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 AT1G55580.1
Common NameF20N2.1, LAS, SCL18
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: 445aa    MW: 50009.4 Da    PI: 6.5652
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G55580.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS438.25.9e-134414451374
         GRAS   1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlar.svselykalppsetseknsseelaal................ 81 
                  l++lL+++A++vs++++++aq+lL+ ls ++sp+gd+++Rl++ ft+AL+ r++r +++++++++++++t+e+++s+++ ++                
  AT1G55580.1  41 LRRLLFTAANFVSQSNFTAAQNLLSILSLNSSPHGDSTERLVHLFTKALSVRINRqQQDQTAETVATWTTNEMTMSNSTVFTssvckeqflfrtknnn 138
                  689****************************************************88999***********999666666556779999*******99 PP

         GRAS  82 ........klfsevsPilkfshltaNqaIleavege..ervHiiDfdisqGlQWpaLlqaLasRp....egppslRiTgvgspesgskeeleetgerL 165
                            +++++P+++f+hltaNqaIl+a+e++   ++Hi+D+disqGlQWp+L+qaLa+R+    ++ppslRiTg+g+    + + l++tg+rL
  AT1G55580.1 139 sdfescyyLWLNQLTPFIRFGHLTANQAILDATETNdnGALHILDLDISQGLQWPPLMQALAERSsnpsSPPPSLRITGCGR----DVTGLNRTGDRL 232
                  9999866444************************9977899***********************988877799*********....************ PP

         GRAS 166 akfAeelgvpfefnvl..vakrledl..eleeLrvkp..gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerf 257
                  ++fA++lg++f+f++l  v+++l+ l  +++ L+++   gE++aVn+v+ lh+++++++++     ++L+++ksl++++v+++e+ea+h+++sFl+rf
  AT1G55580.1 233 TRFADSLGLQFQFHTLviVEEDLAGLllQIRLLALSAvqGETIAVNCVHFLHKIFNDDGDMIG---HFLSAIKSLNSRIVTMAEREANHGDHSFLNRF 327
                  ***************965444554333366666666566**********************99...******************************** PP

         GRAS 258 lealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdgyrveee 354
                  +ea+++y+a+fdslea+lp++s+er ++E++++g+ei +vva+e++er++rh+++e W+e+++++GF +vp++++a +qaklllr ++ s+gy+++  
  AT1G55580.1 328 SEAVDHYMAIFDSLEATLPPNSRERLTLEQRWFGKEILDVVAAEETERKQRHRRFEIWEEMMKRFGFVNVPIGSFALSQAKLLLRLHYpSEGYNLQFL 425
                  ************************************************************************************************** PP

         GRAS 355 sgslvlgWkdrpLvsvSaWr 374
                  ++sl+lgW++rpL+svS+W+
  AT1G55580.1 426 NNSLFLGWQNRPLFSVSSWK 445
                  *******************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098556.53715424IPR005202Transcription factor GRAS
PfamPF035142.0E-13141445IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010014Biological Processmeristem initiation
GO:0010223Biological Processsecondary shoot formation
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:0000037anatomyshoot apex
PO:0004726anatomyvascular leaf primordium adaxial side
PO:0009005anatomyroot
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009023anatomyleaf axil
PO:0009046anatomyflower
PO:0020100anatomyhypocotyl
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 445 aa     Download sequence    Send to blast
MLTSFKSSSS SSEDATATTT ENPPPLCIAS SSAATSASHH LRRLLFTAAN FVSQSNFTAA  60
QNLLSILSLN SSPHGDSTER LVHLFTKALS VRINRQQQDQ TAETVATWTT NEMTMSNSTV  120
FTSSVCKEQF LFRTKNNNSD FESCYYLWLN QLTPFIRFGH LTANQAILDA TETNDNGALH  180
ILDLDISQGL QWPPLMQALA ERSSNPSSPP PSLRITGCGR DVTGLNRTGD RLTRFADSLG  240
LQFQFHTLVI VEEDLAGLLL QIRLLALSAV QGETIAVNCV HFLHKIFNDD GDMIGHFLSA  300
IKSLNSRIVT MAEREANHGD HSFLNRFSEA VDHYMAIFDS LEATLPPNSR ERLTLEQRWF  360
GKEILDVVAA EETERKQRHR RFEIWEEMMK RFGFVNVPIG SFALSQAKLL LRLHYPSEGY  420
NLQFLNNSLF LGWQNRPLFS VSSWK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3g_A8e-604944427378Protein SCARECROW
5b3h_A8e-604944426377Protein SCARECROW
5b3h_D8e-604944426377Protein SCARECROW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.451990.0flower
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1453367930.0
Genevisible265072_at0.0
Expression AtlasAT1G55580-
AtGenExpressAT1G55580-
ATTED-IIAT1G55580-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the axils of leaf primordia and leaves from P1 to P20/22. In the axil of P1, expressed in 3 to 5 cell layers including the L1 to L3 layers of the shoot apical meristem (SAM). Then, extends from 1 or 2 cell layers in the adaxial-abaxial dimension. From P5 to P22, expression is restricted to a 1 to 2 cell-layer domain located within primordium. In the axils of older leaf primordia, expression decreases until it is no longer detectable in the axils of primordia older than P20/P22. {ECO:0000269|PubMed:12730136}.
UniprotTISSUE SPECIFICITY: Expressed in roots and flowers. {ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the GRAS family of putative transcriptional regulators. It is involved in the initiation of axillary meristems during both the vegetative and reproductive growth phases and functions upstream of REV and AXR1 in the regulation of shoot branching.
UniProtProbable transcription factor required for axillary (lateral) shoot meristem formation during vegetative development. Seems to act upstream of REVOLUTA. {ECO:0000269|PubMed:12730136}.
Function -- GeneRIF ? help Back to Top
  1. Studies on LAS transcript accumulation in mir164 triple mutants and cuc3-2 plants overexpressing miR164 suggest that regulation of axillary meristem formation by miR164 is mediated through CUC1 and CUC2, which in turn regulate LAS.
    [PMID: 18346190]
  2. The LAS/Ls 3' enhancer determines promoter function, irrespective of the 5' promoter. The pattern of LAS transcript accumulation is predominantly determined by the 3' enhancer.
    [PMID: 21722220]
  3. ROX regulates axillary meristem formation redundantly with RAX1 and LAS.
    [PMID: 22372440]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G55580.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT3G15170 (A), AT5G53950 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G62360(A), AT2G37630(A), AT4G37750(A), AT5G60690(A)
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants fail to initiate axillary meristems and do not form lateral shoots during vegetative development. {ECO:0000269|PubMed:12730136}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G55580
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0023280.0AC002328.2 Genomic sequence for Arabidopsis thaliana BAC F20N2 from chromosome I, complete sequence.
GenBankAC0052230.0AC005223.1 Arabidopsis thaliana chromosome I BAC T5A14, complete sequence.
GenBankAY1964820.0AY196482.1 Arabidopsis thaliana lateral suppressor (LAS) mRNA, complete cds.
GenBankBT0265190.0BT026519.1 Arabidopsis thaliana At1g55580 mRNA, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_175954.10.0GRAS family transcription factor
SwissprotQ9ZWC50.0SCL18_ARATH; Scarecrow-like protein 18
TrEMBLA0A178WEV40.0A0A178WEV4_ARATH; SCL18
STRINGAT1G55580.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM113292733
Representative plantOGRP54911421
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. Day RB,Shibuya N,Minami E
    Identification and characterization of two new members of the GRAS gene family in rice responsive to N-acetylchitooligosaccharide elicitor.
    Biochim. Biophys. Acta, 2003. 1625(3): p. 261-8
    [PMID:12591613]
  3. Greb T, et al.
    Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation.
    Genes Dev., 2003. 17(9): p. 1175-87
    [PMID:12730136]
  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. Müller D,Schmitz G,Theres K
    Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis.
    Plant Cell, 2006. 18(3): p. 586-97
    [PMID:16461581]
  6. Keller T,Abbott J,Moritz T,Doerner P
    Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development.
    Plant Cell, 2006. 18(3): p. 598-611
    [PMID:16473968]
  7. Hibara K, et al.
    Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.
    Plant Cell, 2006. 18(11): p. 2946-57
    [PMID:17122068]
  8. Ehrenreich IM,Purugganan MD
    Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
    Plant Physiol., 2008. 146(4): p. 1974-82
    [PMID:18305205]
  9. Raman S, et al.
    Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana.
    Plant J., 2008. 55(1): p. 65-76
    [PMID:18346190]
  10. Goldshmidt A,Alvarez JP,Bowman JL,Eshed Y
    Signals derived from YABBY gene activities in organ primordia regulate growth and partitioning of Arabidopsis shoot apical meristems.
    Plant Cell, 2008. 20(5): p. 1217-30
    [PMID:18469164]
  11. 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]
  12. Raatz B, et al.
    Specific expression of LATERAL SUPPRESSOR is controlled by an evolutionarily conserved 3' enhancer.
    Plant J., 2011. 68(3): p. 400-12
    [PMID:21722220]
  13. Busch BL, et al.
    Shoot branching and leaf dissection in tomato are regulated by homologous gene modules.
    Plant Cell, 2011. 23(10): p. 3595-609
    [PMID:22039213]
  14. Nakano T, et al.
    MACROCALYX and JOINTLESS interact in the transcriptional regulation of tomato fruit abscission zone development.
    Plant Physiol., 2012. 158(1): p. 439-50
    [PMID:22106095]
  15. Yang F,Wang Q,Schmitz G,M
    The bHLH protein ROX acts in concert with RAX1 and LAS to modulate axillary meristem formation in Arabidopsis.
    Plant J., 2012. 71(1): p. 61-70
    [PMID:22372440]
  16. 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]
  17. Zhang B, et al.
    Novel function of a putative MOC1 ortholog associated with spikelet number per spike in common wheat.
    Sci Rep, 2015. 5: p. 12211
    [PMID:26197925]