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

Sopim12g087820.0.1

Organism

Solanum pimpinellifolium

Taxonomic ID

4084

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
Sopim12g087820.0.1	genome	CSHL	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 Sopim12g087820.0.1 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: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
Search in ModeBase

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}.

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HG975524	3e-99	HG975524.1 Solanum lycopersicum chromosome ch12, complete genome.

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

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G09960.2	2e-25	MIKC_MADS family protein

Publications ? help Back to Top
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]