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

XP_009102920.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

Protein Properties

Length: 349aa MW: 40055.9 Da PI: 6.138

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009102920.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	62.5	6.9e-20	166	265	2	99
EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS.-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesg.rsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 +k l++sdv+++gr+vlpk+ ae + +++++e++ l ++d ++ +sW++k++y ++ks++yvl+ ++ eFvk ng+ gD ++++ ++++++ XP_009102920.1 166 VKHLKNSDVGSLGRIVLPKREAEGNlpELSEKEGMVLEMRDVDSvQSWSFKYKYwsNNKSRMYVLE-NTGEFVKKNGVLMGDYLTIY--EDESKN 257 6889*********************99999*****7777***99888888889999.****************..669999 PP .EEEEE-S CS B3 92 lvvkvfrk 99 l+++++++ XP_009102920.1 258 LYFSIRKH 265 9*9986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	5.0E-24	161	268	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.28E-21	164	264	No hit	No description
SuperFamily	SSF101936	2.35E-19	164	264	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	4.7E-20	165	266	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	9.742	165	266	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.3E-16	166	265	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010262	Biological Process	somatic embryogenesis
GO:0010344	Biological Process	seed oilbody biogenesis
GO:0010431	Biological Process	seed maturation
GO:0010601	Biological Process	positive regulation of auxin biosynthetic process
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 349 aa Download sequence Send to blast
MDNFLPFSSS NANSVQELSM DLNKNRSHFS MAQPQHLLPP YSYVACPALD QTGTMNHQPL 60 HSSDAFPQIP VVQTGGEFGY LVCKPGVRQE RGGFLDPHST KMARINRKKA MLRSRNNSNP 120 NSSSNELVDS RRQVALTMKN NAEIAARKDF YRFSSFDNKK LRVLLVKHLK NSDVGSLGRI 180 VLPKREAEGN LPELSEKEGM VLEMRDVDSV QSWSFKYKYW SNNKSRMYVL ENTGEFVKKN 240 GVLMGDYLTI YEDESKNLYF SIRKHPHKQN DGREDESMEV IEMNFYEDIM FDYIPNDEDD 300 SIAMLLGNLN EHYPYPNDLM DLTVNLDQHQ QATSSSPPAD HMSSNDFLW

Sequence ? help Back to Top

Protein Sequence Length: 349 aa Download sequence Send to blast

MDNFLPFSSS NANSVQELSM DLNKNRSHFS MAQPQHLLPP YSYVACPALD QTGTMNHQPL  60
HSSDAFPQIP VVQTGGEFGY LVCKPGVRQE RGGFLDPHST KMARINRKKA MLRSRNNSNP  120
NSSSNELVDS RRQVALTMKN NAEIAARKDF YRFSSFDNKK LRVLLVKHLK NSDVGSLGRI  180
VLPKREAEGN LPELSEKEGM VLEMRDVDSV QSWSFKYKYW SNNKSRMYVL ENTGEFVKKN  240
GVLMGDYLTI YEDESKNLYF SIRKHPHKQN DGREDESMEV IEMNFYEDIM FDYIPNDEDD  300
SIAMLLGNLN EHYPYPNDLM DLTVNLDQHQ QATSSSPPAD HMSSNDFLW

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	1e-58	154	262	2	110	B3 domain-containing transcription factor LEC2
6j9c_D	1e-58	154	262	2	110	B3 domain-containing transcription factor LEC2
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during embryo development. {ECO:0000269\|PubMed:11573014}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription regulator that plays a central role in embryo development. Required for the maintenance of suspensor morphology, specification of cotyledon identity, progression through the maturation phase and suppression of premature germination. Ectopic expression is sufficient to promote somatic embryogenesis. {ECO:0000269\|PubMed:11573014, ECO:0000269\|PubMed:16492731, ECO:0000269\|PubMed:18287041}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00032	PBM	Transfer from AT1G28300	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009102920.1

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	HM370539	0.0	HM370539.1 Brassica napus leafy cotyledon 2 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009102920.1	0.0	PREDICTED: B3 domain-containing transcription factor LEC2-like
Swissprot	Q1PFR7	1e-156	LEC2_ARATH; B3 domain-containing transcription factor LEC2
TrEMBL	E2GMX5	0.0	E2GMX5_BRANA; BnaA07g08500D protein
STRING	Bo7g048240.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9262	23	36

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G28300.1	1e-150	B3 family protein

Publications ? help Back to Top
Yang C, et al. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr. Biol., 2013. 23(14): p. 1324-9 [PMID:23810531] Guo F, et al. Induced expression of AtLEC1 and AtLEC2 differentially promotes somatic embryogenesis in transgenic tobacco plants. PLoS ONE, 2013. 8(8): p. e71714 [PMID:23951228] Jia H,McCarty DR,Suzuki M Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. Plant Physiol., 2013. 163(3): p. 1293-305 [PMID:24043445] Feeney M,Frigerio L,Kohalmi SE,Cui Y,Menassa R Reprogramming cells to study vacuolar development. Front Plant Sci, 2013. 4: p. 493 [PMID:24348496] Kim HU, et al. Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues. FEBS Open Bio, 2013. 4: p. 25-32 [PMID:24363987] Nookaraju A, et al. Enhanced accumulation of fatty acids and triacylglycerols in transgenic tobacco stems for enhanced bioenergy production. Plant Cell Rep., 2014. 33(7): p. 1041-52 [PMID:24585187] Zhang Y,Clemens A,Maximova SN,Guiltinan MJ The Theobroma cacao B3 domain transcription factor TcLEC2 plays a duel role in control of embryo development and maturation. BMC Plant Biol., 2014. 14: p. 106 [PMID:24758406] Rikiishi K,Maekawa M Seed maturation regulators are related to the control of seed dormancy in wheat (Triticum aestivum L.). PLoS ONE, 2014. 9(9): p. e107618 [PMID:25211528] Yamamoto A, et al. Cell-by-cell developmental transition from embryo to post-germination phase revealed by heterochronic gene expression and ER-body formation in Arabidopsis leafy cotyledon mutants. Plant Cell Physiol., 2014. 55(12): p. 2112-25 [PMID:25282558] Shen Y,Devic M,Lepiniec L,Zhou DX Chromodomain, Helicase and DNA-binding CHD1 protein, CHR5, are involved in establishing active chromatin state of seed maturation genes. Plant Biotechnol. J., 2015. 13(6): p. 811-20 [PMID:25581843] Kim HU, et al. Senescence-inducible LEC2 enhances triacylglycerol accumulation in leaves without negatively affecting plant growth. Plant Biotechnol. J., 2015. 13(9): p. 1346-59 [PMID:25790072] Schneider A, et al. Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J., 2016. 85(2): p. 305-19 [PMID:26678037] Baud S, et al. Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed. Plant Physiol., 2016. 171(2): p. 1099-112 [PMID:27208266] Ikeuchi M, et al. PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. Nat Plants, 2015. 1: p. 15089 [PMID:27250255] Fatihi A, et al. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. Plant Sci., 2016. 250: p. 198-204 [PMID:27457996] Tang LP, et al. FUSCA3 interacting with LEAFY COTYLEDON2 controls lateral root formation through regulating YUCCA4 gene expression in Arabidopsis thaliana. New Phytol., 2017. 213(4): p. 1740-1754 [PMID:27878992] Vanhercke T, et al. Step changes in leaf oil accumulation via iterative metabolic engineering. Metab. Eng., 2017. 39: p. 237-246 [PMID:27993560] Han JD, et al. Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program. Front Plant Sci, 2017. 8: p. 439 [PMID:28421087] Horstman A, et al. The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis. Plant Physiol., 2017. 175(2): p. 848-857 [PMID:28830937] Liu C,Tong S,Zhang W,Hou H [Expression of Leafy Cotyledon 2 from Arabidopsis increased the content of lipid in Chlorella sorokiniana]. Sheng Wu Gong Cheng Xue Bao, 2017. 33(6): p. 1037-1045 [PMID:28895365] Wójcik AM,Nodine MD,Gaj MD miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis. Front Plant Sci, 2017. 8: p. 2024 [PMID:29321785] Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis. Plant Cell, 2018. 30(3): p. 600-619 [PMID:29475938] Boulard C, et al. LEC1 (NF-YB9) directly interacts with LEC2 to control gene expression in seed. Biochim Biophys Acta Gene Regul Mech, 2018. 1861(5): p. 443-450 [PMID:29580949]