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Entry version 140 (02 Dec 2020)
Sequence version 1 (01 May 1999)
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Protein

Exosome complex component RRP4 homolog

Gene

RRP4

Organism
Arabidopsis thaliana (Mouse-ear cress)
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, maturation and degradation events. In vitro, is an active and distributive 3'->5' exonuclease requiring a free 3'-OH on the substrate and releasing nucleoside 5'-monophosphates (PubMed:11809881).

Required for normal embryo development (PubMed:18160042).

2 Publications

<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

  • RNA binding Source: GO_Central

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

<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 RRP4 homologCurated
Alternative name(s):
Ribosomal RNA-processing protein 4Curated
Short name:
AtRRP41 Publication
Short name:
AtRrp4p1 Publication
<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:RRP4Curated
Ordered Locus Names:At1g03360Imported
ORF Names:F15K9.4Imported
<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 1

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT1G03360

The Arabidopsis Information Resource

More...
TAIRi
locus:2014535, AT1G03360

<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, Exosome, 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

Embryonic lethality due to embryo developmental arrest at early globular stage.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_00004353171 – 322Exosome complex component RRP4 homologAdd BLAST322

Proteomic databases

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

More...
PaxDbi
Q9ZVT7

PRoteomics IDEntifications database

More...
PRIDEi
Q9ZVT7

ProteomicsDB: a multi-organism proteome resource

More...
ProteomicsDBi
226848

<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 a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified 'at protein level'.<br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed in roots, stems, rosette and cauline leaves, flowers and siliques.1 Publication

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q9ZVT7, baseline and differential

<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 (PubMed:11809881, PubMed:18160042).

Interacts with RPP41 (PubMed:11809881).

2 Publications

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
Q9ZVT7, 8 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT1G03360.1

<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
Q9ZVT7

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>Domaini94 – 172S1 motifPROSITE-ProRule annotationAdd BLAST79
Domaini182 – 237KHSequence analysisAdd BLAST56

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The two RNA-binding domains (S1 motif and KH domain) are separated by a conserved linker of five amino acids (KYGKL) and can bind RNA independently. Both domains are also needed for RNA degradation and interaction with RRP41, another exosome subunit.

<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 RRP4 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3013, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_034114_3_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q9ZVT7

Identification of Orthologs from Complete Genome Data

More...
OMAi
KRWRLDI

Database of Orthologous Groups

More...
OrthoDBi
1121868at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9ZVT7

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR026699, Exosome_RNA_bind1/RRP40/RRP4
IPR004088, KH_dom_type_1
IPR036612, KH_dom_type_1_sf
IPR012340, NA-bd_OB-fold
IPR022967, S1_dom

The PANTHER Classification System

More...
PANTHERi
PTHR21321, PTHR21321, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF15985, KH_6, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00316, S1, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249, SSF50249, 1 hit
SSF54791, SSF54791, 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.

Q9ZVT7-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVMRKLQLPL SQTQKVRFER AIERLQSLSS SANSDASVIV TDSIPVNHDD
60 70 80 90 100
AFLKGHGTSE VDGELLATVC GVVERVDKLV YVRTLRARYK PEVGDIVVGR
110 120 130 140 150
VIEVAQKRWR VELNFNQDGV LMLSSMNMPD GIQRRRTSVD ELNMRNIFVE
160 170 180 190 200
HDVVCAEVRN FQHDGSLQLQ ARSQKYGKLE KGQLLKVDPY LVKRSKHHFH
210 220 230 240 250
YVESLGIDLI IGCNGFIWVG EHVEVRDPMA IDDQKDEEMI SSSSTGKEQS
260 270 280 290 300
HIPLETRQTI CRIGNAIRVL SNLGFTVTLE VIMETVNLSN SKNIDIHDML
310 320
GSEFHVVVAE NEAERRRTKR KK
Length:322
Mass (Da):36,574
Last modified:May 1, 1999 - 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:iA6B87D8C0BF17786
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
AC005278 Genomic DNA Translation: AAC72108.1
CP002684 Genomic DNA Translation: AEE27563.1
BT010533 mRNA Translation: AAQ65156.1
AK176232 mRNA Translation: BAD43995.1

Protein sequence database of the Protein Information Resource

More...
PIRi
C86165

NCBI Reference Sequences

More...
RefSeqi
NP_171835.1, NM_100218.5

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT1G03360.1; AT1G03360.1; AT1G03360

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
839521

Gramene; a comparative resource for plants

More...
Gramenei
AT1G03360.1; AT1G03360.1; AT1G03360

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT1G03360

<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
AC005278 Genomic DNA Translation: AAC72108.1
CP002684 Genomic DNA Translation: AEE27563.1
BT010533 mRNA Translation: AAQ65156.1
AK176232 mRNA Translation: BAD43995.1
PIRiC86165
RefSeqiNP_171835.1, NM_100218.5

3D structure databases

SMRiQ9ZVT7
ModBaseiSearch...

Protein-protein interaction databases

IntActiQ9ZVT7, 8 interactors
STRINGi3702.AT1G03360.1

Proteomic databases

PaxDbiQ9ZVT7
PRIDEiQ9ZVT7
ProteomicsDBi226848

Genome annotation databases

EnsemblPlantsiAT1G03360.1; AT1G03360.1; AT1G03360
GeneIDi839521
GrameneiAT1G03360.1; AT1G03360.1; AT1G03360
KEGGiath:AT1G03360

Organism-specific databases

AraportiAT1G03360
TAIRilocus:2014535, AT1G03360

Phylogenomic databases

eggNOGiKOG3013, Eukaryota
HOGENOMiCLU_034114_3_0_1
InParanoidiQ9ZVT7
OMAiKRWRLDI
OrthoDBi1121868at2759
PhylomeDBiQ9ZVT7

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9ZVT7

Gene expression databases

ExpressionAtlasiQ9ZVT7, baseline and differential

Family and domain databases

InterProiView protein in InterPro
IPR026699, Exosome_RNA_bind1/RRP40/RRP4
IPR004088, KH_dom_type_1
IPR036612, KH_dom_type_1_sf
IPR012340, NA-bd_OB-fold
IPR022967, S1_dom
PANTHERiPTHR21321, PTHR21321, 1 hit
PfamiView protein in Pfam
PF15985, KH_6, 1 hit
SMARTiView protein in SMART
SM00316, S1, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
SSF54791, SSF54791, 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 nameiRRP4_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: Q9ZVT7
<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: January 20, 2016
Last sequence update: May 1, 1999
Last modified: December 2, 2020
This is version 140 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 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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