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Entry version 114 (16 Oct 2019)
Sequence version 1 (01 Mar 2002)
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Protein

DNA repair protein RAD4

Gene

RAD4

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 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

May have a role in the nucleotide excision repair (NER) pathway.1 Publication

<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

Biological processDNA damage, DNA repair

<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:
DNA repair protein RAD4Imported
<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:RAD4
Ordered Locus Names:At5g16630Imported
ORF Names:MTG13.7Imported
<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 5

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT5G16630

The Arabidopsis Information Resource

More...
TAIRi
locus:2174160 AT5G16630

<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

<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_00004334811 – 865DNA repair protein RAD4Add BLAST865

Proteomic databases

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

More...
PaxDbi
Q8W489

<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
Q8W489 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q8W489 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_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

Interacts with CML19. Calcium is required for this interaction.

1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
3702.AT5G16630.2

<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 biasi39 – 119Asp-richPROSITE-ProRule annotationAdd BLAST81
Compositional biasi441 – 445Poly-AlaSequence analysis5
Compositional biasi521 – 526Poly-SerSequence analysis6
Compositional biasi748 – 751Poly-GluSequence analysis4

<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 XPC family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2179 Eukaryota
COG5535 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000144515

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8W489

KEGG Orthology (KO)

More...
KOi
K10838

Identification of Orthologs from Complete Genome Data

More...
OMAi
EEKWVCV

Database of Orthologous Groups

More...
OrthoDBi
750482at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q8W489

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.70.2460, 1 hit
3.90.260.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR018327 BHD_2
IPR004583 DNA_repair_Rad4
IPR038765 Papain-like_cys_pep_sf
IPR018325 Rad4/PNGase_transGLS-fold
IPR018326 Rad4_beta-hairpin_dom1
IPR018328 Rad4_beta-hairpin_dom3
IPR042488 Rad4_BHD3_sf
IPR002931 Transglutaminase-like
IPR036985 Transglutaminase-like_sf

The PANTHER Classification System

More...
PANTHERi
PTHR12135 PTHR12135, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF10403 BHD_1, 1 hit
PF10404 BHD_2, 1 hit
PF10405 BHD_3, 1 hit
PF03835 Rad4, 1 hit
PF01841 Transglut_core, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01030 BHD_1, 1 hit
SM01031 BHD_2, 1 hit
SM01032 BHD_3, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54001 SSF54001, 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 has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

Q8W489-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKSRSESKNC RLAQASRVAV NKVLDKSSAR GSRGKKKQDD NCDSAKRDKG
60 70 80 90 100
VNGKGKQALD ARLIDNVLED RGCGNVDDDE MNDSDWEDCP IPSLDSTVDD
110 120 130 140 150
NNVDDTRELT IEFDDDVPDA KKQKNAYRAT AEDKVRAELV HKVHLLCLLA
160 170 180 190 200
RGRIVDSACN DPLIQAALLS LLPSYLTKVS NLEKVTVKDI APLLRWVREN
210 220 230 240 250
FSVSCSPSSE KSFRTSLAFA LESRKGTAEE LAALAVALLR ALKLTTRFVS
260 270 280 290 300
ILDVASLKPG ADRNESSGQN RAKMKHGIFR TSTLMVPKQQ AISSYPKKSS
310 320 330 340 350
SHVKNKSPFE KPQLGNPLGS DQVQDNAVNS SCEAGMSIKS DGTRRKGDVE
360 370 380 390 400
FERQIAMALS ATADNQQSSQ VNNTKKVREI TKISNSSSVS DQVISTAFGS
410 420 430 440 450
KKVDSPLCWL EVYCNGENMD GKWVHVDAVN GMIDAEQNIE AAAAACKTVL
460 470 480 490 500
RYVVAFAAGG AKDVTRRYCT KWHTISSKRV SSVWWDMVLA PLVHLESGAT
510 520 530 540 550
HDEDIALRNF NGLNPVSSRA SSSSSSFGIR SALEDMELAT RALTESLPTN
560 570 580 590 600
QQAYKSHEIY AIEKWLHKNQ ILHPKGPVLG FCSGHPVYPR TCVQTLKTKE
610 620 630 640 650
RWLRDGLQLK ANEVPSKILK RNSKFKKVKD FEDGDNNIKG GSSCMELYGK
660 670 680 690 700
WQMEPLCLPP AVNGIVPKNE RGQVDVWSEK CLPPGTVHLR FPRIFAVAKR
710 720 730 740 750
FGIDYAPAMV GFEYRSGGAT PIFEGIVVCT EFKDTILEAY AEEQEKKEEE
760 770 780 790 800
ERRRNEAQAA SRWYQLLSSI LTRERLKNRY ANNSNDVEAK SLEVNSETVV
810 820 830 840 850
KAKNVKAPEK QRVAKRGEKS RVRKSRNEDE SHEHVFLDEE ETFDEETSVK
860
TKRCKCGFSV EVEQM
Length:865
Mass (Da):96,285
Last modified:March 1, 2002 - 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:iBA1607F048A5F33C
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
A0A1R7T387A0A1R7T387_ARATH
DNA repair protein Rad4 family
RAD4 ATRAD4, MTG13.7, MTG13_7, At5g16630
637Annotation score:

Annotation score:2 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
AB008270 Genomic DNA No translation available.
CP002688 Genomic DNA Translation: AED92319.1
CP002688 Genomic DNA Translation: AED92320.1
AY062755 mRNA Translation: AAL32833.1
BT010359 mRNA Translation: AAQ56802.1

NCBI Reference Sequences

More...
RefSeqi
NP_001031894.1, NM_001036817.3
NP_197166.2, NM_121669.3

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT5G16630.1; AT5G16630.1; AT5G16630
AT5G16630.2; AT5G16630.2; AT5G16630

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
831525

Gramene; a comparative resource for plants

More...
Gramenei
AT5G16630.1; AT5G16630.1; AT5G16630
AT5G16630.2; AT5G16630.2; AT5G16630

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT5G16630

<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
AB008270 Genomic DNA No translation available.
CP002688 Genomic DNA Translation: AED92319.1
CP002688 Genomic DNA Translation: AED92320.1
AY062755 mRNA Translation: AAL32833.1
BT010359 mRNA Translation: AAQ56802.1
RefSeqiNP_001031894.1, NM_001036817.3
NP_197166.2, NM_121669.3

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi3702.AT5G16630.2

Proteomic databases

PaxDbiQ8W489

Genome annotation databases

EnsemblPlantsiAT5G16630.1; AT5G16630.1; AT5G16630
AT5G16630.2; AT5G16630.2; AT5G16630
GeneIDi831525
GrameneiAT5G16630.1; AT5G16630.1; AT5G16630
AT5G16630.2; AT5G16630.2; AT5G16630
KEGGiath:AT5G16630

Organism-specific databases

AraportiAT5G16630
TAIRilocus:2174160 AT5G16630

Phylogenomic databases

eggNOGiKOG2179 Eukaryota
COG5535 LUCA
HOGENOMiHOG000144515
InParanoidiQ8W489
KOiK10838
OMAiEEKWVCV
OrthoDBi750482at2759
PhylomeDBiQ8W489

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q8W489

Gene expression databases

ExpressionAtlasiQ8W489 baseline and differential
GenevisibleiQ8W489 AT

Family and domain databases

Gene3Di3.30.70.2460, 1 hit
3.90.260.10, 1 hit
InterProiView protein in InterPro
IPR018327 BHD_2
IPR004583 DNA_repair_Rad4
IPR038765 Papain-like_cys_pep_sf
IPR018325 Rad4/PNGase_transGLS-fold
IPR018326 Rad4_beta-hairpin_dom1
IPR018328 Rad4_beta-hairpin_dom3
IPR042488 Rad4_BHD3_sf
IPR002931 Transglutaminase-like
IPR036985 Transglutaminase-like_sf
PANTHERiPTHR12135 PTHR12135, 1 hit
PfamiView protein in Pfam
PF10403 BHD_1, 1 hit
PF10404 BHD_2, 1 hit
PF10405 BHD_3, 1 hit
PF03835 Rad4, 1 hit
PF01841 Transglut_core, 1 hit
SMARTiView protein in SMART
SM01030 BHD_1, 1 hit
SM01031 BHD_2, 1 hit
SM01032 BHD_3, 1 hit
SUPFAMiSSF54001 SSF54001, 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 nameiRAD4_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: Q8W489
<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: July 22, 2015
Last sequence update: March 1, 2002
Last modified: October 16, 2019
This is version 114 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. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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