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

RrC4759_p3

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

MYB_related

Protein Properties

Length: 367aa MW: 41482.7 Da PI: 8.3408

Description

MYB_related family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4759_p3	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	58.9	1.2e-18	14	61	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g+WTteEd++l+ +++++G g W+ I+++ g++R++k+c++rw +yl RrC4759_p3 14 KGAWTTEEDKKLISYIHEHGEGGWRDIPQKAGLKRCGKSCRLRWTNYL 61 79********************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	3.1E-24	5	64	IPR009057	Homeodomain-like
PROSITE profile	PS51294	24.586	9	65	IPR017930	Myb domain
SMART	SM00717	1.6E-14	13	63	IPR001005	SANT/Myb domain
Pfam	PF00249	2.1E-17	14	61	IPR001005	SANT/Myb domain
SuperFamily	SSF46689	5.14E-22	15	90	IPR009057	Homeodomain-like
CDD	cd00167	1.03E-11	16	61	No hit	No description
PROSITE profile	PS50090	4.147	62	135	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	1.8E-8	65	139	IPR009057	Homeodomain-like

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 367 aa Download sequence Send to blast
MSRKPCCVGE GLKKGAWTTE EDKKLISYIH EHGEGGWRDI PQKAGLKRCG KSCRLRWTNY 60 LKPEIKRGEF SSEEEQIIIM LHAARGNKYV YFQQKGRLYV YRPSSDYHSS FLFLLRQTNF 120 TNKNLDHKNY WNTHLKKRLI DQGIDPVTHK PLASNTNPTV TTTTTTQPGS LHSLDASSPD 180 DQYPRSTSMP SMSLPISSGL NTVSEITTND GTPVKGDSLS CKKSIKKSSS TSRLLNKVAA 240 KATSIKDILS ATTIPYGSFS SGFPEQSPNE EDSSKALVDL DPFSQSLLYT EHEIHATSDL 300 DMDQGYDFSY FLEKIGRDDH HNEEHDMNVG QVIFLTMLVI YMTRTMISSR SKSYECLYIS 360 QQKGFIQ

Sequence ? help Back to Top

Protein Sequence Length: 367 aa Download sequence Send to blast

MSRKPCCVGE GLKKGAWTTE EDKKLISYIH EHGEGGWRDI PQKAGLKRCG KSCRLRWTNY  60
LKPEIKRGEF SSEEEQIIIM LHAARGNKYV YFQQKGRLYV YRPSSDYHSS FLFLLRQTNF  120
TNKNLDHKNY WNTHLKKRLI DQGIDPVTHK PLASNTNPTV TTTTTTQPGS LHSLDASSPD  180
DQYPRSTSMP SMSLPISSGL NTVSEITTND GTPVKGDSLS CKKSIKKSSS TSRLLNKVAA  240
KATSIKDILS ATTIPYGSFS SGFPEQSPNE EDSSKALVDL DPFSQSLLYT EHEIHATSDL  300
DMDQGYDFSY FLEKIGRDDH HNEEHDMNVG QVIFLTMLVI YMTRTMISSR SKSYECLYIS  360
QQKGFIQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1h8a_C	5e-14	12	90	25	102	MYB TRANSFORMING PROTEIN
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Major regulator of short-chained aliphatic glucosinolates (GLSs) biosynthesis. Together with MYB29/HAG3 and MYB76/HAG2, promotes aliphatic glucosinolate biosynthesis but represses indolic glucosinolate biosynthesis. Prevents insect performance (e.g. lepidopteran insect Mamestra brassicae and Spodoptera exigua) by promoting glucosinolates. {ECO:0000269\|PubMed:17420480, ECO:0000269\|PubMed:17521412, ECO:0000269\|PubMed:18042203, ECO:0000269\|PubMed:18446225, ECO:0000269\|PubMed:20348214, ECO:0000269\|PubMed:23580754, ECO:0000269\|PubMed:23792303, ECO:0000269\|PubMed:23943862}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Slightly induced by glucose, gibberellic acid (GA), jasmonic acid (JA) and salicylic acid (SA). Transiently induced in inflorescence by mechanical stimuli such as touch or wounding, including herbivory-wounding. Up-regulated by sulfur-deficient stress. {ECO:0000269\|PubMed:16463103, ECO:0000269\|PubMed:17521412, ECO:0000269\|PubMed:23115560, ECO:0000269\|PubMed:23792303}.

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	AC232542	1e-172	AC232542.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH005L20, complete sequence.
GenBank	FJ584289	1e-172	FJ584289.1 Brassica rapa subsp. pekinensis MYB domain protein 28-3 gene, complete cds.
GenBank	JQ666168	1e-172	JQ666168.1 Brassica juncea R2R3 DNA binding transcription factor MYB28-3 (MYB28-3) mRNA, complete cds.
GenBank	JQ700567	1e-172	JQ700567.1 Brassica juncea R2R3 DNA binding transcription factor MYB28-3 (MYB28-3) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018440936.1	0.0	PREDICTED: transcription factor MYB28-like
Swissprot	Q9SPG2	1e-146	MYB28_ARATH; Transcription factor MYB28
TrEMBL	C5HYG1	1e-164	C5HYG1_BRARP; MYB domain protein 28-3
STRING	Bra029311.1-P	1e-165	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3787	18	60

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G61420.2	1e-133	myb domain protein 28

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Kim K,Jiang K,Teng SL,Feldman LJ,Huang H Using biologically interrelated experiments to identify pathway genes in Arabidopsis. Bioinformatics, 2012. 28(6): p. 815-22 [PMID:22271267] Augustine R,Majee M,Gershenzon J,Bisht NC Four genes encoding MYB28, a major transcriptional regulator of the aliphatic glucosinolate pathway, are differentially expressed in the allopolyploid Brassica juncea. J. Exp. Bot., 2013. 64(16): p. 4907-21 [PMID:24043856] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Li F, et al. Genome-wide association study dissects the genetic architecture of seed weight and seed quality in rapeseed (Brassica napus L.). DNA Res., 2014. 21(4): p. 355-67 [PMID:24510440] Frerigmann H,Gigolashvili T Update on the role of R2R3-MYBs in the regulation of glucosinolates upon sulfur deficiency. Front Plant Sci, 2014. 5: p. 626 [PMID:25426131] Burow M, et al. The Glucosinolate Biosynthetic Gene AOP2 Mediates Feed-back Regulation of Jasmonic Acid Signaling in Arabidopsis. Mol Plant, 2015. 8(8): p. 1201-12 [PMID:25758208] Martínez-Ballesta M, et al. The impact of the absence of aliphatic glucosinolates on water transport under salt stress in Arabidopsis thaliana. Front Plant Sci, 2015. 6: p. 524 [PMID:26236322] Seo MS, et al. Functional analysis of three BrMYB28 transcription factors controlling the biosynthesis of glucosinolates in Brassica rapa. Plant Mol. Biol., 2016. 90(4-5): p. 503-16 [PMID:26820138] Bulgakov VP,Veremeichik GN,Grigorchuk VP,Rybin VG,Shkryl YN The rolB gene activates secondary metabolism in Arabidopsis calli via selective activation of genes encoding MYB and bHLH transcription factors. Plant Physiol. Biochem., 2016. 102: p. 70-9 [PMID:26913794] Mostafa I, et al. New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants. J Proteomics, 2016. 138: p. 1-19 [PMID:26915584] Smith JD,Woldemariam MG,Mescher MC,Jander G,De Moraes CM Glucosinolates from Host Plants Influence Growth of the Parasitic Plant Cuscuta gronovii and Its Susceptibility to Aphid Feeding. Plant Physiol., 2016. 172(1): p. 181-97 [PMID:27482077] Aarabi F, et al. Sulfur deficiency-induced repressor proteins optimize glucosinolate biosynthesis in plants. Sci Adv, 2016. 2(10): p. e1601087 [PMID:27730214] Mostafa I, et al. Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29. Front Plant Sci, 2017. 8: p. 534 [PMID:28443122] Simon MK,Skinner DJ,Gallagher TL,Gasser CS Integument Development in Arabidopsis Depends on Interaction of YABBY Protein INNER NO OUTER with Coactivators and Corepressors. Genetics, 2017. 207(4): p. 1489-1500 [PMID:28971961] 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]