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 Solyc04g005320.2.1
Common NameLOC101253992
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: 239aa    MW: 27522.1 Da    PI: 8.5995
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc04g005320.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF96.51.1e-30959151
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                        krienk+nrqvtf+kRrng+lKKA+ELS+LC+aeva+iifs++gklye++s
  Solyc04g005320.2.1  9 KRIENKINRQVTFAKRRNGLLKKAYELSILCEAEVALIIFSNRGKLYEFCS 59
                        79***********************************************96 PP
2K-box92.76.2e-31821739100
               K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                         ++++++++ +qe+ kLk+++e Lq++qRh+lGedL++L+ k+L+qLe+qL++sl+ iRs++++ +l+q+++lq+ke++l e+n++L++kle
  Solyc04g005320.2.1  82 QSSKDSQNNYQEYMKLKARVEVLQQSQRHILGEDLGQLNTKDLEQLERQLDSSLRLIRSRRTQNMLDQLSDLQQKEQSLLEINRSLKTKLE 172
                         678889***********************************************************************************98 PP

               K-box 100 e 100
                         e
  Solyc04g005320.2.1 173 E 173
                         7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.081161IPR002100Transcription factor, MADS-box
SMARTSM004327.9E-41160IPR002100Transcription factor, MADS-box
CDDcd002656.61E-44278No hitNo description
SuperFamilySSF554551.23E-33284IPR002100Transcription factor, MADS-box
PRINTSPR004043.1E-32323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.7E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004043.1E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004043.1E-323859IPR002100Transcription factor, MADS-box
PfamPF014868.4E-2683171IPR002487Transcription factor, K-box
PROSITE profilePS5129715.38687177IPR002487Transcription factor, K-box
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
Sequence ? help Back to Top
Protein Sequence    Length: 239 aa     Download sequence    Send to blast
MGRGKVELKR IENKINRQVT FAKRRNGLLK KAYELSILCE AEVALIIFSN RGKLYEFCST  60
SSMSDTLERY HRCSYGDLET GQSSKDSQNN YQEYMKLKAR VEVLQQSQRH ILGEDLGQLN  120
TKDLEQLERQ LDSSLRLIRS RRTQNMLDQL SDLQQKEQSL LEINRSLKTK LEENSVAHWH  180
ITGEQNVQFR QQPAQSEGFF QPLQCNTNIV PNRYNVAPLD SIEPSTQNAT GILPGWML*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A2e-259217122101Developmental protein SEPALLATA 3
4ox0_B2e-259217122101Developmental protein SEPALLATA 3
4ox0_C2e-259217122101Developmental protein SEPALLATA 3
4ox0_D2e-259217122101Developmental 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. SlCMB1 is a new component to the current model of regulatory network that regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening. [SlCMB1]
    [PMID: 29467500]
  2. SlCMB1 is an important regulator involved in the development of inflorescence architecture and sepal size. [SICMB1]
    [PMID: 29807608]
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc04g005320.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004237061.11e-177MADS-box protein 04g005320 isoform X1
SwissprotK4BND81e-178MADS4_SOLLC; MADS-box protein 04g005320
TrEMBLA0A314KXN21e-144A0A314KXN2_NICAT; Developmental protein sepallata 1
STRINGSolyc04g005320.2.11e-176(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
AT3G02310.18e-88MIKC_MADS family protein
Publications ? help Back to Top
  1. 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]
  2. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  3. 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]
  4. Zhang J, et al.
    A tomato MADS-box protein, SlCMB1, regulates ethylene biosynthesis and carotenoid accumulation during fruit ripening.
    Sci Rep, 2018. 8(1): p. 3413
    [PMID:29467500]
  5. Zhang J, et al.
    Suppression of a tomato SEPALLATA MADS-box gene, SlCMB1, generates altered inflorescence architecture and enlarged sepals.
    Plant Sci., 2018. 272: p. 75-87
    [PMID:29807608]