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

Thecc1EG007713t1

Common Name

TCM_007713

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

MIKC_MADS

Protein Properties

Length: 234aa MW: 27574.3 Da PI: 8.0796

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG007713t1	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	84.5	6.2e-27	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++ rqvtfskRr+g+lKK +ELSvLCda++ +i+fsstgk+ y+s Thecc1EG007713t1 9 KRIENQTTRQVTFSKRRAGLLKKTHELSVLCDAQIGLIVFSSTGKMCQYCS 59 79***********************************************96 PP
2	K-box	77.7	3e-26	71	170	1	99
K-box 1 yqkssgks.leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenk 92 yqk +g++ e+ + e+l++ela L+ke++ Lq + R++ Ged++s+ ++eL qLeq+Le+s++k+R++Knell +q+++l++ke+ l+een Thecc1EG007713t1 71 YQKVTGTRiPEHDNREHLYNELAVLRKETRRLQLSMRRYTGEDMSSIPFEELDQLEQELERSVNKVRERKNELLQQQLDNLRRKERILEEENS 163 678888888888999*****************************************************************************9 PP K-box 93 aLrkkle 99 ++ + ++ Thecc1EG007713t1 164 NMYRWIQ 170 9987766 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	30.011	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.4E-39	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.96E-31	2	80	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.19E-40	2	76	No hit	No description
PRINTS	PR00404	2.2E-27	3	23	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	1.1E-23	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.2E-27	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.2E-27	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.9E-24	81	169	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.926	85	175	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:0008360	Biological Process	regulation of cell shape
GO:0019252	Biological Process	starch biosynthetic process
GO:0043068	Biological Process	positive regulation of programmed cell death
GO:0048316	Biological Process	seed development
GO:0048481	Biological Process	plant ovule development
GO:0080155	Biological Process	regulation of double fertilization forming a zygote and endosperm
GO:2000029	Biological Process	regulation of proanthocyanidin biosynthetic process
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: 234 aa Download sequence Send to blast
MGRGKIPIKR IENQTTRQVT FSKRRAGLLK KTHELSVLCD AQIGLIVFSS TGKMCQYCSE 60 PFRMEQIIER YQKVTGTRIP EHDNREHLYN ELAVLRKETR RLQLSMRRYT GEDMSSIPFE 120 ELDQLEQELE RSVNKVRERK NELLQQQLDN LRRKERILEE ENSNMYRWIQ EHRAAIEYQQ 180 GGIEAKPVEH QQVLDQFPFY GEPSSVLQLA TIPQQFHSYQ LQLAQPNLQD SNV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	5e-19	1	71	1	69	MEF2C
5f28_B	5e-19	1	71	1	69	MEF2C
5f28_C	5e-19	1	71	1	69	MEF2C
5f28_D	5e-19	1	71	1	69	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	HM236443	0.0	HM236443.1 Gossypium hirsutum MADS27 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007043265.2	1e-172	PREDICTED: protein TRANSPARENT TESTA 16
Refseq	XP_017971303.1	1e-172	PREDICTED: protein TRANSPARENT TESTA 16
Swissprot	Q8RYD9	2e-97	TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBL	A0A061E415	1e-171	A0A061E415_THECC; K-box region and MADS-box transcription factor family protein isoform 1
STRING	EOX99096	1e-172	(Theobroma cacao)

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	2e-93	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Thecc1EG007713t1
Entrez Gene	18608483

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] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] 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]