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

RrC30821_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

M-type_MADS

Protein Properties

Length: 81aa MW: 8880.38 Da PI: 10.9019

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC30821_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	85.5	3.1e-27	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+ienk+ rqvtfskRr g++KKA+ELSvLCda + +i+fs+tgkl y+s RrC30821_p1 9 KKIENKTSRQVTFSKRRSGLIKKASELSVLCDAHIGLIVFSTTGKLTQYCS 59 78***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	2.1E-39	1	60	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	30.628	1	61	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.36E-35	2	63	No hit	No description
SuperFamily	SSF55455	3.27E-29	2	61	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.2E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.7E-29	38	59	IPR002100	Transcription factor, MADS-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 81 aa Download sequence Send to blast
MGRGKIEIKK IENKTSRQVT FSKRRSGLIK KASELSVLCD AHIGLIVFST TGKLTQYCSE 60 PSKLAPSSSS SSSLFLFSLR L

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	1e-19	1	59	1	59	MEF2C
5f28_B	1e-19	1	59	1	59	MEF2C
5f28_C	1e-19	1	59	1	59	MEF2C
5f28_D	1e-19	1	59	1	59	MEF2C
Search in ModeBase

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}.

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	HQ699312	3e-92	HQ699312.1 Brassica napus clone BnaC.TT16b transparent TESTA16 protein gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018465676.1	3e-38	PREDICTED: protein TRANSPARENT TESTA 16-like isoform X1
Refseq	XP_018465678.1	4e-38	PREDICTED: protein TRANSPARENT TESTA 16-like isoform X3
Swissprot	Q8RYD9	3e-31	TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBL	A0A3N6R668	6e-35	A0A3N6R668_BRACR; Uncharacterized protein
STRING	Bra013028.1-P	6e-34	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM78	28	413

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G23260.3	3e-33	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] 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]