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 Lus10016758
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family Trihelix
Protein Properties Length: 864aa    MW: 95716.7 Da    PI: 7.7927
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10016758genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix55.41.6e-17767848186
     trihelix   1 rWtkqevlaLiearremeerlrr.gklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +e+++Li++r  +++r+ + +  +++lWe++s+ ++e+g+er+p qCk+ w +l ++y++ k+g +++     ++++yf+q++
  Lus10016758 767 KWKPEEIKKLIKMRGILHSRFISvKGGRMALWEDISSSLMEEGIERTPGQCKSLWASLVQKYEESKNGPESG-----KEWQYFEQVK 848
                  7********************9835689****************************************9996.....67*****985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.102.2E-6778328IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.28E-7079493IPR001279Metallo-beta-lactamase
SMARTSM008497.6E-2591288IPR001279Metallo-beta-lactamase
PfamPF007536.5E-1092246IPR001279Metallo-beta-lactamase
PfamPF075219.9E-7430465IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.399760825IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.8E-4762827IPR009057Homeodomain-like
PfamPF138379.9E-16765849No hitNo description
CDDcd122037.75E-19766832No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 864 aa     Download sequence    Send to blast
MSTFSLTAPS LCPYYRPGLA KFSVSCCTGS PTKIGSRRVS KAPPRKRPSR RMEGAGKSME  60
DSVKRKMEQF YEGTDGPPLR IVPIGGLGEI GMNCMLVGNY DRYILIDAGV MFPDDEDLGV  120
QKILPDTTFI KRWSHKIEAV VITHGHEDHI GALPWVIPAL DANTPIFASS FTMELIKKRL  180
KEHGFFLPSR LKVFRTRKRF TAGPFEIEPI TVTHSIPDCS GLILRCSDGI ILHTGDWKID  240
ESPLDGKPFD REALEELSKE GVTLMMSDST NVLSPGRTTS ETVVADSLLR HISAAKGRVI  300
TTQFASNIWR LGSVKAAADL TGRKLVFVGM SLRTYLDAAW KDGKAPIDPA TLVKAEDIDQ  360
YAPKDLLIVT TGSQAEPRAA LNLASYGTSY AFKLKKEDII LYSAKVIPGN ESRVMKMMNR  420
ITEIGSTIVM GRNEQLHTSG HGYRGELEEV LKIVKPQHFL PIHGELLFLK EHELLGKSTG  480
VHHTTVIKNG EMLGVSHLRN RRVLSNGFIS LGKENLQLMY SDGDKAFGTA TELCIEERLR  540
IATDGIIVVS MEILRPQGVD SVSENNIKGR IRITTRCLWL DKGKLLDALH KAAHAALSSC  600
PLNCPLAHME RTVAEVLRKM VRKYSGKRPE MIVIAMENPA GVLSEELSAK LAGKSEMGFG  660
ISALRKVIDK HPERKNKPQI DENGYGYIED APLEDSEGEN AVEEDNSSSS ERLDGRSVED  720
DNFWRSMMSS LPGDPSEEEA NVRGGGNDSS EDNDAEKTRQ KSGKRNKWKP EEIKKLIKMR  780
GILHSRFISV KGGRMALWED ISSSLMEEGI ERTPGQCKSL WASLVQKYEE SKNGPESGKE  840
WQYFEQVKSI LSDHEPEPTA AAK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A6e-867963719560RIBONUCLEASE J
5a0t_B6e-867963719560RIBONUCLEASE J
5a0v_A6e-867963719560RIBONUCLEASE J
5a0v_B6e-867963719560RIBONUCLEASE 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
PlantRegMapLus10016758
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002511207.20.0uncharacterized protein LOC8266322 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLB9RAI20.0B9RAI2_RICCO; Uncharacterized protein
STRINGLus100167580.0(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF50993450
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]