PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc05g012020.2.1
Common NameMADS-RIN
Organism
Solanum lycopersicum
Taxonomic ID
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
Solyc05g012020.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF983.9e-31959151
                        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
2K-box95.77.2e-32791735100
               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
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.417161IPR002100Transcription factor, MADS-box
SMARTSM004329.2E-42160IPR002100Transcription factor, MADS-box
CDDcd002652.22E-45278No hitNo description
SuperFamilySSF554556.93E-34284IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-33323IPR002100Transcription factor, MADS-box
PfamPF003194.4E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-332338IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-333859IPR002100Transcription factor, MADS-box
PfamPF014864.3E-2782171IPR002487Transcription factor, K-box
PROSITE profilePS5129715.13487177IPR002487Transcription factor, K-box
Gene3DG3DSA:3.10.150.105.9E-5151217No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000146anatomyabscission zone
PO:0009031anatomysepal
PO:0009049anatomyinflorescence
PO:0009052anatomyflower 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
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A7e-289217122101Developmental protein SEPALLATA 3
4ox0_B7e-289217122101Developmental protein SEPALLATA 3
4ox0_C7e-289217122101Developmental protein SEPALLATA 3
4ox0_D7e-289217122101Developmental protein SEPALLATA 3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable MADS-box transcription factor that functions with J2 and EJ2 in meristem maturation. {ECO:0000269|PubMed:28528644}.
Function -- GeneRIF ? help Back to Top
  1. Optimal expression and purification system for obtaining active RIN with DNA binding activity.
    [PMID: 18175904]
  2. The susceptibility of ripe fruit to the necrotrophic pathogen Botrytis cinerea is dependent on NOR but not on RIN. [RIN]
    [PMID: 19465579]
  3. These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression.
    [PMID: 21276270]
  4. RIN recruitment to target loci is dependent on a normally functioning allele at the ripening-specific transcription factor COLORLESS NONRIPENING gene locus.
    [PMID: 21941001]
  5. Findings suggest that the regulatory effect of RIN on fruit ripening is achieved by targeting specific molecular pathways.
    [PMID: 22098335]
  6. RIN directly regulates the expression of the ripening-associated transcription factors.
    [PMID: 22160566]
  7. RIN participates in the regulation of ripening processes such as climacteric ethylene production and lycopene accumulation. [RIN]
    [PMID: 23518588]
  8. 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]
  9. 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]
  10. 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]
  11. 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
SourceLink
PlantRegMapSolyc05g012020.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4485220.0Lycopersicon esculentum MADS-box transcription factor MADS-RIN (MADS-RIN) mRNA, complete cds
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001234670.10.0MADS-box transcription factor RIN isoform 1
SwissprotK4BND81e-121MADS4_SOLLC; MADS-box protein 04g005320
TrEMBLQ8S4L41e-180Q8S4L4_SOLLC; MADS-box transcription factor
STRINGSolyc05g012020.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA4024625
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G02310.13e-92MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]