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_00191.1_g00036.1

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: 599aa MW: 65357.4 Da PI: 4.9934

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00191.1_g00036.1	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	1e-12	428	473	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_00191.1_g00036.1 428 NHVEAERQRREKLNQRFYSLRAVVPNV-----SKMDKASLLGDAISYINEL 473 799*********************6.....5*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	1.2E-53	63	258	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	17.282	424	473	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.31E-14	427	478	No hit	No description
SuperFamily	SSF47459	4.06E-18	427	498	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.5E-10	428	473	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	2.0E-18	428	494	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.5E-16	430	479	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: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: 599 aa Download sequence Send to blast
MSSTDVQVTD HHLNQSTNGT NLWSTTEDDA SVMEPFIGSE HSSLWPQPPL TPPPPPHVTE 60 DTLQQRLQAL IEGARESWTY AVFWQLSHGF AGEDSTTAAA LLSWGDGYYK GEEEERKKRK 120 PNNPVSAAEQ EHRKRVIREL NSLISGGGGG TVSGSSSDEA GDEDVTDAEW FFLVSMTQSF 180 FASDGSGLPG RAFSNSQTIW LSGSNALAGS SCERARQGQV YGLETMVCVP TENGVVELGS 240 LEVIHQSSDL VDKVNGFFSF NGGGGGVSGS WAFNLNPDQG ENDPATTWIN EPDVTGIEPV 300 LGVNTGNNNN STSSNSDSQT ASKLCNGSSV EHPKQQQQHQ NPQISSSGFV EGDSKKKKRC 360 LVSDKEEEML SFTSVLPLAT KTNDSDHSDL EASVAKGQKS GGRTVVEPEK KPRKRGRKPA 420 NGREESLNHV EAERQRREKL NQRFYSLRAV VPNVSKMDKA SLLGDAISYI NELKAKLEKA 480 ECDKEELKKK IDGMSQEVAS GNVKSSVKDQ KCVDQDSGVS VEVEIDVKII GWDAMIRIQC 540 GKKNHPGAKF MEALRELELE VNHASLSVVN EFMIQQATVK MGNQFFTQDK LKAALMERV

Sequence ? help Back to Top

Protein Sequence Length: 599 aa Download sequence Send to blast

MSSTDVQVTD HHLNQSTNGT NLWSTTEDDA SVMEPFIGSE HSSLWPQPPL TPPPPPHVTE  60
DTLQQRLQAL IEGARESWTY AVFWQLSHGF AGEDSTTAAA LLSWGDGYYK GEEEERKKRK  120
PNNPVSAAEQ EHRKRVIREL NSLISGGGGG TVSGSSSDEA GDEDVTDAEW FFLVSMTQSF  180
FASDGSGLPG RAFSNSQTIW LSGSNALAGS SCERARQGQV YGLETMVCVP TENGVVELGS  240
LEVIHQSSDL VDKVNGFFSF NGGGGGVSGS WAFNLNPDQG ENDPATTWIN EPDVTGIEPV  300
LGVNTGNNNN STSSNSDSQT ASKLCNGSSV EHPKQQQQHQ NPQISSSGFV EGDSKKKKRC  360
LVSDKEEEML SFTSVLPLAT KTNDSDHSDL EASVAKGQKS GGRTVVEPEK KPRKRGRKPA  420
NGREESLNHV EAERQRREKL NQRFYSLRAV VPNVSKMDKA SLLGDAISYI NELKAKLEKA  480
ECDKEELKKK IDGMSQEVAS GNVKSSVKDQ KCVDQDSGVS VEVEIDVKII GWDAMIRIQC  540
GKKNHPGAKF MEALRELELE VNHASLSVVN EFMIQQATVK MGNQFFTQDK LKAALMERV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rru_A	1e-81	25	254	8	227	Transcription factor MYC3
4ywc_A	1e-81	25	254	8	227	Transcription factor MYC3
4ywc_B	1e-81	25	254	8	227	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	409	417	KKPRKRGRK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in jasmonic acid (JA) gene regulation. With MYC2 and MYC3, 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:21321051, ECO:0000269\|PubMed:21335373, ECO:0000269\|PubMed:23943862}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00086	PBM	Transfer from AT4G17880	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00191.1_g00036.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. Not induced by jasmonic acid. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:21335373}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC183492	0.0	AC183492.1 Brassica oleracea Contig G, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018471791.1	0.0	PREDICTED: transcription factor MYC4
Swissprot	O49687	0.0	MYC4_ARATH; Transcription factor MYC4
TrEMBL	A0A078I392	0.0	A0A078I392_BRANA; BnaC01g10420D protein
STRING	Bo1g017990.1	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
AT4G17880.1	0.0	bHLH family protein

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] 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] 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]