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

Solyc11g028020.1.1

Common Name

LOC543842

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon

Family

MIKC_MADS

Protein Properties

Length: 224aa MW: 26061.7 Da PI: 9.7566

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc11g028020.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	98	3.7e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien++nrqvtf+kRrng+lKKA+ELSvLCdae+a+i+fs++g+lyeys+ Solyc11g028020.1.1 9 KRIENNTNRQVTFCKRRNGLLKKAYELSVLCDAEIALIVFSTRGRLYEYSN 59 79***********************************************95 PP
2	K-box	100	3.5e-33	79	173	6	100
K-box 6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 ++e +a+ +qqe++kL+++i+++q+++Rhl+Ge+L+sL+++eL+qLe++Le+++++iRskK+e +l+++e+l k+e +l++en Lr+ Solyc11g028020.1.1 79 AYTTQELNAQFYQQESKKLRQQIQMMQNTNRHLVGEGLSSLNVRELKQLENRLERGITRIRSKKHEAILAETEDLHKREIQLEQENAFLRS 169 33478999*********************************************************************************** PP K-box 97 klee 100 k++e Solyc11g028020.1.1 170 KIAE 173 *986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.852	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	3.6E-41	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	5.1E-33	2	79	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.36E-43	2	78	No hit	No description
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-32	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.7E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-32	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	1.3E-32	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	2.9E-26	83	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.69	87	177	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:0048283	Biological Process	indeterminate inflorescence morphogenesis
GO:0048481	Biological Process	plant ovule development
GO:0080155	Biological Process	regulation of double fertilization forming a zygote and endosperm
GO:0090376	Biological Process	seed trichome differentiation
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: 224 aa Download sequence Send to blast
MGRGKIEIKR IENNTNRQVT FCKRRNGLLK KAYELSVLCD AEIALIVFST RGRLYEYSNN 60 NVKATIERYK KATAETSSAY TTQELNAQFY QQESKKLRQQ IQMMQNTNRH LVGEGLSSLN 120 VRELKQLENR LERGITRIRS KKHEAILAET EDLHKREIQL EQENAFLRSK IAENERLQEL 180 SMMPSGGEEY NAFQQYLARN MLQLNMMETA LPSYDPLSPD HKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_Q	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_R	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
1tqe_S	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_A	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_B	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_C	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_D	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_E	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
6c9l_F	3e-21	1	69	1	69	Myocyte-specific enhancer factor 2B
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.3820	0.0	flower

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in flowers and seeds (Ref.1). Expressed in endotesta cell layer of developing seeds (PubMed:28369525). {ECO:0000269\|PubMed:28369525, ECO:0000269\|Ref.1}.

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor involved in seed development (PubMed:21447172, Ref.1, PubMed:29853599). Plays a role in seed morphogenesis by promoting the correct development of endotesta cell layer, which directs the further development of the seed coat, the endosperm, and consequently the embryo (Ref.1, PubMed:29853599). {ECO:0000269\|PubMed:21447172, ECO:0000269\|PubMed:29853599, ECO:0000269\|Ref.1}.

Function -- GeneRIF ? help Back to Top
Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, and a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation. [PMID: 28992179]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc11g028020.1.1

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	AY098736	0.0	Lycopersicon esculentum TAGL11 transcription factor mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234194.1	1e-163	agamous-like MADS-box protein AGL11
Swissprot	F6I457	1e-108	AG11C_VITVI; Agamous-like MADS-box protein AGL11
TrEMBL	Q8H280	1e-162	Q8H280_SOLLC; TAGL11 transcription factor
STRING	Solyc11g028020.1.1	1e-163	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA40	24	625
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G09960.1	3e-99	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Solyc11g028020.1.1
Entrez Gene	543842

Publications ? help Back to Top
Busi MV, et al. MADS-box genes expressed during tomato seed and fruit development. Plant Mol. Biol., 2003. 52(4): p. 801-15 [PMID:13677468] Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] Jaillon O, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 2007. 449(7161): p. 463-7 [PMID:17721507] Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater JM,Carmona MJ Genome-wide analysis of MIKCC-type MADS box genes in grapevine. Plant Physiol., 2009. 149(1): p. 354-69 [PMID:18997115] Mejía N, et al. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC Plant Biol., 2011. 11: p. 57 [PMID:21447172] Grimplet J,Martínez-Zapater JM,Carmona MJ Structural and functional annotation of the MADS-box transcription factor family in grapevine. BMC Genomics, 2016. 17: p. 80 [PMID:26818751] Malabarba J, et al. The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine. J. Exp. Bot., 2017. 68(7): p. 1493-1506 [PMID:28369525] Huang B, et al. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits. J. Exp. Bot., 2017. 68(17): p. 4869-4884 [PMID:28992179] Royo C, et al. The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11. Plant Physiol., 2018. 177(3): p. 1234-1253 [PMID:29853599]