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

Solyc01g105800.2.1

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

MIKC_MADS

Protein Properties

Length: 280aa MW: 32104.7 Da PI: 9.1124

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc01g105800.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	82.5	2.7e-26	73	123	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 k+i+n + rqvtfskRr g++KKA+ELS+LCda++ +i+fs tgkl+eyss Solyc01g105800.2.1 73 KKIDNLTARQVTFSKRRRGLFKKAQELSTLCDADIGLIVFSATGKLFEYSS 123 68***********************************************96 PP
2	K-box	42.8	2.3e-15	148	238	9	99
K-box 9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 l++++ s ++ +a L++ + re+R+l Ge+L+ L l eL++Le+ +e +++++ + K + ++++i+ l+kke +lqeen +L+k+ + Solyc01g105800.2.1 148 LHSSNILSEKKTHAMLNRDFVEKNRELRQLHGEELQGLGLDELMKLEKLVEGGISRVLKIKGDKFMKEISSLKKKEAKLQEENSQLKKQSQ 238 6777777888888888888888899**************************************************************9976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00432	7.7E-39	65	124	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS50066	28.777	65	125	IPR002100	Transcription factor, MADS-box
CDD	cd00265	1.87E-36	67	140	No hit	No description
PRINTS	PR00404	8.4E-26	67	87	IPR002100	Transcription factor, MADS-box
SuperFamily	SSF55455	3.14E-29	67	145	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	67	121	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	3.9E-24	74	121	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.4E-26	87	102	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	8.4E-26	102	123	IPR002100	Transcription factor, MADS-box
PROSITE profile	PS51297	11.911	153	243	IPR002487	Transcription factor, K-box
Pfam	PF01486	8.0E-13	157	236	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: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: 280 aa Download sequence Send to blast
MEQITIQLKS SNSNSHEEIQ LLLCNQKYPN YYFFSFYCNN IPFFSFFSSQ LQISSPFLAN 60 FSKEMVRQKI QIKKIDNLTA RQVTFSKRRR GLFKKAQELS TLCDADIGLI VFSATGKLFE 120 YSSSSMMQLI EKHKMQSERD GMDNPEQLHS SNILSEKKTH AMLNRDFVEK NRELRQLHGE 180 ELQGLGLDEL MKLEKLVEGG ISRVLKIKGD KFMKEISSLK KKEAKLQEEN SQLKKQSQAR 240 LNEEGQNVIE QGHSADSITN NRSLVNDSDT SLKLCLAFP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5f28_A	3e-17	65	133	1	69	MEF2C
5f28_B	3e-17	65	133	1	69	MEF2C
5f28_C	3e-17	65	133	1	69	MEF2C
5f28_D	3e-17	65	133	1	69	MEF2C
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Les.23416	0.0	leaf\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During vegetative phase expressed in young leaves and apical meristem until early stage of bolting. Early in development of the inflorescence present in the coflorescence and flower primordia but not in the main apical meristem. Present throughout the floral meristem during early stages of flower development. Later disappears prior to emergence of sepal primordia. {ECO:0000269\|PubMed:19656343}.
Uniprot	TISSUE SPECIFICITY: Detected in roots and leaves. Expressed at very low levels in flowers and siliques. Present in floral meristems. {ECO:0000269\|PubMed:19656343}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription repressor that inhibit floral transition in the autonomous flowering pathway, independent of photoperiod and temperature. Acts in a dosage-dependent manner. Together with AGL24 and AP1, controls the identity of the floral meristem and regulates expression of class B, C and E genes. Promotes EFM expression to suppress flowering (PubMed:25132385). {ECO:0000269\|PubMed:16679456, ECO:0000269\|PubMed:18694458, ECO:0000269\|PubMed:19656343, ECO:0000269\|PubMed:25132385}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc01g105800.2.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by the floral homeotic genes AP1 and SEP3 in emerging floral meristems. Up-regulated by HUA2. {ECO:0000269\|PubMed:15659097, ECO:0000269\|PubMed:17428825, ECO:0000269\|PubMed:18694458}.

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	AC233131	1e-103	Solanum lycopersicum strain Heinz 1706 chromosome 1 clone hba-37d10 map 1, complete sequence

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004230624.1	1e-153	MADS-box protein SVP
Swissprot	Q9FVC1	1e-61	SVP_ARATH; MADS-box protein SVP
TrEMBL	M1D727	1e-146	M1D727_SOLTU; Uncharacterized protein
STRING	Solyc01g105800.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA938	23	77
Representative plant	OGRP16	17	761

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G22540.1	6e-52	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Solyc01g105800.2.1

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] Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae). PLoS ONE, 2013. 8(6): p. e67243 [PMID:23840638] Jaudal M, et al. Overexpression of Medicago SVP genes causes floral defects and delayed flowering in Arabidopsis but only affects floral development in Medicago. J. Exp. Bot., 2014. 65(2): p. 429-42 [PMID:24249713] Müller-Xing R,Clarenz O,Pokorny L,Goodrich J,Schubert D Polycomb-Group Proteins and FLOWERING LOCUS T Maintain Commitment to Flowering in Arabidopsis thaliana. Plant Cell, 2014. 26(6): p. 2457-2471 [PMID:24920331] Hwan Lee J,Sook Chung K,Kim SK,Ahn JH Post-translational regulation of SHORT VEGETATIVE PHASE as a major mechanism for thermoregulation of flowering. Plant Signal Behav, 2014. 9(4): p. e28193 [PMID:25764420] Chen Z, et al. Overexpression of AtAP1M3 regulates flowering time and floral development in Arabidopsis and effects key flowering-related genes in poplar. Transgenic Res., 2015. 24(4): p. 705-15 [PMID:25820621] Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. BMC Plant Biol., 2015. 15: p. 41 [PMID:25848674] Müller-Xing R,Schubert D,Goodrich J Non-inductive conditions expose the cryptic bract of flower phytomeres in Arabidopsis thaliana. Plant Signal Behav, 2015. 10(4): p. e1010868 [PMID:25924005] Marín-González E, et al. SHORT VEGETATIVE PHASE Up-Regulates TEMPRANILLO2 Floral Repressor at Low Ambient Temperatures. Plant Physiol., 2015. 169(2): p. 1214-24 [PMID:26243615] Bechtold U, et al. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. Plant Cell, 2016. 28(2): p. 345-66 [PMID:26842464] Fernández V,Takahashi Y,Le Gourrierec J,Coupland G Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days. Plant J., 2016. 86(5): p. 426-40 [PMID:27117775] Wilson DC,Kempthorne CJ,Carella P,Liscombe DK,Cameron RK Age-Related Resistance in Arabidopsis thaliana Involves the MADS-Domain Transcription Factor SHORT VEGETATIVE PHASE and Direct Action of Salicylic Acid on Pseudomonas syringae. Mol. Plant Microbe Interact., 2017. 30(11): p. 919-929 [PMID:28812948] Zou YP, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. Genome Biol., 2017. 18(1): p. 239 [PMID:29284515] Richter R, et al. Floral regulators FLC and SOC1 directly regulate expression of the B3-type transcription factor TARGET OF FLC AND SVP 1 at the Arabidopsis shoot apex via antagonistic chromatin modifications. PLoS Genet., 2019. 15(4): p. e1008065 [PMID:30946745]