PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA03G19920.1
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 Trihelix
Protein Properties Length: 787aa    MW: 86986 Da    PI: 8.5211
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA03G19920.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix452.9e-147197752586
         trihelix  25 klkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                      k ++ lWee+s+ m ++g++r+p qCk+ w +l ++y++ k+ e++     ++t+pyf +++
  ONIVA03G19920.1 719 KGRMVLWEEISSSMLSQGISRTPAQCKSLWTSLVQKYEESKKDEES-----VKTWPYFLDMD 775
                      567889************************************9998.....689******98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.4E-6580330IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.33E-7181495IPR001279Metallo-beta-lactamase
SMARTSM008497.6E-2493290IPR001279Metallo-beta-lactamase
PfamPF127061.1E-9104240IPR001279Metallo-beta-lactamase
PfamPF075211.1E-6438467IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PfamPF138372.1E-11721776No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 787 aa     Download sequence    Send to blast
MVALASLSSL SPCGLARRRS ASSAASISCC AAPPPPSAKG SQESRTPRRR VRKTEGATKS  60
LEDSVKRKME QFYEGLDGPP LRVLPIGGLG EIGMNCMLVG NYDRYILIDA GVMFPDFDEF  120
GVQKIIPDTT FIKKWSHKIE AVIITHGHED HIGALPWVIP ALDSSTPIFA SSFTMELIKR  180
RLKEFGIFLS SRLKVFRVRK RFQAGPFEVE PLRVTHSIPD CCGLVLRCAD GIIFHTGDWK  240
IDESPVDGKI FDRQALEELS KEGVTLMMSD STNVLSPGRS ISESVVAGSL LRHISEAKGR  300
VITTQFASNI HRIGSIKAAA DLTGRKLVFV GMSLRTYLDA AFRDGKSPID PSTLVKVEDM  360
DAYAPNDLLV VTTGSQAEPR AALNLASFGG SHALKLSKED VLLYSAKVIP GNESRVMKML  420
NRLTELGPKI VMGKDAGLHT SGHAYHDELE EVLQIVKPQH FLPVHGELLF LKEHELLGRS  480
TGIRHTTVIK NGEMLGVSHL RNRRVLSNGF VALGKEDLRL MYSDGDKAFG TSTDLCIDER  540
LRIASDGVIF VSMEIFRPQK ELASSQSGLK GKFKITTRCL WLDNGRLLDA LYKAAYAALS  600
SCPVNCPLSH MERMVSEILR KMAFEQEFRS LEESDKSRPE NTEGEAKENL PDVLRTTRDD  660
ATTSSNGEAF FSSDLHKPKT LEHFWDSFKS PTAVKIARIV NGSAQGSKSK IGKISITVKG  720
RMVLWEEISS SMLSQGISRT PAQCKSLWTS LVQKYEESKK DEESVKTWPY FLDMDRVLSS  780
QGEMATQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-838155419483RIBONUCLEASE J
5a0t_B3e-838155419483RIBONUCLEASE J
5a0v_A3e-838155419483RIBONUCLEASE J
5a0v_B3e-838155419483RIBONUCLEASE J
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015627210.10.0ribonuclease J isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0E0GMY40.0A0A0E0GMY4_ORYNI; Uncharacterized protein
STRINGOBART02G19580.10.0(Oryza barthii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]