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

Rsa1.0_02220.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 566aa MW: 62280.2 Da PI: 4.8036

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_02220.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	39.5	9.9e-13	395	440	4	54
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 +h e+Er+RR+++N++f Lr ++P+ K++Ka+ L A+ YI++L Rsa1.0_02220.1_g00001.1 395 NHVEAERQRREKLNQRFYSLRAVVPNV-----SKMDKASLLGDAISYINEL 440 799*********************6.....5*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	1.3E-54	64	252	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	17.282	391	440	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	3.93E-18	394	458	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.72E-15	394	445	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.4E-18	395	459	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.6E-10	395	440	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.2E-16	397	446	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006952	Biological Process	defense response
GO:0009718	Biological Process	anthocyanin-containing compound biosynthetic process
GO:0009753	Biological Process	response to jasmonic acid
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0043425	Molecular Function	bHLH transcription factor binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 566 aa Download sequence Send to blast
MDDHRSRVSL SPPDPHMSNY FLNQTTPPAD NDNAVEAFIG TNHWSQQTQP PPPQTLSQFN 60 EDTLQQRLQT LIESAGERWT YAIFWQISHE FDSPTGENTV ILGWGDGYYR GEEDKEKKKK 120 QSLSSNPAEQ EHRKRVIREL NSLIAGGGGA GVSDEANDEE VTDTEWFFLV SMTQSFVNGV 180 GLPGESFLNS RVIWLSGSGA LTGSGCERAR QGEVYGLQTI VCIAAENGVV ELGSSEVISQ 240 SSDLMDKVNG LFNGNGNGEA SSWGFNLNPD QGENDPALWL SEPNVTGIEP VVQETPPPGA 300 IENAGGDLNF SSSGLNQSGN FKQGSSSSKK RSPVVSKDEE MLSFTTVVRS AAKSVDSDHS 360 DIEASVVKEA IIVEPEKKPR KRGRKPANGR EEPLNHVEAE RQRREKLNQR FYSLRAVVPN 420 VSKMDKASLL GDAISYINEL KTKLQQAEAD KEEVQKQLDG MGKEGGGSRR AKERKSNRDS 480 ESSVEMEIDV KIIGWDVMIR VQCGKKNHPG ARFMEALKEL DLEVNHASLS VVNDLMIQQA 540 TVKMGSQFFN HDQLKAALML KVGEDI

Sequence ? help Back to Top

Protein Sequence Length: 566 aa Download sequence Send to blast

MDDHRSRVSL SPPDPHMSNY FLNQTTPPAD NDNAVEAFIG TNHWSQQTQP PPPQTLSQFN  60
EDTLQQRLQT LIESAGERWT YAIFWQISHE FDSPTGENTV ILGWGDGYYR GEEDKEKKKK  120
QSLSSNPAEQ EHRKRVIREL NSLIAGGGGA GVSDEANDEE VTDTEWFFLV SMTQSFVNGV  180
GLPGESFLNS RVIWLSGSGA LTGSGCERAR QGEVYGLQTI VCIAAENGVV ELGSSEVISQ  240
SSDLMDKVNG LFNGNGNGEA SSWGFNLNPD QGENDPALWL SEPNVTGIEP VVQETPPPGA  300
IENAGGDLNF SSSGLNQSGN FKQGSSSSKK RSPVVSKDEE MLSFTTVVRS AAKSVDSDHS  360
DIEASVVKEA IIVEPEKKPR KRGRKPANGR EEPLNHVEAE RQRREKLNQR FYSLRAVVPN  420
VSKMDKASLL GDAISYINEL KTKLQQAEAD KEEVQKQLDG MGKEGGGSRR AKERKSNRDS  480
ESSVEMEIDV KIIGWDVMIR VQCGKKNHPG ARFMEALKEL DLEVNHASLS VVNDLMIQQA  540
TVKMGSQFFN HDQLKAALML KVGEDI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rru_A	1e-109	34	248	17	227	Transcription factor MYC3
4ywc_A	1e-109	34	248	17	227	Transcription factor MYC3
4ywc_B	1e-109	34	248	17	227	Transcription factor MYC3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	376	384	KKPRKRGRK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. With MYC2 and MYC4, controls additively subsets of JA-dependent responses. Can form complexes with all known glucosinolate-related MYBs to regulate glucosinolate biosynthesis. Binds to the G-box (5'-CACGTG-3') of promoters. Activates multiple TIFY/JAZ promoters. {ECO:0000269\|PubMed:12136026, ECO:0000269\|PubMed:21242320, ECO:0000269\|PubMed:21321051, ECO:0000269\|PubMed:21335373, ECO:0000269\|PubMed:23943862}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00085	PBM	Transfer from AT5G46760	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_02220.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Barely up-regulated by jasmonic acid. {ECO:0000269\|PubMed:21242320, ECO:0000269\|PubMed:21335373}.

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_018457039.1	0.0	PREDICTED: transcription factor MYC3
Swissprot	Q9FIP9	0.0	MYC3_ARATH; Transcription factor MYC3
TrEMBL	A0A397XV80	0.0	A0A397XV80_BRACM; Uncharacterized protein
TrEMBL	A0A3P6E5A0	0.0	A0A3P6E5A0_BRAOL; Uncharacterized protein
STRING	Bo9g065530.1	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
AT5G46760.1	0.0	bHLH family protein

Publications ? help Back to Top
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] 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] 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] Yu J, et al. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. J. Exp. Bot., 2016. 67(3): p. 751-62 [PMID:26547795] 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] Thatcher LF, et al. Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum. J. Exp. Bot., 2016. 67(8): p. 2367-86 [PMID:26896849] 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] Gimenez-Ibanez S, et al. JAZ2 controls stomata dynamics during bacterial invasion. New Phytol., 2017. 213(3): p. 1378-1392 [PMID:28005270] Zhang F, et al. Structural insights into alternative splicing-mediated desensitization of jasmonate signaling. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(7): p. 1720-1725 [PMID:28137867] 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] 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] 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] 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] Han X, et al. Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons. Plant Physiol., 2018. 176(4): p. 2871-2885 [PMID:29496884]