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Entry version 172 (26 Feb 2020)
Sequence version 1 (01 Oct 1996)
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Protein

Exosome complex component CSL4

Gene

CSL4

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

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.3 Publications

Miscellaneous

Present with 5550 molecules/cell in log phase SD medium.1 Publication

Caution

According to PubMed:17173052 and PubMed:17174896, only DIS3/RRP44 subunit of the exosome core has exonuclease activity.Curated

<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 functionRNA-binding
Biological processrRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-33232-MONOMER

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-SCE-429958 mRNA decay by 3' to 5' exoribonuclease
R-SCE-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-SCE-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-SCE-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

<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:
Exosome complex component CSL4
Alternative name(s):
CEP1 synthetic lethal protein 4
<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:CSL4
Synonyms:SKI4
Ordered Locus Names:YNL232W
ORF Names:N1154
<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 Database Resources

More...
EuPathDBi
FungiDB:YNL232W

Saccharomyces Genome Database

More...
SGDi
S000005176 CSL4

<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

Cytoplasm, Exosome, 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_00000794031 – 292Exosome complex component CSL4Add BLAST292

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 residuei94PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
P53859

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

More...
PaxDbi
P53859

PRoteomics IDEntifications database

More...
PRIDEi
P53859

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P53859

<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 RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which associates with catalytic subunits DIS3 and RRP6 in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits and peripheral S1 domain-containing components CSL4, RRP4 and RRP40 located on the top of the ring structure.

2 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection%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

Show more details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
35606, 444 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant

Database of interacting proteins

More...
DIPi
DIP-6785N

Protein interaction database and analysis system

More...
IntActi
P53859, 18 interactors

Molecular INTeraction database

More...
MINTi
P53859

STRING: functional protein association networks

More...
STRINGi
4932.YNL232W

Miscellaneous databases

RNAct, Protein-RNA interaction predictions for model organisms.

More...
RNActi
P53859 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

Secondary structure

1292
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

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SMRi
P53859

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

<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 CSL4 family.Curated

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_067135_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P53859

KEGG Orthology (KO)

More...
KOi
K07573

Identification of Orthologs from Complete Genome Data

More...
OMAi
LMYPIDW

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR039771 Csl4
IPR019495 EXOSC1_C
IPR012340 NA-bd_OB-fold

The PANTHER Classification System

More...
PANTHERi
PTHR12686 PTHR12686, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF10447 EXOSC1, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249 SSF50249, 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.

P53859-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MACNFQFPEI AYPGKLICPQ YGTENKDGED IIFNYVPGPG TKLIQYEHNG
60 70 80 90 100
RTLEAITATL VGTVRCEEEK KTDQEEEREG TDQSTEEEKS VDASPNDVTR
110 120 130 140 150
RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR
160 170 180 190 200
ANVEILAVED KPSPIDSGIG SNGSGIVAAG GGSGAATFSV SQASSDLGET
210 220 230 240 250
FRGIIRSQDV RSTDRDRVKV IECFKPGDIV RAQVLSLGDG TNYYLTTARN
260 270 280 290
DLGVVFARAA NGAGGLMYAT DWQMMTSPVT GATEKRKCAK PF
Length:292
Mass (Da):31,583
Last modified:October 1, 1996 - 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:i52D3416EA183583B
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
Z69381 Genomic DNA Translation: CAA93366.1
Z71508 Genomic DNA Translation: CAA96137.1
BK006947 Genomic DNA Translation: DAA10326.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S63198

NCBI Reference Sequences

More...
RefSeqi
NP_014167.1, NM_001183070.1

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YNL232W_mRNA; YNL232W; YNL232W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
855489

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YNL232W

<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
Z69381 Genomic DNA Translation: CAA93366.1
Z71508 Genomic DNA Translation: CAA96137.1
BK006947 Genomic DNA Translation: DAA10326.1
PIRiS63198
RefSeqiNP_014167.1, NM_001183070.1

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
4IFDX-ray2.80I1-292[»]
4OO1X-ray3.30I1-292[»]
5C0WX-ray4.60I1-292[»]
5C0XX-ray3.81I1-292[»]
5G06electron microscopy4.20I1-292[»]
5JEAX-ray2.65I1-292[»]
5K36X-ray3.10I1-292[»]
5OKZX-ray3.20I/S/c/m1-292[»]
5VZJX-ray3.30I1-292[»]
6FSZelectron microscopy4.60II1-292[»]
SMRiP53859
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi35606, 444 interactors
ComplexPortaliCPX-599 Nuclear/nucleolar exosome complex, DIS3-RRP6 variant
CPX-603 Cytoplasmic exosome complex, DIS3 variant
DIPiDIP-6785N
IntActiP53859, 18 interactors
MINTiP53859
STRINGi4932.YNL232W

PTM databases

iPTMnetiP53859

Proteomic databases

MaxQBiP53859
PaxDbiP53859
PRIDEiP53859

Genome annotation databases

EnsemblFungiiYNL232W_mRNA; YNL232W; YNL232W
GeneIDi855489
KEGGisce:YNL232W

Organism-specific databases

EuPathDBiFungiDB:YNL232W
SGDiS000005176 CSL4

Phylogenomic databases

HOGENOMiCLU_067135_0_0_1
InParanoidiP53859
KOiK07573
OMAiLMYPIDW

Enzyme and pathway databases

BioCyciYEAST:G3O-33232-MONOMER
ReactomeiR-SCE-429958 mRNA decay by 3' to 5' exoribonuclease
R-SCE-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-SCE-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-SCE-6791226 Major pathway of rRNA processing in the nucleolus and cytosol

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P53859
RNActiP53859 protein

Family and domain databases

InterProiView protein in InterPro
IPR039771 Csl4
IPR019495 EXOSC1_C
IPR012340 NA-bd_OB-fold
PANTHERiPTHR12686 PTHR12686, 1 hit
PfamiView protein in Pfam
PF10447 EXOSC1, 1 hit
SUPFAMiSSF50249 SSF50249, 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 nameiCSL4_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: P53859
Secondary accession number(s): D6W0W0
<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: October 1, 1996
Last sequence update: October 1, 1996
Last modified: February 26, 2020
This is version 172 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 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, Reference proteome

Documents

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