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 AT5G41920.1
Common NameMJC20.2, SCL23
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: 405aa    MW: 44893.1 Da    PI: 5.8629
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G41920.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS383.42.7e-117414002374
         GRAS   2 velLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlar.svselykalppsetseknsseelaalklfsevsPilkfshlta 98 
                   +lLl+cAe v++++l++a++lL+++se++sp g++ +R++ayf++AL++r+ +   s+ ++ l+ ++ +  +s++ ++al++++ vsP++kfsh+ta
  AT5G41920.1  41 LSLLLQCAEYVATDHLREASTLLSEISEICSPFGSSPERVVAYFAQALQTRVISsYLSGACSPLSEKPLTVVQSQKIFSALQTYNSVSPLIKFSHFTA 138
                  689************************************************9997889999*********999************************* PP

         GRAS  99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrv 196
                  NqaI +a++ge+ vHiiD+d++qGlQWpaL++ LasRp++  s+RiTg+gs    s++ l +tg+rLa+fA++l++pfef+++     + +++++L++
  AT5G41920.1 139 NQAIFQALDGEDSVHIIDLDVMQGLQWPALFHILASRPRKLRSIRITGFGS----SSDLLASTGRRLADFASSLNLPFEFHPIEGIIGNLIDPSQLAT 232
                  ***************************************************....9**************************866688899******* PP

         GRAS 197 kpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadh.nsesFlerflealeyysalfdsleaklpreseerikvErellgre 293
                  ++gEa++V+++   hrl+d +++  +    +L+++++l+P++++vveqe+++ +++sFl rf+eal+yysalfd+l  +l++es er +vE+ +lg e
  AT5G41920.1 233 RQGEAVVVHWMQ--HRLYDVTGNNLE----TLEILRRLKPNLITVVEQELSYdDGGSFLGRFVEALHYYSALFDALGDGLGEESGERFTVEQIVLGTE 324
                  ***********9..****88888777....**********************8999****************************************** PP

         GRAS 294 ivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  i+n+va+ g + r+     +kW+e l+++GF+pv+l+ + a+qa lll + +++gy++ ee+g+l lgWkd +L+++SaW+
  AT5G41920.1 325 IRNIVAHGGGR-RK----RMKWKEELSRVGFRPVSLRGNPATQAGLLLGMLPWNGYTLVEENGTLRLGWKDLSLLTASAWK 400
                  *******9997.34....467***********************************************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098556.73714380IPR005202Transcription factor GRAS
PfamPF035149.5E-11541400IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048366Biological Processleaf development
GO:0090610Biological Processbundle sheath cell fate specification
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:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0025022anatomycollective leaf structure
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:0007115developmental stageLP.04 four leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 405 aa     Download sequence    Send to blast
MTTKRIDRDL PSSDDPSSAK RRIEFPEETL ENDGAAAIKL LSLLLQCAEY VATDHLREAS  60
TLLSEISEIC SPFGSSPERV VAYFAQALQT RVISSYLSGA CSPLSEKPLT VVQSQKIFSA  120
LQTYNSVSPL IKFSHFTANQ AIFQALDGED SVHIIDLDVM QGLQWPALFH ILASRPRKLR  180
SIRITGFGSS SDLLASTGRR LADFASSLNL PFEFHPIEGI IGNLIDPSQL ATRQGEAVVV  240
HWMQHRLYDV TGNNLETLEI LRRLKPNLIT VVEQELSYDD GGSFLGRFVE ALHYYSALFD  300
ALGDGLGEES GERFTVEQIV LGTEIRNIVA HGGGRRKRMK WKEELSRVGF RPVSLRGNPA  360
TQAGLLLGML PWNGYTLVEE NGTLRLGWKD LSLLTASAWK SQPFD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_A1e-1444639924377Protein SCARECROW
5b3h_D1e-1444639924377Protein SCARECROW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.678480.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453587340.0
Genevisible249279_at0.0
Expression AtlasAT5G41920-
AtGenExpressAT5G41920-
ATTED-IIAT5G41920-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, cotyledons, shoot apex, leaves and flowers.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. Mutations in three GRAS family transcription factors, SHORT-ROOT (SHR), SCARECROW (SCR) and SCARECROW-LIKE 23 (SCL23), affect BS cell fate in Arabidopsis thaliana.
    [PMID: 24517883]
  2. Data show that SCARECROW-LIKE23 (SCL23) is a mobile protein that controls movement of SHORT-ROOT (SHR) and acts redundantly with SCARCROW (SCR) to specify endodermal fate in the root meristem.
    [PMID: 26415082]
  3. results provide new insights into the regulatory role of the SHR-SCR-SCL23 network in the endodermis development in both roots and shoots.
    [PMID: 27353361]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G41920.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9FHZ1
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G41920
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0170670.0AB017067.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MJC20.
GenBankBT0297600.0BT029760.1 Arabidopsis thaliana At5g41920 mRNA, complete cds.
GenBankCP0026880.0CP002688.1 Arabidopsis thaliana chromosome 5 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_199007.10.0GRAS family transcription factor
SwissprotQ9FHZ10.0SCL23_ARATH; Scarecrow-like protein 23
TrEMBLA0A178UEI10.0A0A178UEI1_ARATH; Uncharacterized protein
STRINGAT5G41920.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM125122631
Representative plantOGRP21831437
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Bolle C
    The role of GRAS proteins in plant signal transduction and development.
    Planta, 2004. 218(5): p. 683-92
    [PMID:14760535]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  8. Cui H,Kong D,Liu X,Hao Y
    SCARECROW, SCR-LIKE 23 and SHORT-ROOT control bundle sheath cell fate and function in Arabidopsis thaliana.
    Plant J., 2014. 78(2): p. 319-27
    [PMID:24517883]
  9. Long Y, et al.
    SCARECROW-LIKE23 and SCARECROW jointly specify endodermal cell fate but distinctly control SHORT-ROOT movement.
    Plant J., 2015. 84(4): p. 773-84
    [PMID:26415082]
  10. Yoon EK, et al.
    Conservation and Diversification of the SHR-SCR-SCL23 Regulatory Network in the Development of the Functional Endodermis in Arabidopsis Shoots.
    Mol Plant, 2016. 9(8): p. 1197-1209
    [PMID:27353361]