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 Bradi3g45230.1.p
Common NameBRADI_3g45230, LOC100825739
Organism
Brachypodium distachyon
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: 876aa    MW: 96628.9 Da    PI: 8.9705
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bradi3g45230.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix68.11.7e-21783863186
          trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                       +W+ +e++ Li++r em+e++++ k ++ lWee+s+ m  +g++r+p qCk+ w +l ++y++ k+  ++      +t+pyf+ ++
  Bradi3g45230.1.p 783 KWKPEEIKSLIQLRGEMNEKFQTVKGRMVLWEEISASMLNQGITRTPAQCKSLWTSLVQKYEESKKDGEG-----MKTWPYFSAMD 863
                       7*************************************************************99988887.....479******98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.104.4E-6884334IPR001279Metallo-beta-lactamase
SuperFamilySSF562813.69E-7385499IPR001279Metallo-beta-lactamase
SMARTSM008491.4E-2597294IPR001279Metallo-beta-lactamase
PfamPF127061.1E-10109244IPR001279Metallo-beta-lactamase
PfamPF075211.2E-6442471IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.898776840IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.3E-5780842IPR009057Homeodomain-like
SMARTSM007170.0012780842IPR001005SANT/Myb domain
PfamPF138372.6E-18782864No hitNo description
CDDcd122032.07E-23782847No 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: 876 aa     Download sequence    Send to blast
MVALASLSSL CPCGLARRRS ASASASTSTS ISCCAVATPP SGKGSHESRI PRRRFRRTEG  60
ATKSMEDSVK RKLEQFYEGL DGPPLRVLPI GGLGEIGMNC MLVGNYDRYI LIDAGVMFPD  120
YDEFGVQKII PDTTFIKKWS HKIEAVIITH GHEDHIGALP WVIPALDSNT PIFASSFTME  180
LIKKRLKEFG IFLSSRLKSF RVRNRFQAGP FEVEPIRVTH SIPDCCGLVL RCGDGTIFHT  240
GDWKIDESPV DGKIFDREAL EELSKEGVTL MMSDSTNILS PGRSTSESVV ASSLLRHISE  300
AKGRVITTQF ASNIHRIGSI KAAADLTGRR LAFVGMSLRT YLEAAFRDGK APLDPSTLVK  360
AEDMDAYDPK SLLVVTTGSQ AEPRAALNLA SYGGSHALKL SKEDVLLYSA KVIPGNESRV  420
MKMLNRLTDL GPKIIMGKDS GLHTSGHAYH DELEEVLQIV KPQHFLPVHG ELLFLKEHEL  480
LGRSTGIRHT TVIKNGEMLG VSHLRNRKVL SNGFVALGKQ EFKLMYSDGD KAFGTSTDLC  540
IDERLRIASD GIIFVSMEIF RPQKELASPQ SGLKGKFKIT TRCLWLDNGR LLDALYKAAH  600
AALSSCPLNC PLSHMERMVS EILRKMVRKY SGKRPDVIVV ASENTTIGFT EEVTNKSPGK  660
FGPFSATRHL SRSPDRSLED SDKTRLDNPE GEAADSTPEV MRTTSDDVTT STNGESFFSS  720
DLHQPKALDH FWESFKSPTA VKIARIVNAS AQGNKPKLGK ISIIDKDSSM SVPAPAKSPR  780
KNKWKPEEIK SLIQLRGEMN EKFQTVKGRM VLWEEISASM LNQGITRTPA QCKSLWTSLV  840
QKYEESKKDG EGMKTWPYFS AMDSFLSCEG EMATK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-848564319560RIBONUCLEASE J
5a0t_B1e-848564319560RIBONUCLEASE J
5a0v_A1e-848564319560RIBONUCLEASE J
5a0v_B1e-848564319560RIBONUCLEASE 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
PlantRegMapBradi3g45230.1.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_010235506.10.0uncharacterized protein LOC100825739 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLI1IAB60.0I1IAB6_BRADI; Uncharacterized protein
STRINGBRADI3G45230.10.0(Brachypodium distachyon)
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]