PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Lsa011476
Organism
Lactuca sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactucinae; Lactuca
Family Trihelix
Protein Properties Length: 859aa    MW: 95577.3 Da    PI: 8.4454
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
gnl|UG|Lsa#S58695685PU_refUnigeneView CDS
PUT-187a-Lactuca_sativa-38733PU_unrefplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.59.5e-20764844186
   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                rW+ +ev++Li++r e+++r++  k +++lWee+s +++ +g++rsp qCk+ w +l ++y++ k+ ++++     ++++y+++++
  Lsa011476 764 RWKPEEVKKLIKFRGELNSRFQVVKGRMALWEEISGNLSTQGYNRSPGQCKSLWASLLQKYEESKKESESK-----RSWQYYEDMD 844
                8*************************************************************999988874.....57*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.102.7E-6580330IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.5E-6981495IPR001279Metallo-beta-lactamase
SMARTSM008491.1E-2393290IPR001279Metallo-beta-lactamase
PfamPF127065.3E-9105240IPR001279Metallo-beta-lactamase
PfamPF075213.0E-8433467IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.602.3E-6756823IPR009057Homeodomain-like
PROSITE profilePS500908.537757821IPR017877Myb-like domain
PfamPF138371.3E-18762846No hitNo description
CDDcd122031.02E-20763822No 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: 859 aa     Download sequence    Send to blast
MEMASFSGIS HCHHHRLWWQ PNTSKLPVSC SMPPPSFTGT SHGSKVGYKR SGRFEGAGKS  60
MEDSVKRKME KFYEGQNGPP LRVLPIGGLG EIGMNCMLVG NFDRYILIDA GVMFPDYEDL  120
GVQKIIPDTT FIKKWSHKIE AVVITHGHED HIGALPWVIP ALDSRTPIFS STFTMELIKK  180
RLKESGIFVP SRLKTFKTKK KFMAGPFEIE PIRVTHSIPD CSGLVLRCSD GVILHTGDWK  240
IDESPLDGQV FDREGLEQLS KEGVTLMMSD STNVLSPGRT LSETVVANSL LRNISAAKGR  300
VITTQFSSNI HRLGSVKAAA DATGRKLVFV GMSLRTYLDA AWKDGKAPID PSTLVKVEDI  360
DGYAPKDLLI VTTGSQAEPR AALNLASFGS SHFFKLSKED LILYSAKVIP GNESRVMKMM  420
NRLSEIGPTI VMGKNEQLHT SGHAYREELE EVLRIVKPQH FLPIHGELLF LKEHELLGKS  480
TGIHHTAVIK NGEMLGVSHL RNRRVLSNGF IALGKENLQL MYSDGDKAFG TSADLCVDER  540
MKIATDGIII VSIEIMRPQS TENTALLKET IKGKIRITTR CLWNDNGKLL DALHSAAHAA  600
LSSCPIKSPL PHMERTVSEV LRKMVRKYSG KRPEVITHAI ENPIAVIADE ISEKLSGVNV  660
NVKVNNGFEM PLGKSVDGSL KKRKSSKFQE EKKDLDNEIK GDEGLLSEEE TTTSVSDSTG  720
IAVSDSDEFW KPYTDSDSVE QSESDSKDDS DSSNTSKKPL KRNRWKPEEV KKLIKFRGEL  780
NSRFQVVKGR MALWEEISGN LSTQGYNRSP GQCKSLWASL LQKYEESKKE SESKRSWQYY  840
EDMDNIFSTS SDATMINKQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-838164119560RIBONUCLEASE J
5a0t_B1e-838164119560RIBONUCLEASE J
5a0v_A1e-838164119560RIBONUCLEASE J
5a0v_B1e-838164119560RIBONUCLEASE 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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023731535.10.0uncharacterized protein LOC111879314
RefseqXP_023731536.10.0uncharacterized protein LOC111879314
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2J6KKP10.0A0A2J6KKP1_LACSA; Uncharacterized protein
STRINGXP_002511207.10.0(Ricinus communis)
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]