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 Brast04G178400.2.p
Organism
Brachypodium stacei
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium
Family Trihelix
Protein Properties Length: 722aa    MW: 79969.8 Da    PI: 9.2194
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Brast04G178400.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix68.51.3e-21629709186
            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+ ++
  Brast04G178400.2.p 629 KWKPEEIKSLIQLRGEMNEKFQTVKGRMVLWEEISGSMLKQGITRTPAQCKSLWTSLVQKYEESKKDEES-----MKTWPYFSAMD 709
                         7******************************************************************998.....579******98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.2E-369180IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.42E-4516345IPR001279Metallo-beta-lactamase
PfamPF075211.0E-6288317IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.793622686IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.1E-5626688IPR009057Homeodomain-like
SMARTSM007170.0063626688IPR001005SANT/Myb domain
CDDcd122039.18E-23628693No hitNo description
PfamPF138377.4E-18628710No 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: 722 aa     Download sequence    Send to blast
MAMKITSVIP ALDSSTPIFA SSFTMELIKK RLKEFGIFLS SRLKSFRVRN RFQAGPFEVE  60
PIRVTHSIPD CCGLVLRCGD GTIFHTGDWK IDESPVDGKI FDRQALEELS KEGVTLMMSD  120
STNILSPGRS TSESVVASSL LRHISEAKGR VITTQFASNI HRIGSIKAAA DLTGRRLAFV  180
GMSLRTYLEA AFRDGKAPLD PSTLVKAEDM DAYDPKSLLV VTTGSQAEPR AALNLASYGG  240
SHALKLSKED VLLYSAKVIP GNESRVMKML NRLTDLGPKI VMGKDSGLHT SGHAYHDELE  300
EVLQIVKPQH FLPVHGELLF LKEHELLGRS TGIRHTTVIK NGEMLGVSHL RNRKVLSNGF  360
VALGKQEFKL MYSDGDKAFG TSTDLCIDER LRIASDGIIF VSMEIFRPQK ELASPQSGLK  420
GKFKITTRCL WLDNGRLLDA LYKAAHAALS SCPLNCPLSH MERMVSEILR KMVRKYSGKR  480
PDVIVVASEN TTVGFTEEVT DKSPGKFGPF SATRHLSRSP DRSLEDSDKT RLENPEGEAA  540
ESIPEVMRTT SDDATTSTNG ESFFSSDLHQ PKTLDHFWES FKSPTAVKIA RIVNSSAQGN  600
KPKFGKISMI DKDSSMPVPA PAKSPRKNKW KPEEIKSLIQ LRGEMNEKFQ TVKGRMVLWE  660
EISGSMLKQG ITRTPAQCKS LWTSLVQKYE ESKKDEESMK TWPYFSAMDS FLSCEGEMAT  720
K*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-5917489104560RIBONUCLEASE J
5a0t_B4e-5917489104560RIBONUCLEASE J
5a0v_A4e-5917489104560RIBONUCLEASE J
5a0v_B4e-5917489104560RIBONUCLEASE 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapBrast04G178400.2.p
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
GenBankAK2496120.0AK249612.1 Hordeum vulgare subsp. vulgare cDNA clone: FLbaf47b03, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003575091.20.0uncharacterized protein LOC100825739 isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLI1IAB60.0I1IAB6_BRADI; Uncharacterized protein
STRINGBRADI3G45230.10.0(Brachypodium distachyon)
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]