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 Brast04G178400.1.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: 878aa    MW: 96972.3 Da    PI: 8.9692
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Brast04G178400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix68.11.7e-21785865186
            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+ ++
  Brast04G178400.1.p 785 KWKPEEIKSLIQLRGEMNEKFQTVKGRMVLWEEISGSMLKQGITRTPAQCKSLWTSLVQKYEESKKDEES-----MKTWPYFSAMD 865
                         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-6786336IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.51E-7287501IPR001279Metallo-beta-lactamase
SMARTSM008495.5E-2599296IPR001279Metallo-beta-lactamase
PfamPF127061.5E-10111246IPR001279Metallo-beta-lactamase
PfamPF075211.3E-6444473IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.793778842IPR017877Myb-like domain
SMARTSM007170.0063782844IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.604.0E-5782844IPR009057Homeodomain-like
CDDcd122035.12E-23784849No hitNo description
PfamPF138379.7E-18784866No 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: 878 aa     Download sequence    Send to blast
MVALASLSSL CPCGLARRRS ASASASASTS TSISCCAVAT PPSGKGSHES RIPRRRFRRT  60
EGATKSMEDS VKRKMEQFYE GLDGPPLRVL PIGGLGEIGM NCMLVGNYDR YILIDAGVMF  120
PDYDEFGVQK IIPDTTFIKK WSHKIEAVII THGHEDHIGA LPWVIPALDS STPIFASSFT  180
MELIKKRLKE FGIFLSSRLK SFRVRNRFQA GPFEVEPIRV THSIPDCCGL VLRCGDGTIF  240
HTGDWKIDES PVDGKIFDRQ ALEELSKEGV TLMMSDSTNI LSPGRSTSES VVASSLLRHI  300
SEAKGRVITT QFASNIHRIG SIKAAADLTG RRLAFVGMSL RTYLEAAFRD GKAPLDPSTL  360
VKAEDMDAYD PKSLLVVTTG SQAEPRAALN LASYGGSHAL KLSKEDVLLY SAKVIPGNES  420
RVMKMLNRLT DLGPKIVMGK DSGLHTSGHA YHDELEEVLQ IVKPQHFLPV HGELLFLKEH  480
ELLGRSTGIR HTTVIKNGEM LGVSHLRNRK VLSNGFVALG KQEFKLMYSD GDKAFGTSTD  540
LCIDERLRIA SDGIIFVSME IFRPQKELAS PQSGLKGKFK ITTRCLWLDN GRLLDALYKA  600
AHAALSSCPL NCPLSHMERM VSEILRKMVR KYSGKRPDVI VVASENTTVG FTEEVTDKSP  660
GKFGPFSATR HLSRSPDRSL EDSDKTRLEN PEGEAAESIP EVMRTTSDDA TTSTNGESFF  720
SSDLHQPKTL DHFWESFKSP TAVKIARIVN SSAQGNKPKF GKISMIDKDS SMPVPAPAKS  780
PRKNKWKPEE IKSLIQLRGE MNEKFQTVKG RMVLWEEISG SMLKQGITRT PAQCKSLWTS  840
LVQKYEESKK DEESMKTWPY FSAMDSFLSC EGEMATK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-858764519560RIBONUCLEASE J
5a0t_B9e-858764519560RIBONUCLEASE J
5a0v_A9e-858764519560RIBONUCLEASE J
5a0v_B9e-858764519560RIBONUCLEASE 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
PlantRegMapBrast04G178400.1.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
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]