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

RrC3963_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: 604aa MW: 67695.2 Da PI: 5.0961

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3963_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	47.4	3.5e-15	414	460	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 +h Er+RR+++N++f +Lr+++P+ K +K++iL +++Y+++Lq RrC3963_p1 414 NHALSERKRREKLNDRFMTLRSIIPST-----SKIDKVSILDDTIDYLQELQ 460 79999*******************7.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF14215	9.2E-52	13	202	IPR025610	Transcription factor MYC/MYB N-terminal
PROSITE profile	PS50888	17.155	410	459	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.1E-12	414	460	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.31E-18	414	479	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.58E-16	414	464	No hit	No description
Gene3D	G3DSA:4.10.280.10	7.5E-18	414	471	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.0E-17	416	465	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009957	Biological Process	epidermal cell fate specification
GO:0005634	Cellular Component	nucleus
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 604 aa Download sequence Send to blast
MTTGEKRTVP ENLKKHLAVS VRNIQWSYGI FWSISASQPG MLEWGDGYYN GDIKTRKTIQ 60 AVEVKADQLG LERSEQLREL YESLSLADSS TSGGSQVSRR ASASALSPED LTDTEWYYLV 120 CMSFVFNIGE GITGGALANG EPIWLCNAHT ADSKVFIRSL LAKSASLLTV VCFPFLGGVL 180 EIGTTEHITE DLNVIQCVKT LFLEAHPYGT ISTRSDYQEI FDPLNSDKYI PVFGTEAFPT 240 TSTSGFEQEL EDHDSFINGG NASQVQSWQF VGEELNNCVH QPLNSSDCVS QTLVGTTGRV 300 SCNPRKSRTQ RLGQIQEQSN RLNMDNDVHY QGVISTIFKT THQLILGPQF QNFDKRSSFT 360 RWRRSSLSAK TLGEKSQNMI KKIIFEVPRM HQKELLLPDT PEDNMFKVGD ETGNHALSER 420 KRREKLNDRF MTLRSIIPST SKIDKVSILD DTIDYLQELQ RRVQELESCR EYTDTDMRMP 480 TKRKKPEDED ERASANCLNT KRKESDVNVG EDEPADTGYA GLTDNLRIGL FGNEVVIELR 540 CAWREGILLE IMDVISDLNL DSHSVQSSTG DGLLCLTVNC KHKGTKIATT GMIQEALQGV 600 AWIC

Sequence ? help Back to Top

Protein Sequence Length: 604 aa Download sequence Send to blast

MTTGEKRTVP ENLKKHLAVS VRNIQWSYGI FWSISASQPG MLEWGDGYYN GDIKTRKTIQ  60
AVEVKADQLG LERSEQLREL YESLSLADSS TSGGSQVSRR ASASALSPED LTDTEWYYLV  120
CMSFVFNIGE GITGGALANG EPIWLCNAHT ADSKVFIRSL LAKSASLLTV VCFPFLGGVL  180
EIGTTEHITE DLNVIQCVKT LFLEAHPYGT ISTRSDYQEI FDPLNSDKYI PVFGTEAFPT  240
TSTSGFEQEL EDHDSFINGG NASQVQSWQF VGEELNNCVH QPLNSSDCVS QTLVGTTGRV  300
SCNPRKSRTQ RLGQIQEQSN RLNMDNDVHY QGVISTIFKT THQLILGPQF QNFDKRSSFT  360
RWRRSSLSAK TLGEKSQNMI KKIIFEVPRM HQKELLLPDT PEDNMFKVGD ETGNHALSER  420
KRREKLNDRF MTLRSIIPST SKIDKVSILD DTIDYLQELQ RRVQELESCR EYTDTDMRMP  480
TKRKKPEDED ERASANCLNT KRKESDVNVG EDEPADTGYA GLTDNLRIGL FGNEVVIELR  540
CAWREGILLE IMDVISDLNL DSHSVQSSTG DGLLCLTVNC KHKGTKIATT GMIQEALQGV  600
AWIC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4rqw_A	5e-15	26	202	24	192	Transcription factor MYC3
4rqw_B	5e-15	26	202	24	192	Transcription factor MYC3
4rs9_A	5e-15	26	202	24	192	Transcription factor MYC3
4yz6_A	5e-15	26	202	24	192	Transcription factor MYC3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	418	423	ERKRRE
2	419	424	RKRREK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator, when associated with MYB75/PAP1, MYB90/PAP2 or TT2. Involved in epidermal cell fate specification. Regulates negatively stomata formation but promotes trichome formation. Together with MYB66/WER, promotes the formation of non-hair cells in root epidermis cells in the N position. Whereas together with CPC, promotes the formation of hair cells in root epidermis cells in the H position by inhibiting non-hair cell formation. Seems also to play a role in the activation of anthocyanin biosynthesis, probably together with MYB75/PAP1. Involved in seed mucilage production. Activates the transcription of GL2. {ECO:0000269\|PubMed:12917293, ECO:0000269\|PubMed:12956536, ECO:0000269\|PubMed:14627722, ECO:0000269\|PubMed:15361138, ECO:0000269\|PubMed:15590742}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By UV treatment. Negatively regulated by MYB66/WER, GL3 and BHLH2 in the developing non-hair cells, and positively regulated by CPC and TRY in the developing hair cells. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15590742}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353217	0.0	AK353217.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-32-J06.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018453342.1	0.0	PREDICTED: transcription factor EGL1 isoform X1
Swissprot	Q9CAD0	0.0	EGL1_ARATH; Transcription factor EGL1
TrEMBL	A0A078F5I3	0.0	A0A078F5I3_BRANA; BnaC09g12820D protein
STRING	Bra027796.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2592	28	67

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G63650.3	0.0	bHLH family protein

Publications ? help Back to Top
Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Liu Z,Shi MZ,Xie DY Regulation of anthocyanin biosynthesis in Arabidopsis thaliana red pap1-D cells metabolically programmed by auxins. Planta, 2014. 239(4): p. 765-81 [PMID:24370633] Nayidu NK, et al. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS ONE, 2014. 9(4): p. e95877 [PMID:24755905] Cheng Y, et al. Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases. Elife, 2018. [PMID:24771765] Ranocha P,Francoz E,Burlat V,Dunand C Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Plant Signal Behav, 2014. 9(11): p. e977734 [PMID:25531128] Nemie-Feyissa D,Heidari B,Blaise M,Lillo C Analysis of interactions between heterologously produced bHLH and MYB proteins that regulate anthocyanin biosynthesis: quantitative interaction kinetics by Microscale Thermophoresis. Phytochemistry, 2015. 111: p. 21-6 [PMID:25659750] Kwak SH,Song SK,Lee MM,Schiefelbein J TORNADO1 regulates root epidermal patterning through the WEREWOLF pathway in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(12): p. e1103407 [PMID:26451798] Dai X, et al. A single amino acid substitution in the R3 domain of GLABRA1 leads to inhibition of trichome formation in Arabidopsis without affecting its interaction with GLABRA3. Plant Cell Environ., 2016. 39(4): p. 897-907 [PMID:26667588] Friede A, et al. The Second Intron Is Essential for the Transcriptional Control of the Arabidopsis thaliana GLABRA3 Gene in Leaves. Front Plant Sci, 2017. 8: p. 1382 [PMID:28848584] Feng K, et al. An R2R3-MYB transcription factor, OjMYB1, functions in anthocyanin biosynthesis in Oenanthe javanica. Planta, 2018. 247(2): p. 301-315 [PMID:28965159] Wen J, et al. The C-terminal domains of Arabidopsis GL3/EGL3/TT8 interact with JAZ proteins and mediate dimeric interactions. Plant Signal Behav, 2018. 13(1): p. e1422460 [PMID:29293407]