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Entry version 126 (11 Dec 2019)
Sequence version 2 (25 Jan 2012)
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Protein

tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like

Gene

At4g38890

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

Catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs.By similarity

<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

FMNBy similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei398FMNBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei429Proton donorBy similarity1
Binding sitei468FMNBy similarity1
Binding sitei498FMNBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri94 – 125C3H1-type 1PROSITE-ProRule annotationAdd BLAST32
Zinc fingeri138 – 163C3H1-type 2PROSITE-ProRule annotationAdd BLAST26
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi344 – 346FMNBy similarity3
Nucleotide bindingi531 – 533FMNBy similarity3
Nucleotide bindingi556 – 557FMNBy similarity2

<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 functionOxidoreductase
Biological processtRNA processing
LigandFlavoprotein, FMN, Metal-binding, Zinc

<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:
tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like (EC:1.3.1.-)
Alternative name(s):
Zinc finger CCCH domain-containing protein 50
Short name:
AtC3H50
tRNA-dihydrouridine synthase 3-like
<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
Ordered Locus Names:At4g38890
ORF Names:F19H22.4
<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 4

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT4G38890

The Arabidopsis Information Resource

More...
TAIRi
locus:2141821 AT4G38890

<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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedCombined sources
<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_00003719602 – 691tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-likeAdd BLAST690

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 residuei2N-acetylserineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

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

More...
PaxDbi
Q9T0J6

PRoteomics IDEntifications database

More...
PRIDEi
Q9T0J6

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q9T0J6

<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
Q9T0J6 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q9T0J6 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

STRING: functional protein association networks

More...
STRINGi
3702.AT4G38890.1

<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 biasi55 – 58Poly-Pro4

<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 Dus family. Dus3 subfamily.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri94 – 125C3H1-type 1PROSITE-ProRule annotationAdd BLAST32
Zinc fingeri138 – 163C3H1-type 2PROSITE-ProRule annotationAdd BLAST26

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2333 Eukaryota
COG0042 LUCA

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q9T0J6

KEGG Orthology (KO)

More...
KOi
K05544

Identification of Orthologs from Complete Genome Data

More...
OMAi
IAANKPW

Database of Orthologous Groups

More...
OrthoDBi
1016307at2759

Family and domain databases

Conserved Domains Database

More...
CDDi
cd02801 DUS_like_FMN, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.70, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR013785 Aldolase_TIM
IPR035587 DUS-like_FMN-bd
IPR001269 tRNA_hU_synthase
IPR018517 tRNA_hU_synthase_CS
IPR000571 Znf_CCCH

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01207 Dus, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01136 UPF0034, 1 hit
PS50103 ZF_C3H1, 2 hits

<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>Sequencei

<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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q9T0J6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSDVIAEHAV DTSVEGDAKA ALPVQSTKQF SVYEATSEEL IERSMAPIKK
60 70 80 90 100
EFLCPPPPSR SVKQNDAADV RAPQSGLVQE KKSKRQLKRE RREQSTINLC
110 120 130 140 150
PQVARTEDVD SCQYKDKCRF NHDIEAFKAQ KADDIEGQCP FVASGMKCAY
160 170 180 190 200
GLSCRFLGSH RDITGNSDDK EKSEMNFFNK ETQRLLWKNK MTFTNADAKL
210 220 230 240 250
KSLGLLGHAK KSNAAEEITA EKTQNGMNGT QATEVAVDSA VSSEHTSEMI
260 270 280 290 300
QDVDIPGPLE TEEVRPMKKA KSEDQKNSKT GDVGGVYDGV KLEEETKKNG
310 320 330 340 350
YPTSKANVED EDSIKIVETD SSLKLHPREK KKLIDFRDKL YLAPLTTVGN
360 370 380 390 400
LPFRRLCKVL GADVTCGEMA MCTNLLQGQA SEWALLRRHS SEDLFGVQIC
410 420 430 440 450
GSYPDTVSRV VELIDRECTV DFIDINMGCP IDMVVNKSAG SALLNKPLRM
460 470 480 490 500
KNIVEVSSSI VETPITIKVR TAFFEGKNRI DSLIADIGNW GATAVTIHGR
510 520 530 540 550
SRQQRYSKSA DWDYIYQCTK NATTNLQVIG NGDVYSYLDW NKHKSDCPEL
560 570 580 590 600
SSCMIARGAL IKPWIFTEIK EQRHWDITSG ERLNIMKDFV RFGLQHWGSD
610 620 630 640 650
TKGVETTRHF LLEWLSYTFR YIPVGLLDVI PQQINWRPPS YFGRDDLETL
660 670 680 690
MMSESAGDWV RISEMLLGKV PEGFTFAPKH KSNAYDRAEN G
Length:691
Mass (Da):77,574
Last modified:January 25, 2012 - 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:i851DDA702F93F227
GO

<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 BAC43063 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.Curated
The sequence CAB38623 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence CAB80552 differs from that shown. Reason: Erroneous gene model prediction.Curated

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
AL035656 Genomic DNA Translation: CAB38623.1 Sequence problems.
AL161594 Genomic DNA Translation: CAB80552.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE86987.1
AK118455 mRNA Translation: BAC43063.1 Different initiation.
BT006228 mRNA Translation: AAP12877.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T06088

NCBI Reference Sequences

More...
RefSeqi
NP_195600.2, NM_120049.4

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT4G38890.1; AT4G38890.1; AT4G38890

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
830044

Gramene; a comparative resource for plants

More...
Gramenei
AT4G38890.1; AT4G38890.1; AT4G38890

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT4G38890

<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
AL035656 Genomic DNA Translation: CAB38623.1 Sequence problems.
AL161594 Genomic DNA Translation: CAB80552.1 Sequence problems.
CP002687 Genomic DNA Translation: AEE86987.1
AK118455 mRNA Translation: BAC43063.1 Different initiation.
BT006228 mRNA Translation: AAP12877.1
PIRiT06088
RefSeqiNP_195600.2, NM_120049.4

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.AT4G38890.1

PTM databases

iPTMnetiQ9T0J6

Proteomic databases

PaxDbiQ9T0J6
PRIDEiQ9T0J6

Genome annotation databases

EnsemblPlantsiAT4G38890.1; AT4G38890.1; AT4G38890
GeneIDi830044
GrameneiAT4G38890.1; AT4G38890.1; AT4G38890
KEGGiath:AT4G38890

Organism-specific databases

AraportiAT4G38890
TAIRilocus:2141821 AT4G38890

Phylogenomic databases

eggNOGiKOG2333 Eukaryota
COG0042 LUCA
InParanoidiQ9T0J6
KOiK05544
OMAiIAANKPW
OrthoDBi1016307at2759

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q9T0J6

Gene expression databases

ExpressionAtlasiQ9T0J6 baseline and differential
GenevisibleiQ9T0J6 AT

Family and domain databases

CDDicd02801 DUS_like_FMN, 1 hit
Gene3Di3.20.20.70, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR035587 DUS-like_FMN-bd
IPR001269 tRNA_hU_synthase
IPR018517 tRNA_hU_synthase_CS
IPR000571 Znf_CCCH
PfamiView protein in Pfam
PF01207 Dus, 1 hit
PROSITEiView protein in PROSITE
PS01136 UPF0034, 1 hit
PS50103 ZF_C3H1, 2 hits

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 nameiDUS3L_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: Q9T0J6
Secondary accession number(s): F4JUH9, Q8GX38
<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: May 5, 2009
Last sequence update: January 25, 2012
Last modified: December 11, 2019
This is version 126 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. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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