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

Solyc12g087820.1.1

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

M-type_MADS

Protein Properties

Length: 107aa MW: 11969.2 Da PI: 11.0288

Description

M-type_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc12g087820.1.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	84.8	5.1e-27	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 kri++k rqv f+kRr+g+lKKA+E+SvLCd++vav+i+s++g+l+e+ss Solyc12g087820.1.1 9 KRIQDKNCRQVAFCKRRKGLLKKAKEISVLCDVDVAVVIISNRGRLHEFSS 59 79***********************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	28.707	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	2.2E-32	1	60	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	1.57E-26	2	76	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.6E-24	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	2.3E-22	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.6E-24	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	2.6E-24	38	59	IPR002100	Transcription factor, MADS-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:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 107 aa Download sequence Send to blast
MGRRKVEIKR IQDKNCRQVA FCKRRKGLLK KAKEISVLCD VDVAVVIISN RGRLHEFSSN 60 NRTSTPCWLD KISPMHQVEL ITLGSSTLGG TMCALLQVTR RALPTF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1tqe_P	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
1tqe_Q	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
1tqe_R	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
1tqe_S	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_A	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_B	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_C	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_D	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_E	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
6c9l_F	6e-16	1	77	1	77	Myocyte-specific enhancer factor 2B
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.21239	1e-101	fruit\| leaf

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. {ECO:0000269\|PubMed:29853599}.
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc12g087820.1.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015060177.1	4e-38	protein MADS AFFECTING FLOWERING 5-like
Swissprot	A0A217EJJ0	3e-23	AG11S_VITVI; Agamous-like MADS-box protein AGL11
Swissprot	F6I457	3e-23	AG11C_VITVI; Agamous-like MADS-box protein AGL11
TrEMBL	A0A0V0HMB7	3e-36	A0A0V0HMB7_SOLCH; Putative agamous-like MADS-box protein AGL27-like
TrEMBL	A0A0V0HME9	4e-36	A0A0V0HME9_SOLCH; Uncharacterized protein
TrEMBL	M1BI81	3e-36	M1BI81_SOLTU; Uncharacterized protein
TrEMBL	M1BI83	3e-36	M1BI83_SOLTU; Uncharacterized protein
STRING	Solyc12g087820.1.1	1e-72	(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
AT4G09960.2	2e-25	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Solyc12g087820.1.1

Publications ? help Back to Top
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] 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]