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Entry version 133 (18 Sep 2019)
Sequence version 1 (01 Dec 2001)
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Protein

40S ribosomal protein S4-1

Gene

RPS4A

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

<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

  • translation Source: GO_Central

<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 functionRibonucleoprotein, Ribosomal protein, RNA-binding, rRNA-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_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:
40S ribosomal protein S4-1
<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:RPS4A
Ordered Locus Names:At2g17360
ORF Names:F5J6.12
<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>OrganismiArabidopsis thaliana (Mouse-ear cress)
<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 identifieri3702 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<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
  • UP000006548 <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 2

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT2G17360

The Arabidopsis Information Resource

More...
TAIRi
locus:2827612 AT2G17360

<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 Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm

<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_00002501811 – 26140S ribosomal protein S4-1Add BLAST261

Proteomic databases

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

More...
PaxDbi
Q93VH9

PRoteomics IDEntifications database

More...
PRIDEi
Q93VH9

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q93VH9

<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
Q93VH9 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q93VH9 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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
1600, 10 interactors

Protein interaction database and analysis system

More...
IntActi
Q93VH9, 8 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT2G17360.1

<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
Q93VH9

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>Domaini42 – 104S4 RNA-bindingAdd BLAST63

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG0378 Eukaryota
COG1471 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000231325

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q93VH9

KEGG Orthology (KO)

More...
KOi
K02987

Identification of Orthologs from Complete Genome Data

More...
OMAi
RINAPKH

Database of Orthologous Groups

More...
OrthoDBi
1065966at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q93VH9

Family and domain databases

Conserved Domains Database

More...
CDDi
cd06087 KOW_RPS4, 1 hit
cd00165 S4, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.30.30.30, 1 hit
2.40.50.740, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00485 Ribosomal_S4e, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR032277 40S_S4_C
IPR005824 KOW
IPR041982 KOW_RPS4
IPR014722 Rib_L2_dom2
IPR000876 Ribosomal_S4e
IPR013845 Ribosomal_S4e_central_region
IPR038237 Ribosomal_S4e_central_sf
IPR013843 Ribosomal_S4e_N
IPR018199 Ribosomal_S4e_N_CS
IPR002942 S4_RNA-bd

The PANTHER Classification System

More...
PANTHERi
PTHR11581 PTHR11581, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF16121 40S_S4_C, 1 hit
PF00467 KOW, 1 hit
PF00900 Ribosomal_S4e, 1 hit
PF08071 RS4NT, 1 hit
PF01479 S4, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF002116 Ribosomal_S4, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00739 KOW, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00528 RIBOSOMAL_S4E, 1 hit
PS50889 S4, 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>Sequence (1+)i

<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.

This entry describes 1 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoform i produced by alternative splicing. AlignAdd to basket
Note: A number of isoforms are produced. According to EST sequences.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Isoform 1 (identifier: Q93VH9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MARGLKKHLK RLNAPKHWML DKLGGAFAPK PSSGPHKSRE CLPLVLIIRN
60 70 80 90 100
RLKYALTYRE VISILMQRHI QVDGKVRTDK TYPAGFMDVV SIPKTNENFR
110 120 130 140 150
LLYDTKGRFR LHSIKDEEAK FKLCKVRSIQ FGQKGIPYLN TYDGRTIRYP
160 170 180 190 200
DPLIKPNDTI KLDLEENKIV EFIKFDVGNV VMVTGGRNRG RVGVIKNREK
210 220 230 240 250
HKGSFETIHI QDSTGHEFAT RLGNVYTIGK GTKPWVSLPK GKGIKLTIIE
260
EARKRLSAQQ A
Length:261
Mass (Da):29,803
Last modified:December 1, 2001 - 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:iB847170791AA67E0
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 is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F4IMI7F4IMI7_ARATH
Ribosomal protein S4 (RPS4A) family...
At2g17360, F5J6.12, F5J6_12
184Annotation 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>

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
CP002685 Genomic DNA Translation: AEC06616.1
AF370469 mRNA Translation: AAK43846.1
AY035131 mRNA Translation: AAK59636.1
AY062983 mRNA Translation: AAL34157.1
AY064625 mRNA Translation: AAL47338.1
AY084230 mRNA Translation: AAM60830.1

Protein sequence database of the Protein Information Resource

More...
PIRi
C84551

NCBI Reference Sequences

More...
RefSeqi
NP_565414.1, NM_127291.4 [Q93VH9-1]

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT2G17360.1; AT2G17360.1; AT2G17360 [Q93VH9-1]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
816243

Gramene; a comparative resource for plants

More...
Gramenei
AT2G17360.1; AT2G17360.1; AT2G17360 [Q93VH9-1]

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT2G17360

Keywords - Coding sequence diversityi

Alternative splicing

<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
CP002685 Genomic DNA Translation: AEC06616.1
AF370469 mRNA Translation: AAK43846.1
AY035131 mRNA Translation: AAK59636.1
AY062983 mRNA Translation: AAL34157.1
AY064625 mRNA Translation: AAL47338.1
AY084230 mRNA Translation: AAM60830.1
PIRiC84551
RefSeqiNP_565414.1, NM_127291.4 [Q93VH9-1]

3D structure databases

SMRiQ93VH9
ModBaseiSearch...

Protein-protein interaction databases

BioGridi1600, 10 interactors
IntActiQ93VH9, 8 interactors
STRINGi3702.AT2G17360.1

PTM databases

iPTMnetiQ93VH9

Proteomic databases

PaxDbiQ93VH9
PRIDEiQ93VH9

Genome annotation databases

EnsemblPlantsiAT2G17360.1; AT2G17360.1; AT2G17360 [Q93VH9-1]
GeneIDi816243
GrameneiAT2G17360.1; AT2G17360.1; AT2G17360 [Q93VH9-1]
KEGGiath:AT2G17360

Organism-specific databases

AraportiAT2G17360
TAIRilocus:2827612 AT2G17360

Phylogenomic databases

eggNOGiKOG0378 Eukaryota
COG1471 LUCA
HOGENOMiHOG000231325
InParanoidiQ93VH9
KOiK02987
OMAiRINAPKH
OrthoDBi1065966at2759
PhylomeDBiQ93VH9

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q93VH9

Gene expression databases

ExpressionAtlasiQ93VH9 baseline and differential
GenevisibleiQ93VH9 AT

Family and domain databases

CDDicd06087 KOW_RPS4, 1 hit
cd00165 S4, 1 hit
Gene3Di2.30.30.30, 1 hit
2.40.50.740, 1 hit
HAMAPiMF_00485 Ribosomal_S4e, 1 hit
InterProiView protein in InterPro
IPR032277 40S_S4_C
IPR005824 KOW
IPR041982 KOW_RPS4
IPR014722 Rib_L2_dom2
IPR000876 Ribosomal_S4e
IPR013845 Ribosomal_S4e_central_region
IPR038237 Ribosomal_S4e_central_sf
IPR013843 Ribosomal_S4e_N
IPR018199 Ribosomal_S4e_N_CS
IPR002942 S4_RNA-bd
PANTHERiPTHR11581 PTHR11581, 1 hit
PfamiView protein in Pfam
PF16121 40S_S4_C, 1 hit
PF00467 KOW, 1 hit
PF00900 Ribosomal_S4e, 1 hit
PF08071 RS4NT, 1 hit
PF01479 S4, 1 hit
PIRSFiPIRSF002116 Ribosomal_S4, 1 hit
SMARTiView protein in SMART
SM00739 KOW, 1 hit
PROSITEiView protein in PROSITE
PS00528 RIBOSOMAL_S4E, 1 hit
PS50889 S4, 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 nameiRS41_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: Q93VH9
Secondary accession number(s): Q7XJS7
<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: September 19, 2006
Last sequence update: December 1, 2001
Last modified: September 18, 2019
This is version 133 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

Complete proteome, Reference proteome

Documents

  1. Ribosomal proteins
    Ribosomal proteins families and list of entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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