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 Bostr.0568s0468.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family Trihelix
Protein Properties Length: 914aa    MW: 100914 Da    PI: 8.5641
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.0568s0468.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix65.61.1e-20821901186
             trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                          +W+ +e+++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  Bostr.0568s0468.1.p 821 KWKPEEIKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLTQKYEECKADERSK-----TSWPHFEDMN 901
                          7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.4E-66110360IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.5E-71111525IPR001279Metallo-beta-lactamase
SMARTSM008494.3E-25123320IPR001279Metallo-beta-lactamase
PfamPF127067.0E-10135270IPR001279Metallo-beta-lactamase
PfamPF075215.6E-7465497IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.84814878IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.2E-5814880IPR009057Homeodomain-like
PfamPF138375.6E-18819903No hitNo description
CDDcd122032.04E-22820885No 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: 914 aa     Download sequence    Send to blast
MMMKPASLQG FSSQASSIYS DVRRPATTTP SKMAAFSALS LCPYTFTFRP SSRIKSTVSC  60
SVTSAPASGT SSSSKTPRRR SGRLEGVGKS MEDSVKRKME QFYEGTDGPP LRVLPIGGLG  120
EIGMNCMLVG NYDRYILIDA GIMFPDYDEP GVQKIMPDTG FIRRWKHKIE AVVITHGHED  180
HIGALPWVIP ALDPNTPIFA SSFTMELIKK RLKEHGIFVQ SRLKIFSTRR RFMAGPFEIE  240
PITVTHSIPD CSGLFLRCAD GNILHTGDWK IDEAPLDGKV FDREALEELS KEGVTLMMSD  300
STNVLSPGRT ISEKVVADAL VRNVMAAKGR VITTQFASNI HRLGSIKAAA DLTGRKLVFV  360
GMSLRTYLEA AWRDGKAPID PSSLVKVEDI EAYAPKDLLI VTTGSQAEPR AALNLASYGS  420
SHAFKLTKED IILYSAKVIP GNESRVMKMM NRIADIGPNI IMGKNEMLHT SGHAYRGELE  480
EVLKIVKPQH FLPIHGELLF LKEHELLGKS TGIRHTTVIK NGEMLGVSHL RNRRVLSNGF  540
SSLGRENLQL MYSDGEKAFG TSSELCIDER LRISSDGIIV LSMEIMRPGV SENNLKGKIR  600
ITTRCMWLDK GRLLDALHKA AHAALSSCPV NCPLSHMERT VSEVLRKIVR KYSGKRPEVI  660
AIATENPMAV RADEVSARLS GDPSVGSGVA ALRKVVDGHN KRSRPKKAPS QEDAPKEVDR  720
TLEDDIIDSA RLLAEEETAA STYTEEVDMP VGSSSEESDD FWKSFINPSS SPSPGETENV  780
NKVTDMEPKT EDKESSRDGD DPSDTSDSET KSSSKRVKRN KWKPEEIKKV IRMRGELHSR  840
FQVVKGRMAL WEEISSNLSA EGINRSPGQC KSLWASLTQK YEECKADERS KTSWPHFEDM  900
NKILSELGTP ASK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-8711166519560RIBONUCLEASE J
5a0t_B4e-8711166519560RIBONUCLEASE J
5a0v_A4e-8711166519560RIBONUCLEASE J
5a0v_B4e-8711166519560RIBONUCLEASE 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
PlantRegMapBostr.0568s0468.1.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
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006279731.10.0uncharacterized protein LOC17874922
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLR0G7Y90.0R0G7Y9_9BRAS; Uncharacterized protein
STRINGBostr.0568s0468.1.p0.0(Boechera stricta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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]