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 XP_009130367.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family GRAS
Protein Properties Length: 543aa    MW: 59133.3 Da    PI: 4.4578
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009130367.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS438.55e-1341785391374
            GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfsh 95 
                     lv++L++cAea++++dl+la+al++ + +la++++ +m ++a+yf+++La+r++     l+      ++     s e a +  f+e +P+lkf+h
  XP_009130367.1 178 LVHALVACAEAIQQQDLNLADALVKSVGTLAASQAGAMGKVATYFAQGLARRIYA--ADLS----GGSS--VGPSFEEALQMHFYESCPYLKFAH 264
                     689***************************************************9..2222....2222..222333344445************ PP

            GRAS  96 ltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledle 190
                     +taNqaIleav +++rvH+iD++++qG+QWpaL+qaLa Rp+gpps+R+Tgvg+p+++s+++l+++g++La+fA+++gv+fef+ l a +   le
  XP_009130367.1 265 FTANQAILEAVTTARRVHVIDLGLNQGMQWPALMQALAVRPGGPPSFRLTGVGPPQTESSDSLQQLGWKLAQFAQAIGVEFEFKGL-AAESLXLE 358
                     *************************************************************************************6.77778899 PP

            GRAS 191 leeLrvkp.gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerik 284
                     +e+++++p  E+l+Vn+v++lhrll++s+s+e+    +L +vk+++P ++++veqea+hn+  Fl+rf eal+yys+lfdsle ++   s++r +
  XP_009130367.1 359 PEMFETRPeSETLVVNSVFELHRLLNRSGSIEK----LLTTVKTVRPSILTMVEQEANHNGVVFLDRFNEALHYYSSLFDSLEDSYTLPSQDR-V 448
                     ********9************************....***********************************************986666665.6 PP

            GRAS 285 vErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374
                     +++++lgr+ivnvva+eg++r+erhetl++W++r++++GF pvpl+++a kqa++ll+ ++ +dgyrvee++g+l+lgW++rpL+++SaW+
  XP_009130367.1 449 MSEVYLGRQIVNVVAAEGTDRVERHETLAQWKARMGSVGFDPVPLGSSAFKQASMLLSVFAgGDGYRVEENDGCLMLGWQTRPLIATSAWK 539
                     77788*************************************************************************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF120416.5E-3343108IPR021914Transcriptional factor DELLA, N-terminal
SMARTSM011297.2E-3843114No hitNo description
PROSITE profilePS5098565.901152518IPR005202Transcription factor GRAS
PfamPF035141.7E-131178539IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009723Biological Processresponse to ethylene
GO:0009737Biological Processresponse to abscisic acid
GO:0009739Biological Processresponse to gibberellin
GO:0009863Biological Processsalicylic acid mediated signaling pathway
GO:0009867Biological Processjasmonic acid mediated signaling pathway
GO:0010187Biological Processnegative regulation of seed germination
GO:0042538Biological Processhyperosmotic salinity response
GO:2000033Biological Processregulation of seed dormancy process
GO:2000377Biological Processregulation of reactive oxygen species metabolic process
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 543 aa     Download sequence    Send to blast
MKRGHGETWD PAPQSQQPSG SCEGSSSVVD NIKGKMADDS NMDELLEVLG YKVRSSEMAE  60
VAQKLEQLEM VLSNDDVGST VLNDTVHYNP SDLSNWVETM LSELNNPEPS DLDPTRICED  120
RSEYGLSAIP GLSAFPKAEE GAEEEASSKR IRLESVGSWG ELTRPVVVVD SQETGVRLVH  180
ALVACAEAIQ QQDLNLADAL VKSVGTLAAS QAGAMGKVAT YFAQGLARRI YAADLSGGSS  240
VGPSFEEALQ MHFYESCPYL KFAHFTANQA ILEAVTTARR VHVIDLGLNQ GMQWPALMQA  300
LAVRPGGPPS FRLTGVGPPQ TESSDSLQQL GWKLAQFAQA IGVEFEFKGL AAESLXLEPE  360
MFETRPESET LVVNSVFELH RLLNRSGSIE KLLTTVKTVR PSILTMVEQE ANHNGVVFLD  420
RFNEALHYYS SLFDSLEDSY TLPSQDRVMS EVYLGRQIVN VVAAEGTDRV ERHETLAQWK  480
ARMGSVGFDP VPLGSSAFKQ ASMLLSVFAG GDGYRVEEND GCLMLGWQTR PLIATSAWKL  540
AGA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A2e-6318553826378Protein SCARECROW
5b3h_A2e-6318553825377Protein SCARECROW
5b3h_D2e-6318553825377Protein SCARECROW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Predominantly expressed in germinating seeds, flowers and siliques. Only detectable in the inflorescence, with high levels in young flower buds and significant levels in siliques. In imbibed seeds, it is restricted to seed coats, elongating regions of pre-emergent and recently emerged radicles, endosperm (especially micropylar endosperm), and embryonic axis. Not expressed in leaves, bolting stems or roots. {ECO:0000269|PubMed:11877383, ECO:0000269|PubMed:18941053, ECO:0000269|PubMed:19500306, ECO:0000269|PubMed:20093430, ECO:0000269|PubMed:20956298}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. No effect of the BOI proteins on its stability. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Upon GA application, it is degraded by the proteasome, allowing the GA signaling pathway. Acts as a major GA-response repressor of seed germination, including seed thermoinhibition. Promotes the biosynthesis of abscisic acid (ABA), especially in seed coats to maintain seed dormancy. Delays flowering and adult leaf production. Also regulates the floral development, petal, stamen and anther development, by repressing the continued growth of floral organs. Its activity is probably regulated by other phytohormones such as auxin and ethylene. Involved in the regulation of seed dormancy and germination, including glucose-induced delay of seed germination. Promotes salt tolerance. Acts as a repressor of positive regulators of trichome initiation. Required during the flagellin-derived peptide flg22-mediated growth inhibition. Contributes to the susceptibility to the biotrophic pathogen P.syringae pv. tomato and to the resistance to the necrotrophic pathogens B.cinerea A.brassicicola, probably by repressing the SA-defense pathway and preventing cell death. Prevents stress-induced reactive oxygen species (ROS) accumulation (e.g. salt stress) by acting on the ROS scavenging system, and delays ROS-induced cell death, thus promoting stress tolerance. {ECO:0000269|PubMed:11877383, ECO:0000269|PubMed:12610625, ECO:0000269|PubMed:14615596, ECO:0000269|PubMed:14973286, ECO:0000269|PubMed:15128937, ECO:0000269|PubMed:16034591, ECO:0000269|PubMed:16400150, ECO:0000269|PubMed:16916886, ECO:0000269|PubMed:17141619, ECO:0000269|PubMed:17384169, ECO:0000269|PubMed:17704233, ECO:0000269|PubMed:18162586, ECO:0000269|PubMed:18450450, ECO:0000269|PubMed:18450451, ECO:0000269|PubMed:18941053, ECO:0000269|PubMed:20093430, ECO:0000269|PubMed:20956298}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009130367.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated transiently following seed imbibition to decline rapidly as germination proceeds; this induction is delayed at supraoptimal temperature conditions (e.g. 34 degrees Celsius). Accumulates in seed coats of dormant seeds where germination does not occur after imbibition. Increased levels upon abscisic acid (ABA) treatment. Down-regulated by norflurazon (NF), an ABA biosynthesis inhibitor. Induced by stress such as glucose, salt or mannitol treatment. {ECO:0000269|PubMed:11877383, ECO:0000269|PubMed:16916886, ECO:0000269|PubMed:17384169, ECO:0000269|PubMed:18162586, ECO:0000269|PubMed:18450450, ECO:0000269|PubMed:18941053, ECO:0000269|PubMed:20956298}.
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_009130367.10.0PREDICTED: LOW QUALITY PROTEIN: DELLA protein RGL2
SwissprotQ8GXW10.0RGL2_ARATH; DELLA protein RGL2
TrEMBLA0A0D3CN130.0A0A0D3CN13_BRAOL; Uncharacterized protein
STRINGBo5g149920.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM83728121
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G03450.10.0RGA-like 2
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Gallego-Giraldo C, et al.
    Role of the gibberellin receptors GID1 during fruit-set in Arabidopsis.
    Plant J., 2014. 79(6): p. 1020-1032
    [PMID:24961590]
  3. Fukazawa J, et al.
    DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2920-38
    [PMID:25035403]
  4. Hauvermale AL,Tuttle KM,Takebayashi Y,Seo M,Steber CM
    Loss of Arabidopsis thaliana Seed Dormancy is Associated with Increased Accumulation of the GID1 GA Hormone Receptors.
    Plant Cell Physiol., 2015. 56(9): p. 1773-85
    [PMID:26136598]
  5. Ibarra SE, et al.
    Molecular mechanisms underlying the entrance in secondary dormancy of Arabidopsis seeds.
    Plant Cell Environ., 2016. 39(1): p. 213-21
    [PMID:26177669]
  6. Zhong C, et al.
    Gibberellic Acid-Stimulated Arabidopsis6 Serves as an Integrator of Gibberellin, Abscisic Acid, and Glucose Signaling during Seed Germination in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2288-303
    [PMID:26400990]
  7. Dave A,Vaistij FE,Gilday AD,Penfield SD,Graham IA
    Regulation of Arabidopsis thaliana seed dormancy and germination by 12-oxo-phytodienoic acid.
    J. Exp. Bot., 2016. 67(8): p. 2277-84
    [PMID:26873978]
  8. Kazachkova Y, et al.
    Salt Induces Features of a Dormancy-Like State in Seeds of Eutrema (Thellungiella) salsugineum, a Halophytic Relative of Arabidopsis.
    Front Plant Sci, 2016. 7: p. 1071
    [PMID:27536302]
  9. Liu X, et al.
    The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis.
    Nat Commun, 2016. 7: p. 12768
    [PMID:27624486]
  10. Ravindran P,Verma V,Stamm P,Kumar PP
    A Novel RGL2-DOF6 Complex Contributes to Primary Seed Dormancy in Arabidopsis thaliana by Regulating a GATA Transcription Factor.
    Mol Plant, 2017. 10(10): p. 1307-1320
    [PMID:28917589]