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 Sopim03g111260.0.1
Organism
Solanum pimpinellifolium
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family Trihelix
Protein Properties Length: 853aa    MW: 94411.4 Da    PI: 8.6685
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim03g111260.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.97.6e-20760840186
            trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                         rW+++e+++Li +r e++++++  + +++lWee+s+++ + g+ rsp qCk+ w +l ++y++ k  ek++      ++py+++++
  Sopim03g111260.0.1 760 RWKHDEIKKLIMLRGELHSKFQVVRGRMALWEEISSNLLSIGVDRSPGQCKSLWASLVQKYEENKSDEKRQ-----DKWPYYEEMR 840
                         8****************************************************************999984.....57******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.1E-6777327IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.12E-7178492IPR001279Metallo-beta-lactamase
SMARTSM008491.1E-2590287IPR001279Metallo-beta-lactamase
PfamPF007533.1E-1091236IPR001279Metallo-beta-lactamase
PfamPF075211.6E-7435464IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.724753817IPR017877Myb-like domain
PfamPF138371.2E-16758842No hitNo description
CDDcd122035.69E-22759824No 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
Sequence ? help Back to Top
Protein Sequence    Length: 853 aa     Download sequence    Send to blast
MAAAFSAISL CPYKLCHQLN PRKHFISCYT PSTSSIGIRG SKGPRKRPDK LEGAGRSIDD  60
SVQRRMEQFY EGSDGPPLRV LPIGGLGEIG MNCMLVGNYD RYILIDAGIM FPGYDEPGVQ  120
KIIPDTTFIK KWSHKIEAVI ITHGHEDHIG ALPWVIPALD SHTPIFASSF TMELIKKRLK  180
EFGIFVPSRL KVFKTRRKFT AGPFEVEPIT VTHSIPDCSG IVLRCSDGTI LHTGDWKIDE  240
SPLDGKVFDR EALEELSKEG VTLMMSDSTN VLSPGRTLSE TVVADSLLRR ISAAKGRVIT  300
TQFASNIHRL GSVKAAADLT GRKLVFVGMS LRTYLDAAWK DGKAPIDPST LVKVEDIDAY  360
APKDLLIVTT GSQAEPRAAL NLASYGSSHS LKLNKEDLVL YSAKVIPGND TRVMQMLNRI  420
SDIGSTIVMG KNELLHTSGH AHREELEEVL RIVKPQHFLP VHGELLFLKE HELLGKSTGI  480
RHTAVIKNGE MLGISHLRNR KVLSNGFISL GKEKLQLMYS DGDKAFGTAA ELCIDERLRI  540
ASDGIIVVSM EIMRPQSTDG MTEKALKGKI RITTRCLWLD KGKLLDALHK AAHASLSSCP  600
LNCPLSHMER TVSEVLRKLV RKYSSKRPEV IAVAFENPAG VLADEINGKL SGKSHVGFGI  660
SALRNVLDED QKRRQASGAR AEGGNGNGYP VDDAVEQVKG DDMDIERLMH DGATTSSANS  720
LDEYSTAEEE SESSRKESVQ VDSGFPQSMM KSSKPLKRNR WKHDEIKKLI MLRGELHSKF  780
QVVRGRMALW EEISSNLLSI GVDRSPGQCK SLWASLVQKY EENKSDEKRQ DKWPYYEEMR  840
KILSDLEATA HK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-877863619560RIBONUCLEASE J
5a0t_B3e-877863619560RIBONUCLEASE J
5a0v_A3e-877863619560RIBONUCLEASE J
5a0v_B3e-877863619560RIBONUCLEASE 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9755150.0HG975515.1 Solanum lycopersicum chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010319059.10.0ribonuclease J isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A3Q7GE030.0A0A3Q7GE03_SOLLC; Uncharacterized protein
STRINGSolyc03g111260.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58742331
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]