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_00661.1_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

MYB

Protein Properties

Length: 340aa MW: 38371.3 Da PI: 4.5644

Description

MYB family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00661.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	Myb_DNA-binding	54	4e-17	14	61	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 +g+WT eEd++l+ +++++G g W+ I+++ g++R++k+c++rw +yl Rsa1.0_00661.1_g00001.1 14 KGAWTIEEDKKLISYIQEHGEGGWRDIPQKAGLKRCGKSCRLRWANYL 61 79********************************************97 PP
2	Myb_DNA-binding	46.6	7.8e-15	67	112	1	48
TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS Myb_DNA-binding 1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 rg ++ eE+++++ +++ G++ W+ Iar+++ +Rt++++k++w+++l Rsa1.0_00661.1_g00001.1 67 RGEFSYEEEQIIIMLHASRGNK-WSVIARHLP-KRTDNEIKNYWNTHL 112 899*****************.*****.**********996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.60	4.9E-24	6	64	IPR009057	Homeodomain-like
PROSITE profile	PS51294	23.742	9	65	IPR017930	Myb domain
SuperFamily	SSF46689	3.44E-29	11	108	IPR009057	Homeodomain-like
SMART	SM00717	2.9E-12	13	63	IPR001005	SANT/Myb domain
Pfam	PF00249	4.1E-16	14	61	IPR001005	SANT/Myb domain
CDD	cd00167	8.78E-10	16	61	No hit	No description
Gene3D	G3DSA:1.10.10.60	7.7E-25	65	116	IPR009057	Homeodomain-like
PROSITE profile	PS51294	18.873	66	116	IPR017930	Myb domain
SMART	SM00717	2.5E-13	66	114	IPR001005	SANT/Myb domain
Pfam	PF00249	1.9E-13	67	112	IPR001005	SANT/Myb domain
CDD	cd00167	5.47E-10	69	112	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009414	Biological Process	response to water deprivation
GO:0009611	Biological Process	response to wounding
GO:0009625	Biological Process	response to insect
GO:0009682	Biological Process	induced systemic resistance
GO:0009739	Biological Process	response to gibberellin
GO:0009751	Biological Process	response to salicylic acid
GO:0009753	Biological Process	response to jasmonic acid
GO:0010439	Biological Process	regulation of glucosinolate biosynthetic process
GO:0050832	Biological Process	defense response to fungus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 340 aa Download sequence Send to blast
MSRKACCVGE GLKKGAWTIE EDKKLISYIQ EHGEGGWRDI PQKAGLKRCG KSCRLRWANY 60 LKPDIKRGEF SYEEEQIIIM LHASRGNKWS VIARHLPKRT DNEIKNYWNT HLKKRLLDQG 120 IDPLTHKPLA SNPEPATPKT SDFQDDSNPS NLDEQSHSGS MSPKSLHLSS GSCNSEETPR 180 NYGYLKSKKS SATSELLNKV ATRAASMGNI ISASMEGTLI PSTTLSQPCL NDGFSETSQF 240 QMDELDPFSN SSEYIDHMKE DICMNFDLNN SDYDFSQFLE QFNNDAAEEA DDIIGYDQDL 300 LLSDDVSSTS VDEDSMMRNL TDWSNYLLDD SDFSHDTNQD

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1mse_C	4e-25	12	116	2	105	C-Myb DNA-Binding Domain
1msf_C	4e-25	12	116	2	105	C-Myb DNA-Binding Domain
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Plays a minor rheostat role in aliphatic glucosinolates (GLSs) biosynthesis, mostly short chained. Together with MYB28/HAG1 and MYB76/HAG2, promotes aliphatic glucosinolate biosynthesis but represses indolic glucosinolate biosynthesis. Prevents insect performance (e.g. lepidopteran insect Mamestra brassicae) by promoting glucosinolates. {ECO:0000269\|PubMed:17420480, ECO:0000269\|PubMed:18042203, ECO:0000269\|PubMed:18446225, ECO:0000269\|PubMed:20348214, ECO:0000269\|PubMed:23580754, ECO:0000269\|PubMed:23792303, ECO:0000269\|PubMed:23943862}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00661.1_g00001.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Slightly induced by gibberellic acid (GA), jasmonic acid (JA, MeJA), nitrogen starvation and UV LIGHT treatment. Transiently repressed by salicylic acid (SA). Accumulates upon mechanical stimuli (e.g. wounding) in inflorescence. Down-regulated by sulfur-deficient stress. {ECO:0000269\|PubMed:16463103, ECO:0000269\|PubMed:18042203, ECO:0000269\|PubMed:23792303, ECO:0000269\|PubMed:9839469}.

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	JX316032	0.0	JX316032.1 Brassica juncea R2R3 DNA binding transcription factor MYB29-2 (MYB29-2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018473209.1	0.0	PREDICTED: transcription factor MYB29-like
Swissprot	Q9FLR1	1e-164	MYB29_ARATH; Transcription factor MYB29
TrEMBL	S4TB34	0.0	S4TB34_BRAJU; R2R3 DNA binding transcription factor MYB29-2
STRING	Bra005949.1-P	0.0	(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
AT5G07690.1	1e-155	myb domain protein 29

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] Araki R, et al. Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production. Plant Biotechnol. J., 2013. 11(8): p. 1017-27 [PMID:23910994] 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] 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] 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] Zhang X, et al. The Transcription Factor MYB29 Is a Regulator of ALTERNATIVE OXIDASE1a. Plant Physiol., 2017. 173(3): p. 1824-1843 [PMID:28167700] Mostafa I, et al. Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29. Front Plant Sci, 2017. 8: p. 534 [PMID:28443122] 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]