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 Carubv10015212m
Common NameCARUB_v10015212mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family GRAS
Protein Properties Length: 553aa    MW: 61012.2 Da    PI: 4.5535
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10015212mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS449.91.7e-1371865461374
             GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 
                      lv++L++cAeav++++l+la+al++r+ +la++++ +m ++a+yf +ALa+r+++         ++ et+    s e   +  f+e +P+lkf+
  Carubv10015212m 186 LVHALVACAEAVQQENLSLADALVKRVGTLAASQAGAMGKVASYFSQALARRIYH-------GYNAAETD---GSFEEVLQMHFYESCPYLKFA 269
                      689***************************************************9.......33444443...5555555557*********** PP

             GRAS  95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrled 188
                      h+taNqaIleav +++rvH+iD++++qG+QWpaL+qaLa Rp+gpps+R+Tgvg+p+++++++l+++g++La+fA+++gv+fef+ l+a++l+d
  Carubv10015212m 270 HFTANQAILEAVTTSRRVHVIDLGLNQGMQWPALMQALALRPGGPPSFRLTGVGPPQTENSDSLQQLGWKLAQFAQNIGVEFEFKGLAAESLSD 363
                      ********************************************************************************************** PP

             GRAS 189 leleeLrvkp.gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpresee 281
                      le+e+++++p  E+++Vn+v++lhrll++s+s+e+    +L++vk ++P +v+vveqea+hn+  Fl+rf eal+yys+lfdsle +++  s++
  Carubv10015212m 364 LEPEMFETRPeSETVVVNSVFELHRLLARSGSIEK----LLETVKAVKPSIVTVVEQEANHNGVVFLDRFNEALHYYSSLFDSLEDSYSLPSQD 453
                      **********9************************....************************************************8777766 PP

             GRAS 282 rikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374
                      r ++++++lgr+i nvva+eg +r+erhetl +W++r+++ GF pv+l+++ +kqa++ll+ ++ +dgyrvee++g+l+lgW++rpL+++SaW+
  Carubv10015212m 454 R-VMSEVYLGRQILNVVAAEGYDRVERHETLPQWKNRMRSGGFDPVNLGSSSYKQASMLLSVFAtGDGYRVEENDGCLMLGWQTRPLITTSAWK 546
                      6.567778*************************************************************************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF120414.9E-3447112IPR021914Transcriptional factor DELLA, N-terminal
SMARTSM011299.1E-3947118No hitNo description
PROSITE profilePS5098566.58160525IPR005202Transcription factor GRAS
PfamPF035145.9E-135186546IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
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: 553 aa     Download sequence    Send to blast
MKRGHGETTW DPPPSRCSGE GPSMAVVVDN NNKKSTADDN NNNNMDDELL AVLGYKVRSS  60
EMAEVAQKLE QLEMVLSNDD VGSTVLNDTV HYNPSDLSNW VETMLSELNN PASSDLDPTR  120
TCVARSEYDL RAIPGLSAFP KEEQEVFDDE EASSKRIRLG EPYCESAGES TRSVVLVDSQ  180
ETGVRLVHAL VACAEAVQQE NLSLADALVK RVGTLAASQA GAMGKVASYF SQALARRIYH  240
GYNAAETDGS FEEVLQMHFY ESCPYLKFAH FTANQAILEA VTTSRRVHVI DLGLNQGMQW  300
PALMQALALR PGGPPSFRLT GVGPPQTENS DSLQQLGWKL AQFAQNIGVE FEFKGLAAES  360
LSDLEPEMFE TRPESETVVV NSVFELHRLL ARSGSIEKLL ETVKAVKPSI VTVVEQEANH  420
NGVVFLDRFN EALHYYSSLF DSLEDSYSLP SQDRVMSEVY LGRQILNVVA AEGYDRVERH  480
ETLPQWKNRM RSGGFDPVNL GSSSYKQASM LLSVFATGDG YRVEENDGCL MLGWQTRPLI  540
TTSAWKLAES RR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_A3e-6719354525377Protein SCARECROW
5b3h_D3e-6719354525377Protein SCARECROW
Search in ModeBase
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
PlantRegMapCarubv10015212m
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankATAC0098950.0AC009895.4 Arabidopsis thaliana chromosome III BAC T21P5 genomic sequence, complete sequence.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
GenBankGQ1777580.0GQ177758.1 Arabidopsis thaliana ecotype Ag-0 RGL2 gene, complete sequence.
GenBankGQ1777600.0GQ177760.1 Arabidopsis thaliana ecotype C24 RGL2 gene, complete sequence.
GenBankGQ1777610.0GQ177761.1 Arabidopsis thaliana ecotype Sorbo RGL2 gene, complete sequence.
GenBankGQ1777650.0GQ177765.1 Arabidopsis thaliana ecotype Bay-0 RGL2 gene, complete sequence.
GenBankGQ1777660.0GQ177766.1 Arabidopsis thaliana ecotype Br-0 RGL2 gene, complete sequence.
GenBankGQ1777670.0GQ177767.1 Arabidopsis thaliana ecotype Ct-1 RGL2 gene, complete sequence.
GenBankGQ1777720.0GQ177772.1 Arabidopsis thaliana ecotype Kas-2 RGL2 gene, complete sequence.
GenBankGQ1777730.0GQ177773.1 Arabidopsis thaliana ecotype Ll-0 RGL2 gene, complete sequence.
GenBankGQ1777750.0GQ177775.1 Arabidopsis thaliana ecotype Ms-0 RGL2 gene, complete sequence.
GenBankGQ1777810.0GQ177781.1 Arabidopsis thaliana ecotype Nd-1 RGL2 gene, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006299072.10.0DELLA protein RGL2
SwissprotQ8GXW10.0RGL2_ARATH; DELLA protein RGL2
TrEMBLR0I2570.0R0I257_9BRAS; Uncharacterized protein
STRINGXP_006299072.10.0(Capsella rubella)
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]