PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G50420.1
Common NameF11F12.22, SCL3, SCL-3
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family GRAS
Protein Properties Length: 482aa    MW: 54152.8 Da    PI: 6.3959
Description scarecrow-like 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G50420.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS533.28.3e-163544791374
         GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 
                  l++lLl+cA++v+sg+l++a+a+L++ls+laspdgd+mqR+aayfteALa+r+++s+++lykal++++t+++n+see+++++lf+e++Pilk+s+l++
  AT1G50420.1  54 LIHLLLTCANHVASGSLQNANAALEQLSHLASPDGDTMQRIAAYFTEALANRILKSWPGLYKALNATQTRTNNVSEEIHVRRLFFEMFPILKVSYLLT 151
                  689*********************************************************************************************** PP

         GRAS  99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrv 196
                  N+aIlea+ege++vH+iD+d+s+++QW+aLlqa++sRpegpp+lRiTgv++    +ke le++++rL + Ae+l++pf+fn+ v++rl++l++e+Lrv
  AT1G50420.1 152 NRAILEAMEGEKMVHVIDLDASEPAQWLALLQAFNSRPEGPPHLRITGVHH----QKEVLEQMAHRLIEEAEKLDIPFQFNP-VVSRLDCLNVEQLRV 244
                  ***************************************************....9**************************.7************** PP

         GRAS 197 kpgEalaVnlvlqlhrll.......................................................desvsles..erdevLklvkslsPk 237
                  k+gEalaV++vlqlh++l                                                       ++s++l+s  ++d++L+++++lsPk
  AT1G50420.1 245 KTGEALAVSSVLQLHTFLasdddlmrkncalrfqnnpsgvdlqrvlmmshgsaaearendmsnnngyspsgdsASSLPLPSsgRTDSFLNAIWGLSPK 342
                  ***********************************************************************9977777777779************** PP

         GRAS 238 vvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaak 335
                  v+vv+eq++dhn+++++er+le+l++y+alfd+le+k+pr+s++rikvE++l+g+ei+n+++ceg+errerhe+lekW++r++ aGF++vpls++a+ 
  AT1G50420.1 343 VMVVTEQDSDHNGSTLMERLLESLYTYAALFDCLETKVPRTSQDRIKVEKMLFGEEIKNIISCEGFERRERHEKLEKWSQRIDLAGFGNVPLSYYAML 440
                  ************************************************************************************************** PP

         GRAS 336 qaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  qa++ll+ +++dgyr++eesg++v++W+drpL+svSaWr
  AT1G50420.1 441 QARRLLQGCGFDGYRIKEESGCAVICWQDRPLYSVSAWR 479
                  **************************************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098560.10728459IPR005202Transcription factor GRAS
PfamPF035142.9E-16054479IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009739Biological Processresponse to gibberellin
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0006036anatomyroot epidermis
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 482 aa     Download sequence    Send to blast
MVAMFQEDNG TSSVASSPLQ VFSTMSLNRP TLLASSSPFH CLKDLKPEER GLYLIHLLLT  60
CANHVASGSL QNANAALEQL SHLASPDGDT MQRIAAYFTE ALANRILKSW PGLYKALNAT  120
QTRTNNVSEE IHVRRLFFEM FPILKVSYLL TNRAILEAME GEKMVHVIDL DASEPAQWLA  180
LLQAFNSRPE GPPHLRITGV HHQKEVLEQM AHRLIEEAEK LDIPFQFNPV VSRLDCLNVE  240
QLRVKTGEAL AVSSVLQLHT FLASDDDLMR KNCALRFQNN PSGVDLQRVL MMSHGSAAEA  300
RENDMSNNNG YSPSGDSASS LPLPSSGRTD SFLNAIWGLS PKVMVVTEQD SDHNGSTLME  360
RLLESLYTYA ALFDCLETKV PRTSQDRIKV EKMLFGEEIK NIISCEGFER RERHEKLEKW  420
SQRIDLAGFG NVPLSYYAML QARRLLQGCG FDGYRIKEES GCAVICWQDR PLYSVSAWRC  480
RK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A1e-36544794375GRAS family transcription factor containing p
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.148260.0flower| leaf| root| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1864900110.0
Genevisible261866_at0.0
Expression AtlasAT1G50420-
AtGenExpressAT1G50420-
ATTED-IIAT1G50420-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, root epidermis, leaves, flowers and siliques. {ECO:0000269|PubMed:10341448, ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a scarecrow-like protein (SCL3) Putative transcription factors interacting with the gene product of VHA-B1 (vacuolar ATPase subunit B1; as shown through yeast two-hybrid assay).
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. A coregulator exchange system between DELLA (as coactivator) and SCL3 (as corepressor) regulates the expression of SCL3.
    [PMID: 24821766]
  2. The balance of the DELLAs and SCL3 protein levels (both are GRAS proteins) regulates downstream gene expression through IDDs binding to DNA. Review.
    [PMID: 25763707]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G50420.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT4G37650 (A)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9LPR8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G50420
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0125610.0AC012561.2 Arabidopsis thaliana chromosome I BAC F11F12 genomic sequence, complete sequence.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBankAY0912600.0AY091260.1 Arabidopsis thaliana putative scarecrow 3 protein (At1g50420) mRNA, complete cds.
GenBankAY0561540.0AY056154.1 Arabidopsis thaliana putative scarecrow 3 protein (At1g50420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_175459.10.0scarecrow-like protein 3
SwissprotQ9LPR80.0SCL3_ARATH; Scarecrow-like protein 3
TrEMBLR0GWE70.0R0GWE7_9BRAS; Uncharacterized protein
STRINGAT1G50420.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP25641433
MalvidsOGEM40982759
Publications ? help Back to Top
  1. Pysh LD,Wysocka-Diller JW,Camilleri C,Bouchez D,Benfey PN
    The GRAS gene family in Arabidopsis: sequence characterization and basic expression analysis of the SCARECROW-LIKE genes.
    Plant J., 1999. 18(1): p. 111-9
    [PMID:10341448]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Ogawa M, et al.
    Gibberellin biosynthesis and response during Arabidopsis seed germination.
    Plant Cell, 2003. 15(7): p. 1591-604
    [PMID:12837949]
  4. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  6. Bolle C
    The role of GRAS proteins in plant signal transduction and development.
    Planta, 2004. 218(5): p. 683-92
    [PMID:14760535]
  7. Goda H, et al.
    Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis.
    Plant Physiol., 2004. 134(4): p. 1555-73
    [PMID:15047898]
  8. Tian C,Wan P,Sun S,Li J,Chen M
    Genome-wide analysis of the GRAS gene family in rice and Arabidopsis.
    Plant Mol. Biol., 2004. 54(4): p. 519-32
    [PMID:15316287]
  9. Gao MJ,Parkin I,Lydiate D,Hannoufa A
    An auxin-responsive SCARECROW-like transcriptional activator interacts with histone deacetylase.
    Plant Mol. Biol., 2004. 55(3): p. 417-31
    [PMID:15604690]
  10. Curtis IS,Hanada A,Yamaguchi S,Kamiya Y
    Modification of plant architecture through the expression of GA 2-oxidase under the control of an estrogen inducible promoter in Arabidopsis thaliana L.
    Planta, 2005. 222(6): p. 957-67
    [PMID:16270204]
  11. Levesque MP, et al.
    Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
    PLoS Biol., 2006. 4(5): p. e143
    [PMID:16640459]
  12. Cho YH,Yoo SD,Sheen J
    Regulatory functions of nuclear hexokinase1 complex in glucose signaling.
    Cell, 2006. 127(3): p. 579-89
    [PMID:17081979]
  13. Zentella R, et al.
    Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.
    Plant Cell, 2007. 19(10): p. 3037-57
    [PMID:17933900]
  14. Lee MH, et al.
    Large-scale analysis of the GRAS gene family in Arabidopsis thaliana.
    Plant Mol. Biol., 2008. 67(6): p. 659-70
    [PMID:18500650]
  15. Rieu I, et al.
    Genetic analysis reveals that C19-GA 2-oxidation is a major gibberellin inactivation pathway in Arabidopsis.
    Plant Cell, 2008. 20(9): p. 2420-36
    [PMID:18805991]
  16. Heo JO, et al.
    Funneling of gibberellin signaling by the GRAS transcription regulator scarecrow-like 3 in the Arabidopsis root.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 2166-71
    [PMID:21245304]
  17. Zhang ZL, et al.
    Scarecrow-like 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(5): p. 2160-5
    [PMID:21245327]
  18. Josse EM, et al.
    A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling.
    Plant Cell, 2011. 23(4): p. 1337-51
    [PMID:21478445]
  19. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  20. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  21. Archacki R, et al.
    BRAHMA ATPase of the SWI/SNF chromatin remodeling complex acts as a positive regulator of gibberellin-mediated responses in arabidopsis.
    PLoS ONE, 2013. 8(3): p. e58588
    [PMID:23536800]
  22. Yoshida H, et al.
    DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(21): p. 7861-6
    [PMID:24821766]
  23. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  24. Yoshida H,Ueguchi-Tanaka M
    DELLA and SCL3 balance gibberellin feedback regulation by utilizing INDETERMINATE DOMAIN proteins as transcriptional scaffolds.
    Plant Signal Behav, 2014. 9(9): p. e29726
    [PMID:25763707]