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 mrna30167.1-v1.0-hybrid
Organism
Fragaria vesca
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family GRAS
Protein Properties Length: 830aa    MW: 92606.5 Da    PI: 5.4884
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna30167.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS91.81.1e-28711824260373
                     GRAS 260 aleyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk 345
                              a+ ++salfd+++++lpr+++ r   E+e++gre+vn+vaceg+er+ r et+++W+ r ++aGF+++pl+ ++++++k  +++ +
  mrna30167.1-v1.0-hybrid 711 AIFHFSALFDMFDSNLPRDDQMRLGFEKEFIGREVVNIVACEGTERTVRPETYKQWQVRNMRAGFRQLPLDREVMNKIKDKVKMGY 796
                              6789********************************************************************************** PP

                     GRAS 346 sdgyrveeesgslvlgWkdrpLvsvSaW 373
                              +  + v+e+  ++++gWk+r +    +W
  mrna30167.1-v1.0-hybrid 797 NPDFVVDEDGRWMLQGWKGRIMCGSACW 824
                              999********************99999 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS513757.0794128IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.182129159IPR002885Pentatricopeptide repeat
Gene3DG3DSA:1.25.40.101.6E-5140177IPR011990Tetratricopeptide-like helical domain
PROSITE profilePS513759.898160194IPR002885Pentatricopeptide repeat
PfamPF130411.3E-9161207IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007568.2E-6163195IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.303195229IPR002885Pentatricopeptide repeat
PROSITE profilePS513758.627230260IPR002885Pentatricopeptide repeat
Gene3DG3DSA:1.25.40.101.6E-5233304IPR011990Tetratricopeptide-like helical domain
TIGRFAMsTIGR007561.6E-4234263IPR002885Pentatricopeptide repeat
PfamPF015350.0056235261IPR002885Pentatricopeptide repeat
PROSITE profilePS5137512.036261295IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007561.6E-5263293IPR002885Pentatricopeptide repeat
PfamPF015351.0E-8263293IPR002885Pentatricopeptide repeat
PfamPF138120.0068326358IPR002885Pentatricopeptide repeat
PROSITE profilePS5137510.26331361IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007564.4E-5333363IPR002885Pentatricopeptide repeat
Gene3DG3DSA:1.25.40.101.6E-5339385IPR011990Tetratricopeptide-like helical domain
PROSITE profilePS5137512.255362396IPR002885Pentatricopeptide repeat
PfamPF130412.1E-13362409IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007564.2E-9364398IPR002885Pentatricopeptide repeat
PROSITE profilePS513757.969397431IPR002885Pentatricopeptide repeat
PROSITE profilePS513758.988432462IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007562.2E-5435464IPR002885Pentatricopeptide repeat
PfamPF130412.8E-10462509IPR002885Pentatricopeptide repeat
PROSITE profilePS5137510.545463493IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007567.3E-7465493IPR002885Pentatricopeptide repeat
PfamPF035143.7E-26711824IPR005202Transcription factor GRAS
PROSITE profilePS5098513.394711805IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 830 aa     Download sequence    Send to blast
MLMLCTTSPN QSWVSPSSYQ YINPNPLKPR FIFFRPNSRT SLFGAKFRVP ATTLAGTTHR  60
KNADKNVKIG VLCELGNLKE AVEMVCGSES SDLDSAAYCS VLELCAGNKS LKDGKRVHSV  120
LCEHGVNVDG YVGAKLVFMY VHCGDLREAR RVFDALSDRK VFLWNLMINE YAKVRDFREG  180
VCLFGKMVEC GVELNSYTFS CVFKCFAALG CVREGEWVHG YLYKLRFGSD SNVVNSLMAF  240
YFKNGRVESA RKVFDALRER DVVSWNSMIS AYVSNGAPEK GIEIFREMVW SGIDVDLATI  300
INVLMACSDC GNVVLGRVVH GYAMKGGFDV DVVLCNSVLD MYSKCGDLSD AVRVFEKMGR  360
RSVVSWTSMI AGYVREGLSD KAIELFCEME KDDVIPDVYT ITSILHACAC SGSLEKGKDI  420
HKYIREHDMD SSLFVCNSLI DMYAKCGSME DADSVFSHMP MKDIVSWNTM IGGFSKNCLP  480
NEALELFSDM QRKFKPDSMT LASVLPACAS LAALDRGQEI HDSSPQKFSP KLQSPPLRAF  540
GDYGLAHLSQ YPSSEPLKDL SFLDPNPSNS ALSSSSSPEG DEFSDSVLKY INQVLMEEDM  600
ESKPCMFHDP LVLQATEESL YESPDGGYSF VSFSDSTHSS SSPGPSSDSC MVNAPFVETR  660
SSILQNPIPE NFVFQSPSRA NSQSSTNRYG EGNGNWMVGS YRREFLVPDV AIFHFSALFD  720
MFDSNLPRDD QMRLGFEKEF IGREVVNIVA CEGTERTVRP ETYKQWQVRN MRAGFRQLPL  780
DREVMNKIKD KVKMGYNPDF VVDEDGRWML QGWKGRIMCG SACWAPSKS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5iww_D7e-766652116332PLS9-PPR
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtPlays a major role in single RNA editing events in chloroplasts. Acts as a site-recognition transacting factor involved in the edition of the unique site (corresponding to cytidine-488) of rpoC1, which is a plastid-encoded subunit of the chloroplast DNA-directed RNA polymerase. May provide the catalytic activity for editing site conversion (PubMed:24194514). Involved in leaf vasculature patterning (PubMed:18643975). {ECO:0000269|PubMed:18643975, ECO:0000269|PubMed:24194514}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapmrna30167.1-v1.0-hybrid
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_011461308.10.0PREDICTED: pentatricopeptide repeat-containing protein DOT4, chloroplastic isoform X2
SwissprotQ9SN391e-165PP320_ARATH; Pentatricopeptide repeat-containing protein DOT4, chloroplastic
TrEMBLA0A2P6Q4V00.0A0A2P6Q4V0_ROSCH; Putative tetratricopeptide-like helical domain, DYW domain-containing protein
STRINGXP_004294643.10.0(Fragaria vesca)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G07530.14e-48SCARECROW-like 14
Publications ? help Back to Top
  1. Serrano-Cartagena J,Robles P,Ponce MR,Micol JL
    Genetic analysis of leaf form mutants from the Arabidopsis Information Service collection.
    Mol. Gen. Genet., 1999. 261(4-5): p. 725-39
    [PMID:10394910]
  2. Aubourg S,Boudet N,Kreis M,Lecharny A
    In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants.
    Plant Mol. Biol., 2000. 42(4): p. 603-13
    [PMID:10809006]
  3. Lurin C, et al.
    Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
    Plant Cell, 2004. 16(8): p. 2089-103
    [PMID:15269332]
  4. Hayes ML,Giang K,Berhane B,Mulligan RM
    Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains.
    J. Biol. Chem., 2013. 288(51): p. 36519-29
    [PMID:24194514]