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 AT1G01260.3
Common NameBHLH13, EN39, F6F3.7, JAM2
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 bHLH
Protein Properties Length: 590aa    MW: 66002 Da    PI: 6.7082
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G01260.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH39.97.5e-13433478454
                  HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS
          HLH   4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 
                  +h e+Er+RR+++N++f  Lr+++P+ +      K++Ka+ L  Av YI++L
  AT1G01260.3 433 NHVEAERQRREKLNQRFYALRSVVPNiS------KMDKASLLGDAVSYINEL 478
                  799***********************66......***************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF142157.1E-5348236IPR025610Transcription factor MYC/MYB N-terminal
PROSITE profilePS5088817.326429478IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.17E-13432483No hitNo description
SuperFamilySSF474599.81E-19432498IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.0E-10433478IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.106.1E-18433492IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.8E-16435484IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
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:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
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: 590 aa     Download sequence    Send to blast
MNIGRLVWNE DDKAIVASLL GKRALDYLLS NSVSNANLLM TLGSDENLQN KLSDLVERPN  60
ASNFSWNYAI FWQISRSKAG DLVLCWGDGY CREPKEGEKS EIVRILSMGR EEETHQTMRK  120
RVLQKLHDLF GGSEEENCAL GLDRVTDTEM FLLSSMYFSF PRGEGGPGKC FASAKPVWLS  180
DVVNSGSDYC VRSFLAKSAG IQTVVLVPTD LGVVELGSTS CLPESEDSIL SIRSLFTSSL  240
PPVRAVALPV TVAEKIDDNR TKIFGKDLHN SGFLQHHQHH QQQQQQPPQQ QQHRQFREKL  300
TVRKMDDRAP KRLDAYPNNG NRFMFSNPGT NNNTLLSPTW VQPENYTRPI NVKEVPSTDE  360
FKFLPLQQSS QRLLPPAQMQ IDFSAASSRA SENNSDGEGG GEWADAVGAD ESGNNRPRKR  420
GRRPANGRAE ALNHVEAERQ RREKLNQRFY ALRSVVPNIS KMDKASLLGD AVSYINELHA  480
KLKVMEAERE RLGYSSNPPI SLDSDINVQT SGEDVTVRIN CPLESHPASR IFHAFEESKV  540
EVINSNLEVS QDTVLHTFVV KSEELTKEKL ISALSREQTN SVQSRTSSGR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5gnj_A4e-26427489264Transcription factor MYC2
5gnj_B4e-26427489264Transcription factor MYC2
5gnj_E4e-26427489264Transcription factor MYC2
5gnj_F4e-26427489264Transcription factor MYC2
5gnj_G4e-26427489264Transcription factor MYC2
5gnj_I4e-26427489264Transcription factor MYC2
5gnj_M4e-26427489264Transcription factor MYC2
5gnj_N4e-26427489264Transcription factor MYC2
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible261050_at0.0
Expression AtlasAT1G01260-
AtGenExpressAT1G01260-
ATTED-IIAT1G01260-
Function -- GeneRIF ? help Back to Top
  1. JAM2 (At1g01260) negatively regulates the JA response in a manner that is mostly antagonistic to MYC2.
    [PMID: 23852442]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00100PBM26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G01260.3
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By UV treatment. {ECO:0000269|PubMed:12679534}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G51600
IntActSearch Q9LNJ5
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G01260
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0236280.0AC023628.3 Arabidopsis thaliana chromosome I BAC F6F3 genomic sequence, complete sequence.
GenBankAF2516980.0AF251698.1 Arabidopsis thaliana putative transcription factor BHLH13 mRNA, complete cds.
GenBankAY0790120.0AY079012.1 Arabidopsis thaliana At1g01260/F6F3_25 mRNA, complete cds.
GenBankAY1207520.0AY120752.1 Arabidopsis thaliana transcription factor MYC7E, putative (At1g01260) mRNA, complete cds.
GenBankBT0045170.0BT004517.1 Arabidopsis thaliana At1g01260/F6F3_25 gene, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001077440.10.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
RefseqNP_001184883.10.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
RefseqNP_171634.10.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ9LNJ50.0BH013_ARATH; Transcription factor bHLH13
TrEMBLA0A178WJW50.0A0A178WJW5_ARATH; JAM2
STRINGAT1G01260.10.0(Arabidopsis thaliana)
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. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
    [PMID:12679534]
  3. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  4. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  5. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
    [PMID:14600211]
  6. Nakabayashi K,Okamoto M,Koshiba T,Kamiya Y,Nambara E
    Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed.
    Plant J., 2005. 41(5): p. 697-709
    [PMID:15703057]
  7. Borsics T,Webb D,Andeme-Ondzighi C,Staehelin LA,Christopher DA
    The cyclic nucleotide-gated calmodulin-binding channel AtCNGC10 localizes to the plasma membrane and influences numerous growth responses and starch accumulation in Arabidopsis thaliana.
    Planta, 2007. 225(3): p. 563-73
    [PMID:16944199]
  8. Li H, et al.
    The bHLH-type transcription factor AtAIB positively regulates ABA response in Arabidopsis.
    Plant Mol. Biol., 2007. 65(5): p. 655-65
    [PMID:17828375]
  9. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]
  10. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  11. Tominaga-Wada R,Iwata M,Nukumizu Y,Wada T
    Analysis of IIId, IIIe and IVa group basic-helix-loop-helix proteins expressed in Arabidopsis root epidermis.
    Plant Sci., 2011. 181(4): p. 471-8
    [PMID:21889054]
  12. Gaudinier A, et al.
    Enhanced Y1H assays for Arabidopsis.
    Nat. Methods, 2011. 8(12): p. 1053-5
    [PMID:22037706]
  13. Sasaki-Sekimoto Y, et al.
    Basic helix-loop-helix transcription factors JASMONATE-ASSOCIATED MYC2-LIKE1 (JAM1), JAM2, and JAM3 are negative regulators of jasmonate responses in Arabidopsis.
    Plant Physiol., 2013. 163(1): p. 291-304
    [PMID:23852442]
  14. Song S, et al.
    The bHLH subgroup IIId factors negatively regulate jasmonate-mediated plant defense and development.
    PLoS Genet., 2013. 9(7): p. e1003653
    [PMID:23935516]
  15. Sasaki-Sekimoto Y,Saito H,Masuda S,Shirasu K,Ohta H
    Comprehensive analysis of protein interactions between JAZ proteins and bHLH transcription factors that negatively regulate jasmonate signaling.
    Plant Signal Behav, 2014. 9(1): p. e27639
    [PMID:24394987]
  16. Fonseca S, et al.
    bHLH003, bHLH013 and bHLH017 are new targets of JAZ repressors negatively regulating JA responses.
    PLoS ONE, 2014. 9(1): p. e86182
    [PMID:24465948]
  17. Ezer D, et al.
    The G-Box Transcriptional Regulatory Code in Arabidopsis.
    Plant Physiol., 2017. 175(2): p. 628-640
    [PMID:28864470]