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 LOC_Os02g33610.1
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 Trihelix
Protein Properties Length: 883aa    MW: 97367.7 Da    PI: 9.1397
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g33610.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix712.1e-22790870186
          trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                       +W+ +e++ Li++r em+e++++ k ++ lWee+s+ m ++g++r+p qCk+ w +l ++y++ k+ e++     ++t+pyf +++
  LOC_Os02g33610.1 790 KWKPEEIKSLIQMRGEMNEQFQTVKGRMVLWEEISSSMLSQGISRTPAQCKSLWTSLVQKYEESKKDEES-----VKTWPYFLDMD 870
                       7*****************************************************************9998.....689******98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.7E-6580330IPR001279Metallo-beta-lactamase
SuperFamilySSF562817.94E-7181506IPR001279Metallo-beta-lactamase
SMARTSM008497.6E-2493290IPR001279Metallo-beta-lactamase
PfamPF127061.3E-9104240IPR001279Metallo-beta-lactamase
PfamPF075211.3E-6449478IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.863783847IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.604.2E-5786849IPR009057Homeodomain-like
SMARTSM007170.0039787849IPR001005SANT/Myb domain
CDDcd122034.20E-22789854No hitNo description
PfamPF138373.1E-17789871No 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: 883 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 PSTLVHLIES  360
RFLLKVKVED MDAYAPNDLL VVTTGSQAEP RAALNLASFG GSHALKLSKE DVLLYSAKVI  420
PGNESRVMKM LNRLTELGPK IVMGKDAGLH TSGHAYHDEL EEVLQIVKPQ HFLPVHGELL  480
FLKEHELLGR STGIRHTTVI KNGEMLGVSH LRNRRVLSNG FVALGKEDLR LMYSDGDKAF  540
GTSTDLCIDE RLRIASDGVI FVSMEIFRPQ KELASSQSGL KGKFKITTRC LWLDNGRLLD  600
ALYKAAYAAL SSCPVNCPLS HMERMVSEIL RKMVRKYSGK RPDVIAVATE NTTVSFVEDS  660
ETKSSGKFGS FSAPRHSSRS SGRSLEESDK SCPENTEGEA KENLPDVLRT TRDDATTSSN  720
GEAFFSSDLH KPKTLEHFWD SFKSPTAVKI ARIVNGSAQG SKSKIGKISI VGKDSSDPSS  780
APVKSSKKNK WKPEEIKSLI QMRGEMNEQF QTVKGRMVLW EEISSSMLSQ GISRTPAQCK  840
SLWTSLVQKY EESKKDEESV KTWPYFLDMD RVLSSQGEMA TQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A8e-828165019560RIBONUCLEASE J
5a0t_B8e-828165019560RIBONUCLEASE J
5a0v_A8e-828165019560RIBONUCLEASE J
5a0v_B8e-828165019560RIBONUCLEASE J
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.509510.0callus| leaf| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329696840.0
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g33610.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g33610
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0596660.0AK059666.1 Oryza sativa Japonica Group cDNA clone:001-031-F01, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015627210.10.0ribonuclease J isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0E0CLN30.0A0A0E0CLN3_9ORYZ; Uncharacterized protein
STRINGOGLUM02G19870.10.0(Oryza glumipatula)
STRINGORUFI02G20630.20.0(Oryza rufipogon)
STRINGONIVA03G19920.20.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP49963542
Representative plantOGRP30821521
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]