PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA04G00640.2
Organism
Oryza nivara
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family C3H
Protein Properties Length: 685aa    MW: 75683.6 Da    PI: 6.5577
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA04G00640.2genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.22.2e-061041161426
                      --TTTTT-SS-SS CS
          zf-CCCH  14 tCkyGdrCkFaHg 26 
                       CkyGd+C+F+H+
  ONIVA04G00640.2 104 SCKYGDSCRFSHD 116
                      7***********6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010310.5387118IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:3.20.20.702.8E-74329572IPR013785Aldolase-type TIM barrel
SuperFamilySSF513951.16E-64333644No hitNo description
CDDcd028011.26E-94333568No hitNo description
PfamPF012075.9E-54336570IPR001269tRNA-dihydrouridine synthase
PROSITE patternPS011360417435IPR018517tRNA-dihydrouridine synthase, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0002943Biological ProcesstRNA dihydrouridine synthesis
GO:0055114Biological Processoxidation-reduction process
GO:0017150Molecular FunctiontRNA dihydrouridine synthase activity
GO:0046872Molecular Functionmetal ion binding
GO:0050660Molecular Functionflavin adenine dinucleotide binding
Sequence ? help Back to Top
Protein Sequence    Length: 685 aa     Download sequence    Send to blast
MAAAAAAAAA APPADPPDSS PAASSPPRPS PEELVARAVA PVKPAFLRPP PVRDAPKDEG  60
KANDGGAVVA EKKSKRQLKR ERKQEQKSSS HLCIEVGKSG NVSSCKYGDS CRFSHDIDAY  120
LAQKPADLEG TCPFTNLDQL CPYGLTCRFL GTHKDIHAAS GNLSEKHEIN ALNKDIQKLL  180
WKNKYKFPKA SAQIKLLGLK EVIKSKPDAA NDDKKVNHDN LDGNDDENKE PLCNPPVNAE  240
CDSTLCEELD RSEGEPLIDN SIPCVEPRPT KKSKVESDEI DKHGAGTLNT NTESEDPNLS  300
NGLEPSNNAS SCRTDLITTP HLREKKIIDF REKLYLAPLT TVGNLPFRRL CKTLGADITC  360
GEMAMCTNLL QGQASEWALL RRHSSEDLFG VQICGAYPDT VARTVELVDN ECSIDFIDIN  420
MGCPIDIVVN KGAGSSLLTK PMRIKSIVQA ASTVTEKPLT VKVRTAFFEG RNRADSIVSD  480
IYDWGASAIT VHGRSRQQRY SKLADWDYIY QCAQKAPDQL HVVGNGDVFS FTDWNKHVSG  540
CSKISTCMIA RGALIKPWIF TEVKEQRHWD ITSGERFNIL KDFVSFGLEH WGSDSKGVET  600
TRYFLLEWLS YTCRYIPVGL LDVIPQRLNW RPPSYCGRDD LETLMISDSA ADWIRISEML  660
LGKVPEGFTF TPKHKSNAYD RAENG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ei9_A2e-2733056427257tRNA-dihydrouridine synthase B
6ei9_B2e-2733056427257tRNA-dihydrouridine synthase B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtCatalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1116990.0AK111699.1 Oryza sativa Japonica Group cDNA clone:J023009K15, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015635918.10.0LOW QUALITY PROTEIN: tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
SwissprotQ7XT070.0DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBLA0A0E0GX690.0A0A0E0GX69_ORYNI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRINGORGLA04G0007500.10.0(Oryza glaberrima)
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]