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 AT2G04890.1
Common NameF1O13.2, SCL21
Organism
Arabidopsis thaliana
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: 413aa    MW: 46467.6 Da    PI: 5.5024
Description SCARECROW-like 21
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G04890.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS448.54.4e-137534134374
         GRAS   4 lLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshltaNqa 101
                  +L++cA+avs+++l +a++++ +l+ ++s +g+p+qRl ay++e+L arla s+s++yk+l+++e +   s e l+++ +++ev+P++kf+++ aN a
  AT2G04890.1  53 VLVACAKAVSENNLLMARWCMGELRGMVSISGEPIQRLGAYMLEGLVARLAASGSSIYKSLQSREPE---SYEFLSYVYVLHEVCPYFKFGYMSANGA 147
                  79****************************************************************9...9*************************** PP

         GRAS 102 IleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpg 199
                  I ea++ eer+HiiDf+i+qG QW+aL+qa+a+Rp+g+p++RiTgvg+        l ++++rL+k+A++++vpf+fn+ v++   ++e+e+L+v+ g
  AT2G04890.1 148 IAEAMKDEERIHIIDFQIGQGSQWIALIQAFAARPGGAPNIRITGVGD-----GSVLVTVKKRLEKLAKKFDVPFRFNA-VSRPSCEVEVENLDVRDG 239
                  ************************************************.....89************************.799*************** PP

         GRAS 200 EalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnv 297
                  Eal Vn++++lh+l+desvs+e++rd++L++vkslsPkvv++veqe+++n+++Fl rfle+l+yy+a+f+s+++ lpr+++eri++E+++++r++vn+
  AT2G04890.1 240 EALGVNFAYMLHHLPDESVSMENHRDRLLRMVKSLSPKVVTLVEQECNTNTSPFLPRFLETLSYYTAMFESIDVMLPRNHKERINIEQHCMARDVVNI 337
                  ************************************************************************************************** PP

         GRAS 298 vacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  +acegaer+erhe l+kW++r+++aGF+p+pls+ + +++++llr ++ +gy +ee++g+l+lgW+dr Lvs +aW+
  AT2G04890.1 338 IACEGAERIERHELLGKWKSRFSMAGFEPYPLSSIISATIRALLRDYS-NGYAIEERDGALYLGWMDRILVSSCAWK 413
                  ***********************************************9.9**************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098565.5924394IPR005202Transcription factor GRAS
PfamPF035141.5E-13453413IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0020100anatomyhypocotyl
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 413 aa     Download sequence    Send to blast
MDNVRGSIML QPLPEIAESI DDAICHELSM WPDDAKDLLL IVEAISRGDL KLVLVACAKA  60
VSENNLLMAR WCMGELRGMV SISGEPIQRL GAYMLEGLVA RLAASGSSIY KSLQSREPES  120
YEFLSYVYVL HEVCPYFKFG YMSANGAIAE AMKDEERIHI IDFQIGQGSQ WIALIQAFAA  180
RPGGAPNIRI TGVGDGSVLV TVKKRLEKLA KKFDVPFRFN AVSRPSCEVE VENLDVRDGE  240
ALGVNFAYML HHLPDESVSM ENHRDRLLRM VKSLSPKVVT LVEQECNTNT SPFLPRFLET  300
LSYYTAMFES IDVMLPRNHK ERINIEQHCM ARDVVNIIAC EGAERIERHE LLGKWKSRFS  360
MAGFEPYPLS SIISATIRAL LRDYSNGYAI EERDGALYLG WMDRILVSSC AWK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A9e-63544138375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453599130.0
Genevisible263633_at0.0
Expression AtlasAT2G04890-
AtGenExpressAT2G04890-
ATTED-IIAT2G04890-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, cotyledons, leaves and flowers. {ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a scarecrow-like protein (SCL21). Member of GRAS gene family.
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. Both PAT1 and SCL21 are involved in phyA-dependent signaling.
    [PMID: 23109688]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G04890.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G48150
IntActSearch Q9S7H5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G04890
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0069550.0AC006955.6 Arabidopsis thaliana chromosome 2 clone F28I8 map RNS1, complete sequence.
GenBankAC0072110.0AC007211.6 Arabidopsis thaliana chromosome 2 BAC F1O13 genomic sequence, complete sequence.
GenBankAF2107320.0AF210732.1 Arabidopsis thaliana scarecrow-like 21 (SCL21) mRNA, complete cds.
GenBankAK1752100.0AK175210.1 Arabidopsis thaliana mRNA for putative SCARECROW gene regulator, complete cds, clone: RAFL21-63-H23.
GenBankBT0264550.0BT026455.1 Arabidopsis thaliana At2g04890 mRNA, complete cds.
GenBankCP0026850.0CP002685.1 Arabidopsis thaliana chromosome 2, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_178566.10.0SCARECROW-like 21
SwissprotQ9S7H50.0SCL21_ARATH; Scarecrow-like protein 21
TrEMBLA0A178VWV40.0A0A178VWV4_ARATH; SCL21
STRINGAT2G04890.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62128141
Representative plantOGRP14091447
Publications ? help Back to Top
  1. Bolle C,Koncz C,Chua NH
    PAT1, a new member of the GRAS family, is involved in phytochrome A signal transduction.
    Genes Dev., 2000. 14(10): p. 1269-78
    [PMID:10817761]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Bolle C
    The role of GRAS proteins in plant signal transduction and development.
    Planta, 2004. 218(5): p. 683-92
    [PMID:14760535]
  4. 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]
  5. 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]
  6. 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]
  7. Roig-Villanova I,Bou J,Sorin C,Devlin PF,Martínez-García JF
    Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis.
    Plant Physiol., 2006. 141(1): p. 85-96
    [PMID:16565297]
  8. Huang G, et al.
    A root-knot nematode secretory peptide functions as a ligand for a plant transcription factor.
    Mol. Plant Microbe Interact., 2006. 19(5): p. 463-70
    [PMID:16673933]
  9. Popescu SC, et al.
    Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays.
    Proc. Natl. Acad. Sci. U.S.A., 2007. 104(11): p. 4730-5
    [PMID:17360592]
  10. 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]
  11. Torres-Galea P,Hirtreiter B,Bolle C
    Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction.
    Plant Physiol., 2013. 161(1): p. 291-304
    [PMID:23109688]