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 BGIOSGA008381-PA
Common NameOsI_07566
Organism
Oryza sativa subsp. indica
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: 871aa    MW: 96031.1 Da    PI: 9.0479
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
BGIOSGA008381-PAgenomeRISView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix71.12.1e-22779859186
          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 +++
  BGIOSGA008381-PA 779 KWKPEEIKSLIQMRGEMNEQFQTVKGRMVLWEEISSSMLSQGISRTPAQCKSLWTSLVQKYEESKKDEES-----VKTWPYFLDMD 859
                       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
SuperFamilySSF562811.89E-7181495IPR001279Metallo-beta-lactamase
SMARTSM008497.6E-2493290IPR001279Metallo-beta-lactamase
PfamPF127061.3E-9104240IPR001279Metallo-beta-lactamase
PfamPF075211.3E-6438467IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.863772836IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.604.1E-5775838IPR009057Homeodomain-like
SMARTSM007170.0039776838IPR001005SANT/Myb domain
CDDcd122033.95E-22778843No hitNo description
PfamPF138373.1E-17778860No 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: 871 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 KMVRKYSGKR PDVIAVATEN TTVSFVEDSE TKSSGKFGSF  660
SAPRHSSRSS GRSLEESDKS CPENTEGEAK ENLPDVLRTT RDDATTSSNG EAFFSSDLHK  720
PKTLEHFWDS FKSPTAVKIA RIVNGSAQGS KSKIGKISIV GKDSSDPSSA PVKSSKKNKW  780
KPEEIKSLIQ MRGEMNEQFQ TVKGRMVLWE EISSSMLSQG ISRTPAQCKS LWTSLVQKYE  840
ESKKDEESVK TWPYFLDMDR VLSSQGEMAT Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-848163919560RIBONUCLEASE J
5a0t_B1e-848163919560RIBONUCLEASE J
5a0v_A1e-848163919560RIBONUCLEASE J
5a0v_B1e-848163919560RIBONUCLEASE 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}.
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 -- 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
TrEMBLB8AJB50.0B8AJB5_ORYSI; Uncharacterized protein
STRINGORUFI02G20630.20.0(Oryza rufipogon)
STRINGONIVA03G19920.20.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP49963542
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]