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 orange1.1g005651m
Common NameCISIN_1g005651mg
Organism
Citrus sinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family bHLH
Protein Properties Length: 686aa    MW: 74642.7 Da    PI: 5.4491
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g005651mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH39.11.4e-12505550454
                        HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS
                HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 
                        +h e+Er+RR+++N++f  Lr ++P+       K++Ka+ L  A+ YI++L
  orange1.1g005651m 505 NHVEAERQRREKLNQRFYALRAVVPNV-----SKMDKASLLGDAISYINEL 550
                        799***********************6.....5***************998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF142151.0E-5469255IPR025610Transcription factor MYC/MYB N-terminal
PROSITE profilePS5088817.39501550IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.49E-15504555No hitNo description
SuperFamilySSF474592.88E-18504570IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000104.5E-10505550IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.101.9E-18505571IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003539.2E-17507556IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009269Biological Processresponse to desiccation
GO:0009611Biological Processresponse to wounding
GO:0009737Biological Processresponse to abscisic acid
GO:0009867Biological Processjasmonic acid mediated signaling pathway
GO:0009963Biological Processpositive regulation of flavonoid biosynthetic process
GO:0010200Biological Processresponse to chitin
GO:0043619Biological Processregulation of transcription from RNA polymerase II promoter in response to oxidative stress
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051090Biological Processregulation of sequence-specific DNA binding transcription factor activity
GO:2000068Biological Processregulation of defense response to insect
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 686 aa     Download sequence    Send to blast
MTDYRLPSTM NLWTDDNGSV MEAFMSSDLT GIWPPSQSSA STADPMKTHI SSSSQQQQQQ  60
QQFFNQETLQ QRLQQLIEGS REGWTYAIFW QSSCDYSGSS MLGWGDGYYK GEGEKGKSSK  120
IKTSSAAEQE HRKKVLRELN SLISGSTSSP TDDAVDEEVT DTEWFFLISM TQSFYVTGGG  180
GGGGLPGQAY FGNSPVWVSG AERLANSGCD RARQGQVFGL QTLVCIPSAN GVVELGSTEV  240
IIQNSDLMNK VRFLFNFNGS MEIGTWPSAM QNPDQGENDP SSWINDPSPT PAPTAGFIEI  300
KDSTAAATTT TTTTTTTTTP AIGSGSASNL SKGIHFELPS SVSLTESVDL QHQQIPQTQS  360
FFTRELNFSE YAYDHNSVKN GSSRLFKPES GEILNFAESK RSSCTGNGNN SLLSNHSQFV  420
AEDSNKKKRS PTSRGSTEEG MLSFTSGVIL PSSGVVKSSG GAGDSDHSDL EASVVKDPDS  480
SRVEPEKKPR KRGRKPANGR EEPLNHVEAE RQRREKLNQR FYALRAVVPN VSKMDKASLL  540
GDAISYINEL RTKLQSAESD KEDLQKELAS VKKELAGGGK DSHSGPSTSD QDLKMSNHAS  600
KLIDLDIEVK IIGWDAMIRI QSSKKNHPAA KLMQALKELD LEVNHASMSV VNDLMIQQAT  660
VKMGSRFYTQ EQLKNVLAAK VGDTQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4rqw_A8e-69642584195Transcription factor MYC3
4rqw_B8e-69642584195Transcription factor MYC3
4rs9_A8e-69642584195Transcription factor MYC3
4yz6_A8e-69642584195Transcription factor MYC3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1486494KKPRKRGRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.164630.0fruit| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at low levels in roots, stems, leaves, flowers and fruits. {ECO:0000269|PubMed:15231736}.
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator that binds to the G-box motif (5'-AACGTG-3') found in the promoter of the jasmonate-induced gene LAPA1 (PubMed:15231736). Acts as negative regulator of blue light-mediated photomorphogenesis and positively regulates root growth (PubMed:24483714). Promotes growth in response to the phytohormones abscisic acid (ABA) and jasmonate (JA) (PubMed:24483714). Binds to the G-box motif (5'-CACGTG-3') of the RBCS-3A gene promoter (PubMed:24483714). Acts downstream of the jasmonate (JA) receptor to orchestrate JA-mediated activation of plant responses (PubMed:28733419). Positively regulates both wound-responsive and pathogen-responsive genes through MYC2-targeted transcription factors (MTFs) involved in early response to JA (PubMed:28733419). With JA2L forms a transcription module that regulates wounding-responsive genes (PubMed:28733419). With ERF.C3 forms a transcription module that regulates pathogen-responsive genes (PubMed:28733419). Plays a critical role in orchestrating JA-mediated defense gene expression during Botrytis cinerea infection (PubMed:28733419). Regulates negatively defense responses to root-knot nematodes, potentially by mediating crosstalk among the hormones strigolactones, abscisic acid (ABA) and jasmonate (JA) (PubMed:30576511). Regulates the termination of JA-mediated defense responses by specifically binding the G-box (5'-CACATG-3') motifs in the promoters of MTB1, MTB2 and MTB3, which are transcription factors that negatively regulates JA signaling (PubMed:30610166). May be involved in JA-induced chilling tolerance, possibly by ameliorating the antioxidant enzyme system of fruit and increasing proline and lycopene levels (PubMed:29528226). {ECO:0000269|PubMed:15231736, ECO:0000269|PubMed:24483714, ECO:0000269|PubMed:28733419, ECO:0000269|PubMed:29528226, ECO:0000269|PubMed:30576511, ECO:0000269|PubMed:30610166}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00084PBMTransfer from AT1G32640Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by methyl jasmonate (PubMed:15231736, PubMed:28733419). Induced by wounding (PubMed:15231736). Induced by infection with the fungal pathogen Botrytis cinerea (PubMed:28733419). Induced in fruit by storage in cold (PubMed:29528226). Induced by hydrogen peroxide and infection with root-knot nematodes (PubMed:30576511). {ECO:0000269|PubMed:15231736, ECO:0000269|PubMed:28733419, ECO:0000269|PubMed:29528226, ECO:0000269|PubMed:30576511}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9216120.0EU921612.1 Citrus unshiu clone GB-CU-206 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006428423.10.0transcription factor MYC2
RefseqXP_006491734.10.0transcription factor MYC2-like
SwissprotA0A3Q7HRZ60.0MYC2_SOLLC; Transcription factor MYC2
TrEMBLA0A067DP670.0A0A067DP67_CITSI; Uncharacterized protein
STRINGXP_006491734.10.0(Citrus sinensis)
STRINGXP_006428423.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM12652896
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G32640.10.0bHLH family protein
Publications ? help Back to Top
  1. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  2. Gupta N,Prasad VB,Chattopadhyay S
    LeMYC2 acts as a negative regulator of blue light mediated photomorphogenic growth, and promotes the growth of adult tomato plants.
    BMC Plant Biol., 2014. 14: p. 38
    [PMID:24483714]
  3. Sun H,Fan HJ,Ling HQ
    Genome-wide identification and characterization of the bHLH gene family in tomato.
    BMC Genomics, 2015. 16: p. 9
    [PMID:25612924]
  4. Du M, et al.
    MYC2 Orchestrates a Hierarchical Transcriptional Cascade That Regulates Jasmonate-Mediated Plant Immunity in Tomato.
    Plant Cell, 2017. 29(8): p. 1883-1906
    [PMID:28733419]
  5. Min D, et al.
    SlMYC2 Involved in Methyl Jasmonate-Induced Tomato Fruit Chilling Tolerance.
    J. Agric. Food Chem., 2018. 66(12): p. 3110-3117
    [PMID:29528226]
  6. Xu X, et al.
    Strigolactones positively regulate defense against root-knot nematodes in tomato.
    J. Exp. Bot., 2019. 70(4): p. 1325-1337
    [PMID:30576511]
  7. Liu Y, et al.
    MYC2 Regulates the Termination of Jasmonate Signaling via an Autoregulatory Negative Feedback Loop.
    Plant Cell, 2019. 31(1): p. 106-127
    [PMID:30610166]