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Entry version 106 (12 Aug 2020)
Sequence version 2 (25 Nov 2008)
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Protein

Carbon catabolite repressor protein 4 homolog 6

Gene

CCR4-6

Organism
Arabidopsis thaliana (Mouse-ear cress)
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

Acts as catalytic component of the CCR4-NOT core complex, which in the nucleus seems to be a general transcription factor, and in the cytoplasm the major mRNA deadenylase involved in mRNA turnover.By similarity

<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

  • Exonucleolytic cleavage of poly(A) to 5'-AMP. EC:3.1.13.4

<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

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 bindingi237MagnesiumBy 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

<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 functionExonuclease, Hydrolase, Nuclease, RNA-binding
Biological processTranscription, Transcription regulation
LigandMagnesium, 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:
Carbon catabolite repressor protein 4 homolog 6 (EC:3.1.13.4)
Short name:
CCR4 homolog 6
<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:CCR4-6
Ordered Locus Names:At5g11350
ORF Names:F2I11_240
<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>OrganismiArabidopsis thaliana (Mouse-ear cress)
<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 identifieri3702 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<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
  • UP000006548 <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 5

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT5G11350

The Arabidopsis Information Resource

More...
TAIRi
locus:2832132, AT5G11350

<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

Cytoplasm, 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_00003550491 – 754Carbon catabolite repressor protein 4 homolog 6Add BLAST754

Proteomic databases

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

More...
PaxDbi
Q8VYU4

PRoteomics IDEntifications database

More...
PRIDEi
Q8VYU4

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
223935

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q8VYU4

<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

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q8VYU4, baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q8VYU4, AT

<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 CCR4-NOT complex, at least composed of CRR4 and CAF1 proteins.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
3702.AT5G11350.1

<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
Q8VYU4

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

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 biasi92 – 178Pro-richAdd BLAST87

<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 CCR4/nocturin family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2338, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_008664_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8VYU4

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q8VYU4

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.60.10.10, 2 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR036691, Endo/exonu/phosph_ase_sf
IPR005135, Endo/exonuclease/phosphatase

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03372, Exo_endo_phos, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF56219, SSF56219, 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>Sequence (1+)i

<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.

This entry has 1 described isoform and 4 potential isoforms that are computationally mapped.Show allAlign All

Q8VYU4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRRSRFVAQV FSDVTFADAS TISAPIFTMS TRAPYRGARG RGRGRGGRSF
60 70 80 90 100
SDRPYNDDAG RDQFVTGDSH FQSVHDANFR FRHGEPYRQH QPPLDQRQQP
110 120 130 140 150
PFNQNYEFRP PPPSRGQWQQ FRQPNQFPSN QNYAACPPPP FYQNQMSRPP
160 170 180 190 200
PQQSFRQRPR SKPSDYREWE YAKTPPSPGS EKFVVLSYNI LADYLANDHW
210 220 230 240 250
RSLYFHIPRN MLSWGWRKSK LVFELSLWSA DIMCLQEVDK FQDLEEEMKH
260 270 280 290 300
RGYSAIWKMR TGNAVDGCAI FWRSNRFKLV HEESIQFNQL GLRDNVAQIC
310 320 330 340 350
VLETLLTSHT KENETPPPES SAGSHRVVIC NIHVLFNPKR GDFKLGQVRT
360 370 380 390 400
LLDKAHAVSK LWDDAPIVLC GDFNCTPKSP LYNFISDRKL DLSGLARDKV
410 420 430 440 450
SGQVSAEFRP PRPENYTTRY QSANKSPQGQ VQPPNLITNA HMENNSNIDV
460 470 480 490 500
GTAPSEKTSE LPCGDTILAG HEATSSSDQV LPCENMASDC QFGIENRKPD
510 520 530 540 550
DSGNLSTAED LSSLTISDTE PQHASSARED LNTDRSVSSG LSETEQTPEE
560 570 580 590 600
ICSSDQDISS SLSTKVDTFV AEMKLDGLKL DEPVVFAQDE ESLGEDGETF
610 620 630 640 650
LAKLHDNNEN LSQKGELVSE VPLKWSSEAL NSDKITYSPS SWTPMEIATA
660 670 680 690 700
TGDPERTTVE HALELKSTYS EVEGQANTRD ENGEPVVTSY HRCFMGTVDY
710 720 730 740 750
IWRSEGLQTV RVLAPIPKQA MQWTPGFPTP KWGSDHIALV SELAFCSSKT

LPKS
Length:754
Mass (Da):84,925
Last modified:November 25, 2008 - 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:iB53A55C92AC288CF
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A178UDZ2A0A178UDZ2_ARATH
DNAse I-like superfamily protein
At5g11350, F2I11.240, F2I11_240
755Annotation score:

Annotation score:1 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>
A0A1P8BDV6A0A1P8BDV6_ARATH
DNAse I-like superfamily protein
At5g11350, F2I11.240, F2I11_240
594Annotation score:

Annotation score:1 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>
A0A1P8BDX5A0A1P8BDX5_ARATH
DNAse I-like superfamily protein
At5g11350, F2I11.240, F2I11_240
738Annotation score:

Annotation score:1 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>
A0A1P8BDY9A0A1P8BDY9_ARATH
DNAse I-like superfamily protein
At5g11350, F2I11.240, F2I11_240
703Annotation score:

Annotation score:1 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>

<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 CAB96670 differs from that shown. Reason: Erroneous gene model prediction.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 conflicti291G → R in AAN28916 (PubMed:14593172).Curated1
Sequence conflicti291G → R in AAL47464 (PubMed:14593172).Curated1

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
AL360314 Genomic DNA Translation: CAB96670.1 Sequence problems.
CP002688 Genomic DNA Translation: AED91664.1
AY069916 mRNA Translation: AAL47464.1
AY143977 mRNA Translation: AAN28916.1

NCBI Reference Sequences

More...
RefSeqi
NP_196696.2, NM_121173.5

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT5G11350.1; AT5G11350.1; AT5G11350

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
831006

Gramene; a comparative resource for plants

More...
Gramenei
AT5G11350.1; AT5G11350.1; AT5G11350

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT5G11350

<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
AL360314 Genomic DNA Translation: CAB96670.1 Sequence problems.
CP002688 Genomic DNA Translation: AED91664.1
AY069916 mRNA Translation: AAL47464.1
AY143977 mRNA Translation: AAN28916.1
RefSeqiNP_196696.2, NM_121173.5

3D structure databases

SMRiQ8VYU4
ModBaseiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G11350.1

PTM databases

iPTMnetiQ8VYU4

Proteomic databases

PaxDbiQ8VYU4
PRIDEiQ8VYU4
ProteomicsDBi223935

Genome annotation databases

EnsemblPlantsiAT5G11350.1; AT5G11350.1; AT5G11350
GeneIDi831006
GrameneiAT5G11350.1; AT5G11350.1; AT5G11350
KEGGiath:AT5G11350

Organism-specific databases

AraportiAT5G11350
TAIRilocus:2832132, AT5G11350

Phylogenomic databases

eggNOGiKOG2338, Eukaryota
HOGENOMiCLU_008664_0_0_1
InParanoidiQ8VYU4
PhylomeDBiQ8VYU4

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q8VYU4

Gene expression databases

ExpressionAtlasiQ8VYU4, baseline and differential
GenevisibleiQ8VYU4, AT

Family and domain databases

Gene3Di3.60.10.10, 2 hits
InterProiView protein in InterPro
IPR036691, Endo/exonu/phosph_ase_sf
IPR005135, Endo/exonuclease/phosphatase
PfamiView protein in Pfam
PF03372, Exo_endo_phos, 1 hit
SUPFAMiSSF56219, SSF56219, 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 nameiCCR4F_ARATH
<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: Q8VYU4
Secondary accession number(s): Q9LFM2
<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: November 25, 2008
Last sequence update: November 25, 2008
Last modified: August 12, 2020
This is version 106 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 programPlant 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. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
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