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

GSBRNA2T00146106001

Common Name

GSBRNA2T00146106001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

MIKC_MADS

Protein Properties

Length: 246aa MW: 29040.9 Da PI: 7.0813

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00146106001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	77.4	1e-24	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+ienk+ rqvtfskRrng++KK ELS+LCda + +i+fs tgkl y+s GSBRNA2T00146106001 9 KKIENKTSRQVTFSKRRNGLIKKTRELSILCDAHIGLIVFSATGKLTQYCS 59 68***********************************************96 PP
2	K-box	55.9	1.8e-19	87	167	15	95
K-box 15 eslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLr 95 l++e++ L++e+ +L+ +R + G dL s+ eL Le+qLe+s+ k+R++K+ell +q+ +l +k ++l+++n+++ GSBRNA2T00146106001 87 DDLRHEIEILRRETCKLELRLRPYHGHDLASIPPHELDGLEHQLEHSVHKVRERKKELLQQQLGNLSRKRRMLEDDNNNMY 167 56899************************************************************************9976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.0E-38	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	30.165	1	61	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.49E-30	2	85	IPR002100	Transcription factor, MADS-box
CDD	cd00265	7.34E-42	2	79	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.9E-27	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.2E-24	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.9E-27	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.9E-27	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	6.2E-19	85	170	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	13.136	86	176	IPR002487	Transcription factor, K-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 246 aa Download sequence Send to blast
MGRGKIEIKK IENKTSRQVT FSKRRNGLIK KTRELSILCD AHIGLIVFSA TGKLTQYCSE 60 HSNMPQLIDR YLTKEGLQLP DLNDDRDDLR HEIEILRRET CKLELRLRPY HGHDLASIPP 120 HELDGLEHQL EHSVHKVRER KKELLQQQLG NLSRKRRMLE DDNNNMYRWL HDEHRTGIEF 180 QQAEIETKPM EYQQFLEHVQ YYNDHHQQQS SVLQLPTLPS EIDLSYHLQL AQPNFQNDPT 240 ITKVD*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	9e-17	1	71	1	69	MEF2C
5f28_B	9e-17	1	71	1	69	MEF2C
5f28_C	9e-17	1	71	1	69	MEF2C
5f28_D	9e-17	1	71	1	69	MEF2C
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	139	156	RKKELLQQQLGNLSRKRR
2	152	157	SRKRRM

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bna.13305	0.0	seed

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed during seed development.
Uniprot	TISSUE SPECIFICITY: Expressed in buds, flowers and immature seeds, but not in roots, stems, leaves, seedlings or siliques valves. Expression in seed coat is confined to the endothelium layer.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation (PubMed:12368498, PubMed:16080001). Necessary for the normal activation of the BANYULS promoter in the endothelium body (PubMed:12368498). Is required, together with AGL11/STK for the maternal control of endothelium formation, which is essential for female gametophyte development and fertilization, and seed formation (PubMed:22176531). Interacts genetically with AGL1/SHP1 and AGL5/SHP2 in a partially antagonistic manner and represses AGL1/SHP1, AGL5/SHP2, and AGL8/FUL during flower development. Is essential for the coordination of cell divisions in ovule, seed coat development and endosperm formation (PubMed:27776173). Mediates the crosstalk between endothelium and nucellus to ensure proper seed formation. Functions redundantly with AGL63/GOA to repress nucellus growth and promote its degeneration. Represses the negative regulator of autophagy and programmed cell death HVA22D in the proximal nucellus (PubMed:27233529). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269\|PubMed:12368498, ECO:0000269\|PubMed:16080001, ECO:0000269\|PubMed:22176531, ECO:0000269\|PubMed:27233529, ECO:0000269\|PubMed:27776173}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00146106001

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	HM449989	0.0	HM449989.1 Brassica napus cultivar DH12075 MADS-box DNA-binding domain transcription factor (TT16.4) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022564734.1	0.0	protein TRANSPARENT TESTA 16-like isoform X1
Refseq	XP_022564738.1	0.0	protein TRANSPARENT TESTA 16-like isoform X5
Swissprot	Q8RYD9	1e-129	TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBL	A0A0D3E1M4	1e-177	A0A0D3E1M4_BRAOL; Uncharacterized protein
STRING	Bo9g014270.1	1e-178	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6506	25	43

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G23260.2	1e-124	MIKC_MADS family protein

Publications ? help Back to Top
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] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Rhodes DH, et al. Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm. J. Agric. Food Chem., 2014. 62(45): p. 10916-27 [PMID:25272193] Xu W, et al. Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds. Plant Cell, 2016. 28(6): p. 1343-60 [PMID:27233529] Ehlers K, et al. The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana. PLoS ONE, 2016. 11(10): p. e0165075 [PMID:27776173] Coen O, et al. Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds. Development, 2017. 144(8): p. 1490-1497 [PMID:28348169] Xu W, et al. TRANSPARENT TESTA 16 and 15 act through different mechanisms to control proanthocyanidin accumulation in Arabidopsis testa. J. Exp. Bot., 2017. 68(11): p. 2859-2870 [PMID:28830101] Fiume E,Coen O,Xu W,Lepiniec L,Magnani E Developmental patterning of sub-epidermal cells in the outer integument of Arabidopsis seeds. PLoS ONE, 2017. 12(11): p. e0188148 [PMID:29141031]