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

Solyc05g012020.2.1

Common Name

MADS-RIN

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: 243aa MW: 27968.4 Da PI: 8.0049

Description

MIKC_MADS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc05g012020.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SRF-TF	98	3.9e-31	9	59	1	51
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krienk+nrqvtf+kRrng+lKKA+ELS+LCdae+a+iifss+gklye++s Solyc05g012020.2.1 9 KRIENKINRQVTFAKRRNGLLKKAYELSILCDAEIALIIFSSRGKLYEFCS 59 79***********************************************96 PP
2	K-box	95.7	7.2e-32	79	173	5	100
K-box 5 sgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLr 95 +g+ ++++++++ +qe+ kLk ++e+Lq++qRhllGedL++L k+L+qLe+qL++sl++iRs+K++++l+q+ elq+ke++l e nk+Lr Solyc05g012020.2.1 79 EGT-QTSSDSQNNYQEYLKLKTRVEMLQQSQRHLLGEDLGQLGTKDLEQLERQLDSSLRQIRSTKTQHILDQLAELQQKEQSLTEMNKSLR 168 455.578889********************************************************************************* PP K-box 96 kklee 100 klee Solyc05g012020.2.1 169 IKLEE 173 *9986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50066	33.417	1	61	IPR002100	Transcription factor, MADS-box
SMART	SM00432	9.2E-42	1	60	IPR002100	Transcription factor, MADS-box
CDD	cd00265	2.22E-45	2	78	No hit	No description
SuperFamily	SSF55455	6.93E-34	2	84	IPR002100	Transcription factor, MADS-box
PROSITE pattern	PS00350	0	3	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.2E-33	3	23	IPR002100	Transcription factor, MADS-box
Pfam	PF00319	4.4E-26	10	57	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.2E-33	23	38	IPR002100	Transcription factor, MADS-box
PRINTS	PR00404	6.2E-33	38	59	IPR002100	Transcription factor, MADS-box
Pfam	PF01486	4.3E-27	82	171	IPR002487	Transcription factor, K-box
PROSITE profile	PS51297	15.134	87	177	IPR002487	Transcription factor, K-box
Gene3D	G3DSA:3.10.150.10	5.9E-5	151	217	No hit	No description

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

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000146	anatomy	abscission zone
PO:0009031	anatomy	sepal
PO:0009049	anatomy	inflorescence
PO:0009052	anatomy	flower pedicel

Sequence ? help Back to Top
Protein Sequence Length: 243 aa Download sequence Send to blast
MGRGKVELKR IENKINRQVT FAKRRNGLLK KAYELSILCD AEIALIIFSS RGKLYEFCSN 60 SSMSKTLERY HRYNYGTLEG TQTSSDSQNN YQEYLKLKTR VEMLQQSQRH LLGEDLGQLG 120 TKDLEQLERQ LDSSLRQIRS TKTQHILDQL AELQQKEQSL TEMNKSLRIK LEELGVTFQT 180 SWHCGEQSVQ YRHEQPSHHE GFFQHVNCNN TLPISYGYDN VQPENAAPST HDATGVVPGW 240 ML*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ox0_A	7e-28	92	171	22	101	Developmental protein SEPALLATA 3
4ox0_B	7e-28	92	171	22	101	Developmental protein SEPALLATA 3
4ox0_C	7e-28	92	171	22	101	Developmental protein SEPALLATA 3
4ox0_D	7e-28	92	171	22	101	Developmental protein SEPALLATA 3
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable MADS-box transcription factor that functions with J2 and EJ2 in meristem maturation. {ECO:0000269\|PubMed:28528644}.

Function -- GeneRIF ? help Back to Top
Optimal expression and purification system for obtaining active RIN with DNA binding activity. [PMID: 18175904] The susceptibility of ripe fruit to the necrotrophic pathogen Botrytis cinerea is dependent on NOR but not on RIN. [RIN] [PMID: 19465579] These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression. [PMID: 21276270] RIN recruitment to target loci is dependent on a normally functioning allele at the ripening-specific transcription factor COLORLESS NONRIPENING gene locus. [PMID: 21941001] Findings suggest that the regulatory effect of RIN on fruit ripening is achieved by targeting specific molecular pathways. [PMID: 22098335] RIN directly regulates the expression of the ripening-associated transcription factors. [PMID: 22160566] RIN participates in the regulation of ripening processes such as climacteric ethylene production and lycopene accumulation. [RIN] [PMID: 23518588] RIN, both directly and indirectly, through SlASR1, regulates the transcription of beta-Hex during fruit ripening. The fruit ripening-specific promoter of beta-Hex could be a useful tool in regulating gene expression during fruit ripening. [PMID: 25129131] RIN-protein-defective mutants produced incomplete-ripening fruits in which pigmentation was significantly lower than that of wild type, while heterologous mutants reached full-ripening red color, confirming the important role of RIN in ripening. [PMID: 26408904] Data suggest that, during tomato fruit ripening and softening, RIN transcription factor (a MADS domain protein) regulates expression of enzymes with roles in cell wall degradation (LeaGal2, alpha-galactosidase-like isoform 2) and ethylene biosynthesis (LeACO4, 1-aminocyclopropane-1-carboxylate oxidase). [PMID: 27247090] RIN is not required for the initiation of ripening and rin is not a null mutation, but rather is a gain-of-function mutation that produces a protein that actively represses ripening [PMID: 29085071]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Solyc05g012020.2.1

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	AF448522	0.0	Lycopersicon esculentum MADS-box transcription factor MADS-RIN (MADS-RIN) mRNA, complete cds

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001234670.1	0.0	MADS-box transcription factor RIN isoform 1
Swissprot	K4BND8	1e-121	MADS4_SOLLC; MADS-box protein 04g005320
TrEMBL	Q8S4L4	1e-180	Q8S4L4_SOLLC; MADS-box transcription factor
STRING	Solyc05g012020.2.1	0.0	(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
AT3G02310.1	3e-92	MIKC_MADS family protein

Link Out ? help Back to Top
Phytozome	Solyc05g012020.2.1
Entrez Gene	543708

Publications ? help Back to Top
Vrebalov J, et al. A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science, 2002. 296(5566): p. 343-6 [PMID:11951045] 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] Zhu HL, et al. Expression and DNA binding activity of the tomato transcription factor RIN (ripening inhibitor). Biosci. Biotechnol. Biochem., 2008. 72(1): p. 250-2 [PMID:18175904] Cantu D, et al. Ripening-regulated susceptibility of tomato fruit to Botrytis cinerea requires NOR but not RIN or ethylene. Plant Physiol., 2009. 150(3): p. 1434-49 [PMID:19465579] Fujisawa M,Nakano T,Ito Y Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biol., 2011. 11: p. 26 [PMID:21276270] Martel C,Vrebalov J,Tafelmeyer P,Giovannoni JJ The tomato MADS-box transcription factor RIPENING INHIBITOR interacts with promoters involved in numerous ripening processes in a COLORLESS NONRIPENING-dependent manner. Plant Physiol., 2011. 157(3): p. 1568-79 [PMID:21941001] Qin G,Wang Y,Cao B,Wang W,Tian S Unraveling the regulatory network of the MADS box transcription factor RIN in fruit ripening. Plant J., 2012. 70(2): p. 243-55 [PMID:22098335] Fujisawa M, et al. Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses. Planta, 2012. 235(6): p. 1107-22 [PMID:22160566] Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Fujisawa M,Ito Y The regulatory mechanism of fruit ripening revealed by analyses of direct targets of the tomato MADS-box transcription factor RIPENING INHIBITOR. Plant Signal Behav, 2013. 8(6): p. e24357 [PMID:23518588] Irfan M, et al. Insights into transcriptional regulation of β-D-N-acetylhexosaminidase, an N-glycan-processing enzyme involved in ripening-associated fruit softening. J. Exp. Bot., 2014. 65(20): p. 5835-48 [PMID:25129131] Ito Y,Nishizawa-Yokoi A,Endo M,Mikami M,Toki S CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem. Biophys. Res. Commun., 2015. 467(1): p. 76-82 [PMID:26408904] Li L,Wang X,Zhang X,Guo M,Liu T Unraveling the target genes of RIN transcription factor during tomato fruit ripening and softening. J. Sci. Food Agric., 2017. 97(3): p. 991-1000 [PMID:27247090] Soyk S, et al. Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell, 2017. 169(6): p. 1142-1155.e12 [PMID:28528644] Ito Y, et al. Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. Nat Plants, 2017. 3(11): p. 866-874 [PMID:29085071]