PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

RrC8230_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

bHLH

Protein Properties

Length: 800aa MW: 87569.5 Da PI: 5.8191

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC8230_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.8	1.7e-12	395	441	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +h e+Er+RR+++N++f Lr ++P+ K++Ka+ L A+ YI++L+ RrC8230_p1 395 NHVEAERQRREKLNQRFYALRAVVPNV-----SKMDKASLLGDAIAYINELE 441 799*********************6.....5**************995 PP
2	HLH	20.4	9.4e-07	775	800	4	29
HHHHHHHHHHHHHHHHHHHHHCTSCC CS HLH 4 ahnerErrRRdriNsafeeLrellPk 29 +h e+Er+RR+++N++f Lr ++P+ RrC8230_p1 775 NHVEAERQRREKLNQRFYALRAVVPN 800 799*********************95 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	5.7E-57	44	228	IPR025610	Transcription factor MYC/MYB N-terminal
SuperFamily	SSF47459	7.85E-17	390	456	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.66E-14	390	441	No hit	No description
PROSITE profile	PS50888	17.111	391	440	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	5.6E-10	395	441	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	9.4E-17	395	461	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.5E-15	397	446	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF14215	3.4E-10	565	608	IPR025610	Transcription factor MYC/MYB N-terminal
CDD	cd00083	8.89E-7	770	800	No hit	No description
PROSITE profile	PS50888	11.458	771	800	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	6.67E-7	771	800	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.0E-6	775	800	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009269	Biological Process	response to desiccation
GO:0009611	Biological Process	response to wounding
GO:0009737	Biological Process	response to abscisic acid
GO:0009867	Biological Process	jasmonic acid mediated signaling pathway
GO:0009963	Biological Process	positive regulation of flavonoid biosynthetic process
GO:0010200	Biological Process	response to chitin
GO:0043619	Biological Process	regulation of transcription from RNA polymerase II promoter in response to oxidative stress
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0051090	Biological Process	regulation of sequence-specific DNA binding transcription factor activity
GO:2000068	Biological Process	regulation of defense response to insect
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 800 aa Download sequence Send to blast
MRNLWATDDN TSMMEAFLTS SDMSALWLQE TSATAPAGFN QETLQQRLQA LIEGTNEGWT 60 YAIFWQPSYD FSGDSVLGWG DGYYKGEEDK GKPKQRSTPL PFSTPADQEY RKKVLRELNS 120 LISGGGGPVD DAVDEEVTDT EWFFLVSMTQ SFASGAGLAG KAFSTGNVVW VSGSDQLSGS 180 SCERAKQGGV FGMQTIACIP SVNGVVELGS TEQIRRSSDL MNKVRLLFNF DVGTNWNLQG 240 ENNPSVWIND PIGASEPGNG QFSSKFENGG SSSTITGNPN HDSTLSPVHS QTLNPNFNNN 300 FSGEMNFSTS SKPRPGEILS FGNNGKRSSM NPDPIQFENK RKNSLGLIDD KVLSFGGGGE 360 TDHSDLEASV VKETPEKRPK KRGRKPANGK EEPLNHVEAE RQRREKLNQR FYALRAVVPN 420 VSKMDKASLL GDAIAYINEL ELNVNKTESE KIKIKNQLEE VKMELAGRKA STCGDLSSSS 480 SSSSATAPVG MEIEVKVIGW DAMIRVESSK RNYPAARLMS ALMDLELEVS HASMSVVNDL 540 MIQQATVKMG FRIYTQDQLR ASLISKIGGV FGMQTIACIP SVNGVVELGS TEQIRRSSDL 600 MNKVRLLFNF DVGTNWNLQG ENNPSVWIND PIGASEPGNG QFSSKFENGG SSSTITGNPN 660 HDSTLSPVHS QTLNPNFNNN FSGEMNFSTS SKPRPGEILS FGNNGKRSSM NPDPIQFENK 720 RKNSLGLIDD KVLSFGGGGE TDHSDLEASV VKETPEKRPK KRGRKPANGK EEPLNHVEAE 780 RQRREKLNQR FYALRAVVPN

Sequence ? help Back to Top

Protein Sequence Length: 800 aa Download sequence Send to blast

MRNLWATDDN TSMMEAFLTS SDMSALWLQE TSATAPAGFN QETLQQRLQA LIEGTNEGWT  60
YAIFWQPSYD FSGDSVLGWG DGYYKGEEDK GKPKQRSTPL PFSTPADQEY RKKVLRELNS  120
LISGGGGPVD DAVDEEVTDT EWFFLVSMTQ SFASGAGLAG KAFSTGNVVW VSGSDQLSGS  180
SCERAKQGGV FGMQTIACIP SVNGVVELGS TEQIRRSSDL MNKVRLLFNF DVGTNWNLQG  240
ENNPSVWIND PIGASEPGNG QFSSKFENGG SSSTITGNPN HDSTLSPVHS QTLNPNFNNN  300
FSGEMNFSTS SKPRPGEILS FGNNGKRSSM NPDPIQFENK RKNSLGLIDD KVLSFGGGGE  360
TDHSDLEASV VKETPEKRPK KRGRKPANGK EEPLNHVEAE RQRREKLNQR FYALRAVVPN  420
VSKMDKASLL GDAIAYINEL ELNVNKTESE KIKIKNQLEE VKMELAGRKA STCGDLSSSS  480
SSSSATAPVG MEIEVKVIGW DAMIRVESSK RNYPAARLMS ALMDLELEVS HASMSVVNDL  540
MIQQATVKMG FRIYTQDQLR ASLISKIGGV FGMQTIACIP SVNGVVELGS TEQIRRSSDL  600
MNKVRLLFNF DVGTNWNLQG ENNPSVWIND PIGASEPGNG QFSSKFENGG SSSTITGNPN  660
HDSTLSPVHS QTLNPNFNNN FSGEMNFSTS SKPRPGEILS FGNNGKRSSM NPDPIQFENK  720
RKNSLGLIDD KVLSFGGGGE TDHSDLEASV VKETPEKRPK KRGRKPANGK EEPLNHVEAE  780
RQRREKLNQR FYALRAVVPN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rru_A	2e-71	3	224	5	227	Transcription factor MYC3
4ywc_A	2e-71	3	224	5	227	Transcription factor MYC3
4ywc_B	2e-71	3	224	5	227	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	756	764	KRPKKRGRK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator. Common transcription factor of light, abscisic acid (ABA), and jasmonic acid (JA) signaling pathways. With MYC3 and MYC4, controls additively subsets of JA-dependent responses. In cooperation with MYB2 is involved in the regulation of ABA-inducible genes under drought stress conditions. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the MYC recognition site (5'-CACATG-3'), and to the G-box (5'-CACNTG-3') and Z-box (5'-ATACGTGT-3') of promoters. Binds directly to the promoters of the transcription factors PLETHORA1 (PLT1) and PLT2 and represses their expression. Negative regulator of blue light-mediated photomorphogenic growth and blue- and far-red-light regulated gene expression. Activates multiple TIFY/JAZ promoters. Positive regulator of lateral root formation. Regulates sesquiterpene biosynthesis. Subjected to proteasome-dependent proteolysis. The presence of the destruction element (DE) involved in turnover is required for the function to regulate gene transcription. {ECO:0000269\|PubMed:12509522, ECO:0000269\|PubMed:15208388, ECO:0000269\|PubMed:15923349, ECO:0000269\|PubMed:21321051, ECO:0000269\|PubMed:21335373, ECO:0000269\|PubMed:21954460, ECO:0000269\|PubMed:22669881, ECO:0000269\|PubMed:23142764, ECO:0000269\|PubMed:23593022, ECO:0000269\|PubMed:23943862, ECO:0000269\|PubMed:9368419}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00084	PBM	Transfer from AT1G32640	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Detected early after abscisic acid (ABA) treatment or after dehydration and high-salt stresses. Induced by UV treatment. Up-regulated by methyl jasmonate and herbivory. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15208388, ECO:0000269\|PubMed:23593022, ECO:0000269\|PubMed:23943862, ECO:0000269\|PubMed:9368419}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018451259.1	0.0	PREDICTED: transcription factor MYC2-like
Swissprot	Q39204	0.0	MYC2_ARATH; Transcription factor MYC2
TrEMBL	A0A0D3DKU7	0.0	A0A0D3DKU7_BRAOL; Uncharacterized protein
STRING	Bo8g028850.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1265	28	96

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G32640.1	0.0	bHLH family protein

Publications ? help Back to Top
Zheng XY, et al. Coronatine promotes Pseudomonas syringae virulence in plants by activating a signaling cascade that inhibits salicylic acid accumulation. Cell Host Microbe, 2012. 11(6): p. 587-96 [PMID:22704619] Guo R, et al. Jasmonic acid and glucose synergistically modulate the accumulation of glucosinolates in Arabidopsis thaliana. J. Exp. Bot., 2013. 64(18): p. 5707-19 [PMID:24151308] Gangappa SN,Srivastava AK,Maurya JP,Ram H,Chattopadhyay S Z-box binding transcription factors (ZBFs): a new class of transcription factors in Arabidopsis seedling development. Mol Plant, 2013. 6(6): p. 1758-68 [PMID:24157607] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Vos IA, et al. Onset of herbivore-induced resistance in systemic tissue primed for jasmonate-dependent defenses is activated by abscisic acid. Front Plant Sci, 2013. 4: p. 539 [PMID:24416038] Liu N,Ding Y,Fromm M,Avramova Z Different gene-specific mechanisms determine the 'revised-response' memory transcription patterns of a subset of A. thaliana dehydration stress responding genes. Nucleic Acids Res., 2014. 42(9): p. 5556-66 [PMID:24744238] Chico JM, et al. Repression of Jasmonate-Dependent Defenses by Shade Involves Differential Regulation of Protein Stability of MYC Transcription Factors and Their JAZ Repressors in Arabidopsis. Plant Cell, 2014. 26(5): p. 1967-1980 [PMID:24824488] Karumuri S,Bandopadhyay R In silico analysis of the structure and interaction of COP1 protein of Arabidopsis thaliana. Indian J. Biochem. Biophys., 2014. 51(5): p. 343-9 [PMID:25630103] Roos J,Bejai S,Mozūraitis R,Dixelius C Susceptibility to Verticillium longisporum is linked to monoterpene production by TPS23/27 in Arabidopsis. Plant J., 2015. 81(4): p. 572-85 [PMID:25640950] Yamada Y,Motomura Y,Sato F CjbHLH1 homologs regulate sanguinarine biosynthesis in Eschscholzia californica cells. Plant Cell Physiol., 2015. 56(5): p. 1019-30 [PMID:25713177] Kazan K Diverse roles of jasmonates and ethylene in abiotic stress tolerance. Trends Plant Sci., 2015. 20(4): p. 219-29 [PMID:25731753] Lenka SK, et al. Jasmonate-responsive expression of paclitaxel biosynthesis genes in Taxus cuspidata cultured cells is negatively regulated by the bHLH transcription factors TcJAMYC1, TcJAMYC2, and TcJAMYC4. Front Plant Sci, 2015. 6: p. 115 [PMID:25767476] Carvalhais LC, et al. Linking Jasmonic Acid Signaling, Root Exudates, and Rhizosphere Microbiomes. Mol. Plant Microbe Interact., 2015. 28(9): p. 1049-58 [PMID:26035128] Gasperini D, et al. Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth. PLoS Genet., 2015. 11(6): p. e1005300 [PMID:26070206] Qi T, et al. Regulation of Jasmonate-Induced Leaf Senescence by Antagonism between bHLH Subgroup IIIe and IIId Factors in Arabidopsis. Plant Cell, 2015. 27(6): p. 1634-49 [PMID:26071420] Wang C, et al. Arabidopsis Elongator subunit 2 positively contributes to resistance to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola. Plant J., 2015. 83(6): p. 1019-33 [PMID:26216741] de Ollas C,Arbona V,Gómez-Cadenas A Jasmonic acid interacts with abscisic acid to regulate plant responses to water stress conditions. Plant Signal Behav, 2015. 10(12): p. e1078953 [PMID:26340066] Yastreb TO,Kolupayev YE,Shvidenko AA,Lugovaya AA,Dmitriev AP [Salt Stress Response in Arabidopsis thaliana Plants with Defective Jasmonate Signaling]. Prikl. Biokhim. Mikrobiol., 2015 Jul-Aug. 51(4): p. 412-6 [PMID:26353406] Liu Z, et al. A Conserved Cytochrome P450 Evolved in Seed Plants Regulates Flower Maturation. Mol Plant, 2015. 8(12): p. 1751-65 [PMID:26388305] Zhu X, et al. Jasmonic acid promotes degreening via MYC2/3/4- and ANAC019/055/072-mediated regulation of major chlorophyll catabolic genes. Plant J., 2015. 84(3): p. 597-610 [PMID:26407000] de Torres Zabala M, et al. Novel JAZ co-operativity and unexpected JA dynamics underpin Arabidopsis defence responses to Pseudomonas syringae infection. New Phytol., 2016. 209(3): p. 1120-34 [PMID:26428397] Kaurilind E,Xu E,Brosché M A genetic framework for H2O2 induced cell death in Arabidopsis thaliana. BMC Genomics, 2015. 16: p. 837 [PMID:26493993] Yu J, et al. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. J. Exp. Bot., 2016. 67(3): p. 751-62 [PMID:26547795] Lu M, et al. AtCNGC2 is involved in jasmonic acid-induced calcium mobilization. J. Exp. Bot., 2016. 67(3): p. 809-19 [PMID:26608645] Chen X,Huang H,Qi T,Liu B,Song S New perspective of the bHLH-MYB complex in jasmonate-regulated plant fertility in arabidopsis. Plant Signal Behav, 2016. 11(2): p. e1135280 [PMID:26829586] Schmiesing A,Emonet A,Gouhier-Darimont C,Reymond P Arabidopsis MYC Transcription Factors Are the Target of Hormonal Salicylic Acid/Jasmonic Acid Cross Talk in Response to Pieris brassicae Egg Extract. Plant Physiol., 2016. 170(4): p. 2432-43 [PMID:26884488] Liu N,Avramova Z Molecular mechanism of the priming by jasmonic acid of specific dehydration stress response genes in Arabidopsis. Epigenetics Chromatin, 2016. 9: p. 8 [PMID:26918031] Takagi H, et al. Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner. J. Exp. Bot., 2016. 67(8): p. 2519-2532 [PMID:26931169] Mira MM, et al. Jasmonic acid is a downstream component in the modulation of somatic embryogenesis by Arabidopsis Class 2 phytoglobin. J. Exp. Bot., 2016. 67(8): p. 2231-46 [PMID:26962208] Valenzuela CE, et al. Salt stress response triggers activation of the jasmonate signaling pathway leading to inhibition of cell elongation in Arabidopsis primary root. J. Exp. Bot., 2016. 67(14): p. 4209-20 [PMID:27217545] Aleman F, et al. An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling. Sci Rep, 2016. 6: p. 28941 [PMID:27357749] An JP, et al. The molecular cloning and functional characterization of MdMYC2, a bHLH transcription factor in apple. Plant Physiol. Biochem., 2016. 108: p. 24-31 [PMID:27404131] Gao C, et al. MYC2, MYC3, and MYC4 function redundantly in seed storage protein accumulation in Arabidopsis. Plant Physiol. Biochem., 2016. 108: p. 63-70 [PMID:27415132] Liu N,Staswick PE,Avramova Z Memory responses of jasmonic acid-associated Arabidopsis genes to a repeated dehydration stress. Plant Cell Environ., 2016. 39(11): p. 2515-2529 [PMID:27451106] Allu AD,Brotman Y,Xue GP,Balazadeh S Transcription factor ANAC032 modulates JA/SA signalling in response to Pseudomonas syringae infection. EMBO Rep., 2016. 17(11): p. 1578-1589 [PMID:27632992] Raya-González J,Velázquez-Becerra C,Barrera-Ortiz S,López-Bucio J,Valencia-Cantero E N,N-dimethyl hexadecylamine and related amines regulate root morphogenesis via jasmonic acid signaling in Arabidopsis thaliana. Protoplasma, 2017. 254(3): p. 1399-1410 [PMID:27696021] Gimenez-Ibanez S, et al. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol., 2017. 213(3): p. 1378-1392 [PMID:28005270] Yuan LB, et al. Jasmonate Regulates Plant Responses to Postsubmergence Reoxygenation through Transcriptional Activation of Antioxidant Synthesis. Plant Physiol., 2017. 173(3): p. 1864-1880 [PMID:28082717] Le Hir R, et al. AtbHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana. Physiol Plant, 2017. 160(3): p. 312-327 [PMID:28369972] Li K,Yang F,Miao Y,Song CP Abscisic acid signaling is involved in regulating the mitogen-activated protein kinase cascade module, AIK1-MKK5-MPK6. Plant Signal Behav, 2017. 12(5): p. e1321188 [PMID:28494202] Lian TF,Xu YP,Li LF,Su XD Crystal Structure of Tetrameric Arabidopsis MYC2 Reveals the Mechanism of Enhanced Interaction with DNA. Cell Rep, 2017. 19(7): p. 1334-1342 [PMID:28514654] Yao L,Zheng Y,Zhu Z Jasmonate suppresses seedling soil emergence in Arabidopsis thaliana. Plant Signal Behav, 2017. 12(6): p. e1330239 [PMID:28534718] Jeong JS,Jung C,Seo JS,Kim JK,Chua NH The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses. Plant Cell, 2017. 29(6): p. 1406-1424 [PMID:28536144] Huang CF, et al. Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(33): p. E6884-E6891 [PMID:28761000] Wang H, et al. The bHLH Transcription Factors MYC2, MYC3, and MYC4 Are Required for Jasmonate-Mediated Inhibition of Flowering in Arabidopsis. Mol Plant, 2017. 10(11): p. 1461-1464 [PMID:28827172] Jang G, et al. Antagonistic interaction between jasmonic acid and cytokinin in xylem development. Sci Rep, 2017. 7(1): p. 10212 [PMID:28860478] Song S, et al. MYC5 is Involved in Jasmonate-Regulated Plant Growth, Leaf Senescence and Defense Responses. Plant Cell Physiol., 2017. 58(10): p. 1752-1763 [PMID:29017003] Ullah A,Sun H,Yang X,Zhang X A novel cotton WRKY gene, GhWRKY6-like, improves salt tolerance by activating the ABA signaling pathway and scavenging of reactive oxygen species. Physiol Plant, 2018. 162(4): p. 439-454 [PMID:29027659] Zhai Q,Li L,An C,Li C Conserved function of mediator in regulating nuclear hormone receptor activation between plants and animals. Plant Signal Behav, 2018. 13(5): p. e1403709 [PMID:29125388] Li B, et al. Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. Plant Cell, 2018. 30(1): p. 178-195 [PMID:29317470] Giri MK,Gautam JK,Rajendra Prasad VB,Chattopadhyay S,Nandi AK Rice MYC2 (OsMYC2) modulates light-dependent seedling phenotype, disease defence but not ABA signalling. J. Biosci., 2017. 42(3): p. 501-508 [PMID:29358563] Han X, et al. Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons. Plant Physiol., 2018. 176(4): p. 2871-2885 [PMID:29496884] Li X,Yang R,Chen H The Arabidopsis thaliana Mediator subunit MED8 regulates plant immunity to Botrytis Cinerea through interacting with the basic helix-loop-helix (bHLH) transcription factor FAMA. PLoS ONE, 2018. 13(3): p. e0193458 [PMID:29513733]