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 Lus10022454
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: 1425aa    MW: 157009 Da    PI: 8.0383
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10022454genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix53.56.4e-1713281409186
     trihelix    1 rWtkqevlaLiearremeerlrr.gklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86  
                   +W+ +e+++Li++r   ++r+ + +  +++lWe++s+ ++e+g+er+p qCk+ w +l ++y++ k+g +++     ++++yf+q++
  Lus10022454 1328 KWKPEEIKKLIKMRGIFHSRFISvKGGRMALWEDISSSLMEEGIERTPGQCKSLWASLVQKYEESKNGPESG-----KEWQYFEQVK 1409
                   7********************9835689****************************************9996.....67****9985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF509787.97E-409340IPR017986WD40-repeat-containing domain
Gene3DG3DSA:2.130.10.108.7E-1710149IPR015943WD40/YVTN repeat-like-containing domain
SMARTSM003207482119IPR001680WD40 repeat
PROSITE profilePS5029420.38287318IPR017986WD40-repeat-containing domain
SMARTSM003201.0E-5122161IPR001680WD40 repeat
PfamPF004000.0028123160IPR001680WD40 repeat
PROSITE profilePS5008210.508129160IPR001680WD40 repeat
Gene3DG3DSA:2.130.10.102.5E-27150340IPR015943WD40/YVTN repeat-like-containing domain
SMARTSM003201174215IPR001680WD40 repeat
PROSITE profilePS500829.74181224IPR001680WD40 repeat
SMARTSM0032048218257IPR001680WD40 repeat
SMARTSM003202.7E-6272309IPR001680WD40 repeat
PfamPF004001.3E-4276309IPR001680WD40 repeat
PROSITE profilePS5008211.979279318IPR001680WD40 repeat
PROSITE patternPS006780296310IPR019775WD40 repeat, conserved site
Gene3DG3DSA:3.60.15.102.7E-66634888IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.14E-686351053IPR001279Metallo-beta-lactamase
SMARTSM008496.4E-24647848IPR001279Metallo-beta-lactamase
PfamPF007533.0E-10648805IPR001279Metallo-beta-lactamase
PfamPF075211.8E-69901025IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.38713211386IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.4E-413231388IPR009057Homeodomain-like
PfamPF138373.3E-1513261410No hitNo description
CDDcd122031.22E-1813271393No 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
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 1425 aa     Download sequence    Send to blast
MDPKGFNSKE GEALVLCGDR NMGTGIELWD LESGDRILHI PTCASPPHGL SCLRSQVLFA  60
SQANKHGSVG GGAIFSWHLN KPHSPIRSYQ IEAIGPLAAT YNGMYLVAGA LSGNAYIWEV  120
TSGRLLKTWR AHHRSFKCIA FSNNDSLVIV GSDDGTILAW PLISLLVVED GGSSSSLLHY  180
SMEHKSSITS LLMPPGSTNS LFISTSLDAT SKVWELVSGR LMQTLEYATG IAAATLHPDE  240
PLLFTGSSID GRIFVNVVDL GLIHDHESIT GVQGQMGVLK GHNGSITALT FSRSGLISAS  300
EDCTVCLWDV GSQQIVWRIN HKKGPVTNLV LVPHSSMLST PNHHQRVSSR FCISLLDKCH  360
RQADPSKGVI AFLPSYSLPI DGGQSSTSLE LQINNSVDRQ ILEIEMSIGK QMWALQMTKH  420
VMKMNKHLQS RLLDLMQSRL LLACHNTDVP RINNKKKKTT NKTQLKTQSR CSSEEELSFQ  480
PGNASLYVFL TSSRSKLQLS TFLKPCCRSL LPYLDFFLLG LSARPYLGPS AQMRLELLGI  540
SSPSPSFNSL SSLNPNMSTF SLTAPSLCPY YRPGLAKFSV SCGTGSPTKI GSSRVSKATP  600
RKRPSRRMEG VGKSMEDSVK RKMEQFYEGA DGPPLRIVPI GGLGEIGMNC MLVGNYDRYI  660
LIDAGVMFPD DEDLGVQKIL PDTTFIKRWS HKSIHKVGAV VITHGHEDHI GALPWVIPAL  720
DANTPIFASS FTMELIKKRL KEHGFFLPSR LKVFRTRKRF TAGPFEIEPI TVTHSIPDCS  780
GLILRCSDGI ILHTGDWKID ESPLDGKPFD REALEELSKE GVTLMMSDST NVLSPGRTTS  840
ETVVADSLLR HISAAKGRVI TTQFASNIWR LGSVKAAADL TGRKLVFVGM SLRTYLDAAW  900
KDGKAPIDPA TLVKAEDIDQ YAPKDLLIVT TGSQAEPRAA LNLASYGTSY AFKLKKEDII  960
LYSAKVIPGN ESRVMKMMNR ITEIGSTIVM GRNEQLHTSG HGYRGELEEV LKIVKPQHFL  1020
PIHGELLFLK EHELLGKSTG VHHTTVIKNG EMLGVSHLRN RRVLSNGFIS LGKENLQLMY  1080
SDGDKAFGTA TELCIEERLR IATDGIIVVS MEILRPQGVD SVSENNIKGR IRITTRCLWL  1140
DKGKLLDALH KAAHAALSSC PLNCPLAHME RTVAEVLRKM VRKYSGKRPE MIVIAMENPA  1200
GVLSEELSAK LAGKSEMGFG ISALRKVIDK HPERRNNKSQ IDENGYGYIE DAPLEDSEEE  1260
DAVEEDNTNS SERLDGRTEE DDNFWRSMIS SLPGDPSEEE ANVRGGGNDS SEDNDAEKTR  1320
QKSGKRNKWK PEEIKKLIKM RGIFHSRFIS VKGGRMALWE DISSSLMEEG IERTPGQCKS  1380
LWASLVQKYE ESKNGPESGK EWQYFEQVKS ILSDHEPEPT AAAK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-81635119719560RIBONUCLEASE J
5a0t_B3e-81635119719560RIBONUCLEASE J
5a0v_A3e-81635119719560RIBONUCLEASE J
5a0v_B3e-81635119719560RIBONUCLEASE 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
PlantRegMapLus10022454
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
STRINGLus100224540.0(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]