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

Carubv10004392m

Common Name

CARUB_v10004392mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 615aa MW: 67103.1 Da PI: 4.5302

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10004392m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.9	1.6e-12	441	486	4	54
HHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 +h e+Er+RR+++N++f Lr ++P+ + K++Ka+ L A+ YI++L Carubv10004392m 441 NHVEAERQRREKLNQRFYSLRAVVPNiS------KMDKASLLGDAISYINEL 486 799*********************66......*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	3.2E-55	66	262	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	17.218	437	486	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.28E-18	440	507	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	9.09E-15	440	491	No hit	No description
Gene3D	G3DSA:4.10.280.10	1.0E-18	441	507	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	5.8E-10	441	486	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.3E-16	443	492	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: 615 aa Download sequence Send to blast
MSPTSVQITD YHLNQSTNGT TNLWSNDEDA SVMEAFIGGS DQSSLFPPPS PPLPPPAQSQ 60 FNEDTLQQRL QALIEGANES WTYAVFWQSS YDFAGEDDGG GESRNTAVLG WGDGYYKGEE 120 ENSRKKKSNP ASAAEQEHRR RVIRELNALI SGGGGVVNNG GGSDEAGDEE VTDTEWFFLV 180 SMTQSFVSGT GLPGQAFSNS NTIWLSGSNA LAGSSCERAR QGQIYGLQTM VCVPCENGVV 240 ELGSSEIIHQ SSDLVDKVDT FFNFNNGGGE SGSWAFNLNP DQGENDPGLW IGEPDSVGVE 300 LGLVAPVMNN TGNNSASNSD SQPISKLCNG SSVEDPKPQV TKSSEMVSFK NGTDENGFSG 360 QSRFMEEDSN KKRSPVSNND EGMLSFTSVL PRPAKSGDSN HSDLEASVVK EAESNRTVVE 420 PEKKPRKRGR KPANGREEPL NHVEAERQRR EKLNQRFYSL RAVVPNISKM DKASLLGDAI 480 SYINELKSKL QKVESDKEEL QKQIEGMSKE AANEKSYVKE RKCANQESGV TIEMEVDVKI 540 IGWDAMIRVQ CSKRNHPGAK FMEALKELDL EVNHASLSVV NDLMIQQATV KMGKEFFTQD 600 QLKVALMEKV GECL*

Sequence ? help Back to Top

Protein Sequence Length: 615 aa Download sequence Send to blast

MSPTSVQITD YHLNQSTNGT TNLWSNDEDA SVMEAFIGGS DQSSLFPPPS PPLPPPAQSQ  60
FNEDTLQQRL QALIEGANES WTYAVFWQSS YDFAGEDDGG GESRNTAVLG WGDGYYKGEE  120
ENSRKKKSNP ASAAEQEHRR RVIRELNALI SGGGGVVNNG GGSDEAGDEE VTDTEWFFLV  180
SMTQSFVSGT GLPGQAFSNS NTIWLSGSNA LAGSSCERAR QGQIYGLQTM VCVPCENGVV  240
ELGSSEIIHQ SSDLVDKVDT FFNFNNGGGE SGSWAFNLNP DQGENDPGLW IGEPDSVGVE  300
LGLVAPVMNN TGNNSASNSD SQPISKLCNG SSVEDPKPQV TKSSEMVSFK NGTDENGFSG  360
QSRFMEEDSN KKRSPVSNND EGMLSFTSVL PRPAKSGDSN HSDLEASVVK EAESNRTVVE  420
PEKKPRKRGR KPANGREEPL NHVEAERQRR EKLNQRFYSL RAVVPNISKM DKASLLGDAI  480
SYINELKSKL QKVESDKEEL QKQIEGMSKE AANEKSYVKE RKCANQESGV TIEMEVDVKI  540
IGWDAMIRVQ CSKRNHPGAK FMEALKELDL EVNHASLSVV NDLMIQQATV KMGKEFFTQD  600
QLKVALMEKV GECL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rru_A	3e-90	20	258	3	227	Transcription factor MYC3
4ywc_A	3e-90	20	258	3	227	Transcription factor MYC3
4ywc_B	3e-90	20	258	3	227	Transcription factor MYC3
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Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	422	430	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	Carubv10004392m

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	AF251689	0.0	AF251689.1 Arabidopsis thaliana putative transcription factor BHLH4 (BHLH4) mRNA, complete cds.
GenBank	AK221507	0.0	AK221507.1 Arabidopsis thaliana mRNA for putative transcription factor BHLH4, complete cds, clone: RAFL07-57-K04.
GenBank	AL021889	0.0	AL021889.2 Arabidopsis thaliana DNA chromosome 4, BAC clone T6K21 (ESSA project).
GenBank	AL161547	0.0	AL161547.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 47.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006283348.1	0.0	transcription factor MYC4
Swissprot	O49687	0.0	MYC4_ARATH; Transcription factor MYC4
TrEMBL	R0F4A8	0.0	R0F4A8_9BRAS; Uncharacterized protein
STRING	XP_006283348.1	0.0	(Capsella rubella)

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

Link Out ? help Back to Top
Phytozome	Carubv10004392m
Entrez Gene	17879015

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]