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 LOC_Os04g41060.1
Common NameOs04g0487550
Organism
Oryza sativa subsp. japonica
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; Oryza sativa
Family C3H
Protein Properties Length: 147aa    MW: 15845.9 Da    PI: 9.605
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g41060.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.91.5e-07117136626
                       -SGGGGTS--TTTTT-SS-SS CS
           zf-CCCH   6 CrffartGtCkyGdrCkFaHg 26 
                       C +f++ G C++Gd C FaHg
  LOC_Os04g41060.1 117 CLDFRK-GGCNHGDACEFAHG 136
                       999999.*************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003563.3E-4112137IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010310.962116138IPR000571Zinc finger, CCCH-type
PfamPF006421.3E-5116136IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.109.5E-6117137IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 147 aa     Download sequence    Send to blast
MTESTKIKYC RADSGSGSKP LSAETKTRLM ADGKKIDEEK KDGTAVRRVL FWFAVLVIRF  60
ALLMAMHYYH DVTSSRCDGA RAGGARTGRS ALSRVRGRRR GGGTPDTRPY CDSGTACLDF  120
RKGGCNHGDA CEFAHGVFDN SSADLA*
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ7XSB2
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g41060.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g41060
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAL6629461e-126AL662946.2 Oryza sativa genomic DNA, chromosome 4, BAC clone: OJ991113_30, complete sequence.
GenBankAP0149601e-126AP014960.1 Oryza sativa Japonica Group DNA, chromosome 4, cultivar: Nipponbare, complete sequence.
GenBankCP0126121e-126CP012612.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 4 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
SwissprotQ7XSB21e-104C3H29_ORYSJ; Putative zinc finger CCCH domain-containing protein 29
TrEMBLA0A0E0PAT51e-102A0A0E0PAT5_ORYRU; Uncharacterized protein
TrEMBLI1PMG61e-102I1PMG6_ORYGL; Uncharacterized protein
STRINGORUFI04G18220.11e-103(Oryza rufipogon)
STRINGOS04T0487550-001e-103(Oryza sativa)
STRINGORGLA04G0138500.11e-103(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP2346255
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G29190.11e-11C3H family protein
Publications ? help Back to Top
  1. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]