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 AT4G00150.1
Common NameATHAM3, F6N15.20, HAM3, LOM3, SCL6, SCL6-IV
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: 558aa    MW: 61167.8 Da    PI: 5.656
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G00150.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS330.92.5e-1012065542374
         GRAS   2 velLlecAeavssgdlelaqalLarlsel.aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfshlta 98 
                  +e+L+++Ae+++s d+ laq +Larl+++ +sp g+p++R+a+yf+eAL++ l++          +++ ++++ + ++aa+k fse+sP+l+f+++t 
  AT4G00150.1 206 TEQLVKAAEVIES-DTCLAQGILARLNQQlSSPVGKPLERAAFYFKEALNNLLHN---------VSQTLNPYSLIFKIAAYKSFSEISPVLQFANFTS 293
                  689******8887.9************998************************9.........55566667789*********************** PP

         GRAS  99 NqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegpp.slRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledl.eleeL 194
                  Nqa+le+++g +r+HiiDfdi++G+QW++L+q+L  R++ +p sl+iT+++sp+++++ el  t+++L++fA+e++++++++vl   +l+ l +++  
  AT4G00150.1 294 NQALLESFHGFHRLHIIDFDIGYGGQWASLMQELVLRDNAAPlSLKITVFASPANHDQLELGFTQDNLKHFASEINISLDIQVL---SLDLLgSISWP 388
                  **************************************99998****************************************8...55555223333 PP

         GRAS 195 rvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgr 292
                  + +++Ea+aVn++ + ++ l          + vL++vk+lsP+++v++++ +++++ +F ++++++l+ ++alf+sl+a   ++ ++++k+Er+l+++
  AT4G00150.1 389 NSSEKEAVAVNISAASFSHL----------PLVLRFVKHLSPTIIVCSDRGCERTDLPFSQQLAHSLHSHTALFESLDAV-NANLDAMQKIERFLIQP 475
                  5667**********988887..........67*********************************************887.56779************ PP

         GRAS 293 eivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374
                  ei+++v  + +     ++ +++W++++ ++GF+pv+ s+++++qa++l+++++++g++ve++++sl+l+W++ +Lv vSaWr
  AT4G00150.1 476 EIEKLVLDRSRP---IERPMMTWQAMFLQMGFSPVTHSNFTESQAECLVQRTPVRGFHVEKKHNSLLLCWQRTELVGVSAWR 554
                  ********9998...55677*************************************************************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098541.544179534IPR005202Transcription factor GRAS
PfamPF035148.6E-99206554IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0048768Biological Processroot hair cell tip growth
GO:0051301Biological Processcell division
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:0000013anatomycauline leaf
PO:0000014anatomyrosette leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009001anatomyfruit
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:0009049anatomyinflorescence
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: 558 aa     Download sequence    Send to blast
MPLPFEEFQG KGISCFSSFS SSFPQPPSSP LLSHRKARGG EEEEEEVPAA EPTSVLDSLI  60
SPTSSSTVSS SHGGNSAVGG GGDATTDEQC GAIGLGDWEE QVPHDHEQSI LGLIMGDSTD  120
PSLELNSILQ TSPTFHDSDY SSPGFGVVDT GFGLDHHSVP PSHVSGLLIN QSQTHYTQNP  180
AAIFYGHHHH TPPPAKRLNP GPVGITEQLV KAAEVIESDT CLAQGILARL NQQLSSPVGK  240
PLERAAFYFK EALNNLLHNV SQTLNPYSLI FKIAAYKSFS EISPVLQFAN FTSNQALLES  300
FHGFHRLHII DFDIGYGGQW ASLMQELVLR DNAAPLSLKI TVFASPANHD QLELGFTQDN  360
LKHFASEINI SLDIQVLSLD LLGSISWPNS SEKEAVAVNI SAASFSHLPL VLRFVKHLSP  420
TIIVCSDRGC ERTDLPFSQQ LAHSLHSHTA LFESLDAVNA NLDAMQKIER FLIQPEIEKL  480
VLDRSRPIER PMMTWQAMFL QMGFSPVTHS NFTESQAECL VQRTPVRGFH VEKKHNSLLL  540
CWQRTELVGV SAWRCRSS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A4e-322055544375GRAS family transcription factor containing p
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.37320.0leaf| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425661780.0
Genevisible255698_at0.0
Expression AtlasAT4G00150-
AtGenExpressAT4G00150-
ATTED-IIAT4G00150-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, leaves, flowers and siliques. {ECO:0000269|PubMed:10341448, ECO:0000269|PubMed:18500650}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. AtHAM1, AtHAM2, and AtHAM3 are expressed in apical meristems and in differentiating and mature tissues of both shoot and root.
    [PMID: 21173022]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G00150.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
IntActSearch O81316
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G00150
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankF6N150.0AF069299.1 Arabidopsis thaliana BAC F6N15.
GenBankCP0026870.0CP002687.1 Arabidopsis thaliana chromosome 4 sequence.
GenBankAY1335370.0AY133537.1 Arabidopsis thaliana At4g00150/F6N15_20 mRNA, complete cds.
GenBankAL1614710.0AL161471.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 1.
GenBankAK1172980.0AK117298.1 Arabidopsis thaliana mRNA, clone: RAFL16-86-D11.
GenBankAF4628310.0AF462831.1 Arabidopsis thaliana AT4g00150/F6N15_20 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_191926.10.0protein LOST MERISTEMS 3
SwissprotO813160.0SCL6_ARATH; Scarecrow-like protein 6
TrEMBLD7M5S20.0D7M5S2_ARALL; Putative uncharacterized protein
STRINGAT4G00150.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP17501242
MalvidsOGEM85742739
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. Llave C,Kasschau KD,Rector MA,Carrington JC
    Endogenous and silencing-associated small RNAs in plants.
    Plant Cell, 2002. 14(7): p. 1605-19
    [PMID:12119378]
  4. Llave C,Xie Z,Kasschau KD,Carrington JC
    Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA.
    Science, 2002. 297(5589): p. 2053-6
    [PMID:12242443]
  5. Kasschau KD, et al.
    P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction.
    Dev. Cell, 2003. 4(2): p. 205-17
    [PMID:12586064]
  6. 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]
  7. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  8. Bolle C
    The role of GRAS proteins in plant signal transduction and development.
    Planta, 2004. 218(5): p. 683-92
    [PMID:14760535]
  9. Chapman EJ,Prokhnevsky AI,Gopinath K,Dolja VV,Carrington JC
    Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step.
    Genes Dev., 2004. 18(10): p. 1179-86
    [PMID:15131083]
  10. Sunkar R,Zhu JK
    Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis.
    Plant Cell, 2004. 16(8): p. 2001-19
    [PMID:15258262]
  11. Yoo BC, et al.
    A systemic small RNA signaling system in plants.
    Plant Cell, 2004. 16(8): p. 1979-2000
    [PMID:15258266]
  12. Souret FF,Kastenmayer JP,Green PJ
    AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.
    Mol. Cell, 2004. 15(2): p. 173-83
    [PMID:15260969]
  13. Bonnet E,Wuyts J,Rouz
    Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes.
    Proc. Natl. Acad. Sci. U.S.A., 2004. 101(31): p. 11511-6
    [PMID:15272084]
  14. 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]
  15. 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]
  16. Axtell MJ,Bartel DP
    Antiquity of microRNAs and their targets in land plants.
    Plant Cell, 2005. 17(6): p. 1658-73
    [PMID:15849273]
  17. Xie Z, et al.
    Expression of Arabidopsis MIRNA genes.
    Plant Physiol., 2005. 138(4): p. 2145-54
    [PMID:16040653]
  18. Nakayama N, et al.
    Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.
    Plant Cell, 2005. 17(9): p. 2486-506
    [PMID:16055634]
  19. Jones L,Keining T,Eamens A,Vaistij FE
    Virus-induced gene silencing of argonaute genes in Nicotiana benthamiana demonstrates that extensive systemic silencing requires Argonaute1-like and Argonaute4-like genes.
    Plant Physiol., 2006. 141(2): p. 598-606
    [PMID:16632593]
  20. 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]
  21. Wagner R,Pfannschmidt T
    Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants.
    Gene, 2006. 381: p. 62-70
    [PMID:16934950]
  22. Lewsey M,Robertson FC,Canto T,Palukaitis P,Carr JP
    Selective targeting of miRNA-regulated plant development by a viral counter-silencing protein.
    Plant J., 2007. 50(2): p. 240-52
    [PMID:17444907]
  23. Ehrenreich IM,Purugganan MD
    Sequence variation of MicroRNAs and their binding sites in Arabidopsis.
    Plant Physiol., 2008. 146(4): p. 1974-82
    [PMID:18305205]
  24. 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]
  25. Wang L,Mai YX,Zhang YC,Luo Q,Yang HQ
    MicroRNA171c-targeted SCL6-II, SCL6-III, and SCL6-IV genes regulate shoot branching in Arabidopsis.
    Mol Plant, 2010. 3(5): p. 794-806
    [PMID:20720155]
  26. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  27. Schulze S,Sch
    LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems.
    Plant J., 2010. 64(4): p. 668-78
    [PMID:21070418]
  28. Engstrom EM, et al.
    Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy.
    Plant Physiol., 2011. 155(2): p. 735-50
    [PMID:21173022]
  29. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
    [PMID:21499259]
  30. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  31. Zhou Y, et al.
    Control of plant stem cell function by conserved interacting transcriptional regulators.
    Nature, 2015. 517(7534): p. 377-80
    [PMID:25363783]