdd BLAST49
Compositional biasi211 – 236Polar residuesSequence analysisAdd BLAST26
Compositional biasi505 – 546Polar residuesSequence analysisAdd BLAST42
Compositional biasi568 – 589Polar residuesSequence analysisAdd BLAST22
Compositional biasi599 – 613Polar residuesSequence analysisAdd BLAST15

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2402, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00940000168478

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_018644_0_1_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
G5EBY0

Identification of Orthologs from Complete Genome Data

More...
OMAi
SGCKSAV

Database of Orthologous Groups

More...
OrthoDBi
1056075at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
G5EBY0

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.90.70.200, 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.

G5EBY0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSSESASSD EETKRRAPAT SDSDSDSDAG PKPGKPLSTD SSASDSDAEK
60 70 80 90 100
PQAKPAKKKT LTKRKRRATG SSDDDQVDDD LFADKEDKAR WKKLTELEKE
110 120 130 140 150
QEIFERMEAR ENAIAREEIA QQLAKKAKKS SEKGVKTEKR RKMNSGGSDA
160 170 180 190 200
GSPKRKASSD SDSEMDAAFH RPSDINRKHK EKNAMDALKN KRKEIEKKNA
210 220 230 240 250
KNEALSIDAV FGANSGSSSS SSSSESSRSS SSSRESSPER VSEKDKIVKK
260 270 280 290 300
DVDGLSELRR ARLSRHKLSL MIHAPFFDST VVGCYVRLGQ GQMSGSGSKY
310 320 330 340 350
RIWKIVGVEE SNKVYELEGK KTNKIIKCQN GGSERPFRMQ FVSNADFEQI
360 370 380 390 400
EFDEWLLACK RHGNLPTVDI MDKKKQDIEK AINHKYSDKE VDLMIKEKSK
410 420 430 440 450
YQTVPRNFAM TKANWSKQKE LAQQRGDIRE AEQIQTKIDE IERQADELEK
460 470 480 490 500
ERSKSISAIA FINHRNRSKI KDQVLSGQLK IEENSQDDPF TRKKGGMRVV
510 520 530 540 550
SGSKSRLDGT LSASSSTTNL SDGGKDKSSS LAKPTQPPPS TQIKKKTDIS
560 570 580 590 600
SLHDFDLDID LGKLKDFSTP ESSGNKRPSI SSSKGVSLSD YRMRRSGGGD
610
AGSSTSAAPS SAV
Length:613
Mass (Da):67,803
Last modified:December 14, 2011 - v1
<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:i198487053A5F78BB
GO

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
Z70752, Z81101 Genomic DNA Translation: CAA94759.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T21325

NCBI Reference Sequences

More...
RefSeqi
NP_505473.1, NM_073072.4

Genome annotation databases

Ensembl metazoan genome annotation project

More...
EnsemblMetazoai
F25B3.6.1; F25B3.6.1; WBGene00009103

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
179345

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
cel:CELE_F25B3.6

<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
Z70752, Z81101 Genomic DNA Translation: CAA94759.1
PIRiT21325
RefSeqiNP_505473.1, NM_073072.4

3D structure databases

SMRiG5EBY0
ModBaseiSearch...

Protein-protein interaction databases

ComplexPortaliCPX-966, PAF1 complex
IntActiG5EBY0, 1 interactor
STRINGi6239.F25B3.6

Proteomic databases

EPDiG5EBY0
PaxDbiG5EBY0
PeptideAtlasiG5EBY0
PRIDEiG5EBY0

Genome annotation databases

EnsemblMetazoaiF25B3.6.1; F25B3.6.1; WBGene00009103
GeneIDi179345
KEGGicel:CELE_F25B3.6

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
179345
WormBaseiF25B3.6 ; CE09619 ; WBGene00009103 ; rtfo-1

Phylogenomic databases

eggNOGiKOG2402, Eukaryota
GeneTreeiENSGT00940000168478
HOGENOMiCLU_018644_0_1_1
InParanoidiG5EBY0
OMAiSGCKSAV
OrthoDBi1056075at2759
PhylomeDBiG5EBY0

Enzyme and pathway databases

ReactomeiR-CEL-112382, Formation of RNA Pol II elongation complex
R-CEL-674695, RNA Polymerase II Pre-transcription Events
R-CEL-75955, RNA Polymerase II Transcription Elongation

Miscellaneous databases

Protein Ontology

More...
PROi
PR:G5EBY0

Gene expression databases

BgeeiWBGene00009103, Expressed in multi-cellular organism and 5 other tissues

Family and domain databases

Gene3Di3.90.70.200, 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

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_CAEEL
<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: G5EBY0
<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: January 7, 2015
Last sequence update: December 14, 2011
Last modified: September 29, 2021
This is version 64 of the entry and version 1 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 programCaenorhabditis annotation project

<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. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
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