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 AT2G45160.1
Common NameATHAM1, HAM1, LOM1, SCL27, T14P1.3
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: 640aa    MW: 70205.7 Da    PI: 5.4346
Description GRAS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G45160.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1GRAS307.14e-942696392374
         GRAS   2 velLlecAeavss.gdle.....laqalLarlsel...aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPi 90 
                  +e+L+++Ae + + g+++     laq +Larl+++   +s++++p+qR+a++++eAL + +++      ++ pp   +++n + ++aa++ fse+sP+
  AT2G45160.1 269 IEQLFNAAELIGTtGNNNgdhtvLAQGILARLNHHlntSSNHKSPFQRAASHIAEALLSLIHN------ESSPPLI-TPENLILRIAAYRSFSETSPF 359
                  678899999886642222344469**********998788888*******************9......4444444.4578***************** PP

         GRAS  91 lkfshltaNqaIleavege..ervHiiDfdisqGlQWpaLlqaLas.....RpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefn 179
                  l+f ++taNq Ile+ +++  +r+HiiDfd+++G+QW +L+q+Las     R++ + sl++T++++p s+  ++ el+ t+e+L+ fA e+++pfe++
  AT2G45160.1 360 LQFVNFTANQSILESCNESgfDRIHIIDFDVGYGGQWSSLMQELASgvggrRRNRASSLKLTVFAPPPSTvsDEFELRFTEENLKTFAGEVKIPFEIE 457
                  ****************99988************************744443557799*********9988899************************* PP

         GRAS 180 vlvakrledleleeLrvkp..gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleakl 275
                  +l ++ l +  ++ L++++  +Ea+aVnl ++             + + +L+++k+lsP++vv++++ +d+n+++F + ++++l+y+++l++sl+a+ 
  AT2G45160.1 458 LLSVELLLNPAYWPLSLRSseKEAIAVNLPVNSVASG--------YLPLILRFLKQLSPNIVVCSDRGCDRNDAPFPNAVIHSLQYHTSLLESLDAN- 546
                  **9999999999999888777*********9666654........5677************************************************. PP

         GRAS 276 preseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaW 373
                    ++++++++Er++++++i++++++++++     e+   Wr  ++++GF+p++ls+ a++qa++ll++ +++g++ve+++ slv++W++++Lv+vSaW
  AT2G45160.1 547 --QNQDDSSIERFWVQPSIEKLLMKRHRW----IERSPPWRILFTQCGFSPASLSQMAEAQAECLLQRNPVRGFHVEKRQSSLVMCWQRKELVTVSAW 638
                  ..89*************************....89999************************************************************ PP

         GRAS 374 r 374
                  +
  AT2G45160.1 639 K 639
                  8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5098541.333243619IPR005202Transcription factor GRAS
PfamPF035141.4E-91269639IPR005202Transcription factor GRAS
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048768Biological Processroot hair cell tip growth
GO:0051301Biological Processcell division
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:0000014anatomyrosette leaf
PO:0000017anatomyvascular leaf primordium
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
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:0020148anatomyshoot apical meristem
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: 640 aa     Download sequence    Send to blast
MPLSFERFQG EGVFGLSSSS FYSDSQKIWS NQDKTEAKQE DLGYVVGGFL PEPTSVLDAL  60
RSPSPLASYS STTTTLSSSH GGGGTTVTNT TVTAGDDNNN NKCSQMGLDD LDGVLSASSP  120
GQEQSILRLI MDPGSAFGVF DPGFGFGSGS GPVSAPVSDN SNLLCNFPFQ EITNPAEALI  180
NPSNHCLFYN PPLSPPAKRF NSGSLHQPVF PLSDPDPGHD PVRRQHQFQF PFYHNNQQQQ  240
FPSSSSSTAV AMVPVPSPGM AGDDQSVIIE QLFNAAELIG TTGNNNGDHT VLAQGILARL  300
NHHLNTSSNH KSPFQRAASH IAEALLSLIH NESSPPLITP ENLILRIAAY RSFSETSPFL  360
QFVNFTANQS ILESCNESGF DRIHIIDFDV GYGGQWSSLM QELASGVGGR RRNRASSLKL  420
TVFAPPPSTV SDEFELRFTE ENLKTFAGEV KIPFEIELLS VELLLNPAYW PLSLRSSEKE  480
AIAVNLPVNS VASGYLPLIL RFLKQLSPNI VVCSDRGCDR NDAPFPNAVI HSLQYHTSLL  540
ESLDANQNQD DSSIERFWVQ PSIEKLLMKR HRWIERSPPW RILFTQCGFS PASLSQMAEA  600
QAECLLQRNP VRGFHVEKRQ SSLVMCWQRK ELVTVSAWKC
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5hyz_A2e-2829863924375GRAS family transcription factor containing protein, expressed
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.270460.0bud| flower| leaf| seed| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306899400.0
Genevisible266131_at0.0
Expression AtlasAT2G45160-
AtGenExpressAT2G45160-
ATTED-IIAT2G45160-
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
UniProtProbable transcription factor involved in plant development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. findings show that LOM1(AT2G45160) and LOM2 (AT3G60630) promote cell differentiation at the periphery of shoot meristems and help to maintain their polar organization
    [PMID: 21070418]
  2. AtHAM1, AtHAM2, and AtHAM3 are expressed in apical meristems and in differentiating and mature tissues of both shoot and root.
    [PMID: 21173022]
  3. Results indicate that the control of HAIRY MERISTEM 1 (HAM1) functions at the single-cell-layer level by miR171a is essential for proper organ formation.
    [PMID: 29574557]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G45160.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G11260, AT1G46480
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G45160
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0537600.0BT053760.1 Arabidopsis thaliana unknown protein (At2g45160) 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_182041.10.0GRAS family transcription factor
SwissprotQ7XJM80.0SCL27_ARATH; Scarecrow-like protein 27
TrEMBLA0A384KUR00.0A0A384KUR0_ARATH; LOM1
TrEMBLB7ZWR80.0B7ZWR8_ARATH; At2g45160
STRINGAT2G45160.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM134171828
Representative plantOGRP17501242
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. Reinhart BJ,Weinstein EG,Rhoades MW,Bartel B,Bartel DP
    MicroRNAs in plants.
    Genes Dev., 2002. 16(13): p. 1616-26
    [PMID:12101121]
  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. Hudson ME,Lisch DR,Quail PH
    The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway.
    Plant J., 2003. 34(4): p. 453-71
    [PMID:12753585]
  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. 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]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. Trinks D, et al.
    Suppression of RNA silencing by a geminivirus nuclear protein, AC2, correlates with transactivation of host genes.
    J. Virol., 2005. 79(4): p. 2517-27
    [PMID:15681452]
  14. Axtell MJ,Bartel DP
    Antiquity of microRNAs and their targets in land plants.
    Plant Cell, 2005. 17(6): p. 1658-73
    [PMID:15849273]
  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. Borges F, et al.
    Comparative transcriptomics of Arabidopsis sperm cells.
    Plant Physiol., 2008. 148(2): p. 1168-81
    [PMID:18667720]
  17. 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]
  18. 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]
  19. Xue XY, et al.
    Interaction between two timing microRNAs controls trichome distribution in Arabidopsis.
    PLoS Genet., 2014. 10(4): p. e1004266
    [PMID:24699192]
  20. Ma Z, et al.
    Arabidopsis miR171-targeted scarecrow-like proteins bind to GT cis-elements and mediate gibberellin-regulated chlorophyll biosynthesis under light conditions.
    PLoS Genet., 2014. 10(8): p. e1004519
    [PMID:25101599]
  21. Zhou Y, et al.
    Control of plant stem cell function by conserved interacting transcriptional regulators.
    Nature, 2015. 517(7534): p. 377-80
    [PMID:25363783]
  22. Huo X,Wang C,Teng Y,Liu X
    Identification of miRNAs associated with dark-induced senescence in Arabidopsis.
    BMC Plant Biol., 2015. 15: p. 266
    [PMID:26530097]
  23. Takanashi H, et al.
    miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis.
    Plant Mol. Biol., 2018. 96(6): p. 627-640
    [PMID:29574557]