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 AT4G17230.1
Common Namedl4650c, FCAALL.225, SCL13
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: 529aa    MW: 58455.2 Da    PI: 5.7346
Description SCARECROW-like 13
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G17230.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS406.13.3e-1241555251374
         GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 
                  l+e+L+e+A+av++gd++ a  +L  l++++s +g+p+qRl +y++e+L+arl +s+s++yk+l+++e +     e ++++++++e++P+ kf++ ta
  AT4G17230.1 155 LKEVLVEAARAVADGDFATAYGFLDVLEQMVSVSGSPIQRLGTYMAEGLRARLEGSGSNIYKSLKCNEPT---GRELMSYMSVLYEICPYWKFAYTTA 249
                  5789*****************************************************************9...9999999****************** PP

         GRAS  99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeL 194
                  N  Ilea++ge+rvHiiDf+i qG Q++ L+q+La+Rp+gpp lR+Tgv++++s+  +   l+ +gerLa +A+++gvpfef+  +  +  +++ e+L
  AT4G17230.1 250 NVEILEAIAGETRVHIIDFQIAQGSQYMFLIQELAKRPGGPPLLRVTGVDDSQSTyaRGGGLSLVGERLATLAQSCGVPFEFHD-AIMSGCKVQREHL 346
                  ***************************************************999999999************************.7888999****** PP

         GRAS 195 rvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgr 292
                   ++pg a++Vn+ + lh+++desvs+e++rd++L+l+kslsPk+v++veqe+++n+++Fl rf+e+l+yy+a+f+s++a  pr++++ri+ E+++++r
  AT4G17230.1 347 GLEPGFAVVVNFPYVLHHMPDESVSVENHRDRLLHLIKSLSPKLVTLVEQESNTNTSPFLSRFVETLDYYTAMFESIDAARPRDDKQRISAEQHCVAR 444
                  ************************************************************************************************** PP

         GRAS 293 eivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  +ivn++ace++er+erhe l+ Wr r+++aGF+  p+s++aa  a+ +l+ ++++ y++  ++g+l+l Wk+rp+ ++S+W+
  AT4G17230.1 445 DIVNMIACEESERVERHEVLGIWRVRMMMAGFTGWPVSTSAAFAASEMLKAYDKN-YKLGGHEGALYLFWKRRPMATCSVWK 525
                  *****************************************************66.*************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098562.865129506IPR005202Transcription factor GRAS
PfamPF035141.1E-121155525IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010200Biological Processresponse to chitin
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
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: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: 529 aa     Download sequence    Send to blast
MQTSQKHHSA AGLHMLYPQV YCSPQFQAKD NKGFSDIPSK ENFFTLESST ASGSLPSYDS  60
PSVSITSGRS PFSPQGSQSC ISDLHHSPDN VYGSPLSGVS SLAYDEAGVK SKIRELEVSL  120
LSGDTKVEEF SGFSPAAGKS WNWDELLALT PQLDLKEVLV EAARAVADGD FATAYGFLDV  180
LEQMVSVSGS PIQRLGTYMA EGLRARLEGS GSNIYKSLKC NEPTGRELMS YMSVLYEICP  240
YWKFAYTTAN VEILEAIAGE TRVHIIDFQI AQGSQYMFLI QELAKRPGGP PLLRVTGVDD  300
SQSTYARGGG LSLVGERLAT LAQSCGVPFE FHDAIMSGCK VQREHLGLEP GFAVVVNFPY  360
VLHHMPDESV SVENHRDRLL HLIKSLSPKL VTLVEQESNT NTSPFLSRFV ETLDYYTAMF  420
ESIDAARPRD DKQRISAEQH CVARDIVNMI ACEESERVER HEVLGIWRVR MMMAGFTGWP  480
VSTSAAFAAS EMLKAYDKNY KLGGHEGALY LFWKRRPMAT CSVWKPNPN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A2e-541595258375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.253230.0bud| flower| root| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2402559640.0
Genevisible245247_at0.0
Expression AtlasAT4G17230-
AtGenExpressAT4G17230-
ATTED-IIAT4G17230-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During development, higher expression levels are detected in young rosette leaves, senescing leaves and petals and sepals at flower stage 15. {ECO:0000269|PubMed:16680434}.
UniprotTISSUE SPECIFICITY: Expressed in roots, hypocotyls, cotyledons, shoot apex, leaves, flowers and siliques. {ECO:0000269|PubMed:10341448, ECO:0000269|PubMed:16680434, ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a scarecrow-like protein (SCL13). Member of GRAS gene family.
UniProtProbable transcription factor that acts as a positive regulator of continuous red light signals downstream of phytochrome B (phyB). Required for the regulation of hypocotyl elongation during de-etiolation. May be required to modulate phytochrome A (phyA) signal transduction in a phyB-independent way. {ECO:0000269|PubMed:16680434}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G17230.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By osmotic and cold stresses, and UV-A/B. {ECO:0000269|PubMed:16680434}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G17230
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCP0026870.0CP002687.1 Arabidopsis thaliana chromosome 4 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001328648.10.0SCARECROW-like 13
RefseqNP_193456.40.0SCARECROW-like 13
SwissprotQ9M0M50.0SCL13_ARATH; Scarecrow-like protein 13
TrEMBLA0A1P8B5A90.0A0A1P8B5A9_ARATH; SCARECROW-like 13
STRINGAT4G17230.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM62128141
Representative plantOGRP14091447
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. Gutierrez RA,Ewing RM,Cherry JM,Green PJ
    Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes.
    Proc. Natl. Acad. Sci. U.S.A., 2002. 99(17): p. 11513-8
    [PMID:12167669]
  4. Ziolkowski PA,Blanc G,Sadowski J
    Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome.
    Nucleic Acids Res., 2003. 31(4): p. 1339-50
    [PMID:12582254]
  5. Hammond JP, et al.
    Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants.
    Plant Physiol., 2003. 132(2): p. 578-96
    [PMID:12805589]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  7. Bolle C
    The role of GRAS proteins in plant signal transduction and development.
    Planta, 2004. 218(5): p. 683-92
    [PMID:14760535]
  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. Lu Y,Zhu J,Liu P
    A two-step strategy for detecting differential gene expression in cDNA microarray data.
    Curr. Genet., 2005. 47(2): p. 121-31
    [PMID:15688252]
  11. Suzuki N, et al.
    Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c.
    Plant Physiol., 2005. 139(3): p. 1313-22
    [PMID:16244138]
  12. Torres-Galea P,Huang LF,Chua NH,Bolle C
    The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling, but can also modulate phytochrome A responses.
    Mol. Genet. Genomics, 2006. 276(1): p. 13-30
    [PMID:16680434]
  13. Ma S,Bohnert HJ
    Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.
    Genome Biol., 2007. 8(4): p. R49
    [PMID:17408486]
  14. Libault M,Wan J,Czechowski T,Udvardi M,Stacey G
    Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor.
    Mol. Plant Microbe Interact., 2007. 20(8): p. 900-11
    [PMID:17722694]
  15. 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]
  16. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  17. Son GH, et al.
    Ethylene-responsive element-binding factor 5, ERF5, is involved in chitin-induced innate immunity response.
    Mol. Plant Microbe Interact., 2012. 25(1): p. 48-60
    [PMID:21936663]
  18. Klopffleisch K, et al.
    Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.
    Mol. Syst. Biol., 2011. 7: p. 532
    [PMID:21952135]