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 Solyc01g060310.1.1
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 M-type_MADS
Protein Properties Length: 140aa    MW: 15117.5 Da    PI: 8.9865
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g060310.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF74.49.4e-241459247
                        ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEE CS
              SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgkly 47
                        +i+n++n qvtfskRr+g++KKA+ELS+LC+a+va++ fs+++k+y
  Solyc01g060310.1.1 14 KIQNQTNLQVTFSKRRAGLFKKASELSTLCGANVAIVSFSPSNKVY 59
                        79******************************************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006624.376565IPR002100Transcription factor, MADS-box
SMARTSM004321.3E-31564IPR002100Transcription factor, MADS-box
CDDcd002658.30E-34673No hitNo description
SuperFamilySSF554555.23E-27678IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-19727IPR002100Transcription factor, MADS-box
PfamPF003192.4E-241459IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-192742IPR002100Transcription factor, MADS-box
PRINTSPR004041.3E-194263IPR002100Transcription factor, MADS-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:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 140 aa     Download sequence    Send to blast
MRKPNGRKKI EIAKIQNQTN LQVTFSKRRA GLFKKASELS TLCGANVAIV SFSPSNKVYA  60
CGHPSVESIV DKFIGENTPP ETDDLNPIIV MGLSFLETDY HLGPTTELAQ VCVPAARQMS  120
GARSIIVVSQ CVLERLIAT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1egw_A1e-17682177MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B1e-17682177MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C1e-17682177MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D1e-17682177MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
3kov_A2e-17682177Myocyte-specific enhancer factor 2A
3kov_B2e-17682177Myocyte-specific enhancer factor 2A
3kov_I2e-17682177Myocyte-specific enhancer factor 2A
3kov_J2e-17682177Myocyte-specific enhancer factor 2A
3p57_A2e-17682177Myocyte-specific enhancer factor 2A
3p57_B2e-17682177Myocyte-specific enhancer factor 2A
3p57_C2e-17682177Myocyte-specific enhancer factor 2A
3p57_D2e-17682177Myocyte-specific enhancer factor 2A
3p57_I2e-17682177Myocyte-specific enhancer factor 2A
3p57_J2e-17682177Myocyte-specific enhancer factor 2A
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during the syncytial endosperm development. {ECO:0000269|PubMed:18334668}.
UniprotTISSUE SPECIFICITY: Expressed in the endosperm but not in the embryo. Detected in young siliques, roots, leaves, stems, young flowers and anthers. {ECO:0000269|PubMed:18334668}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. Required for suppression of cellularization and promotion of nuclear proliferation during early endosperm development. The FERTILIZATION-INDEPENDENT SEED (FIS) polycomb complex is required for suppression of ALG62 expression at the end of the syncytial phase of endosperm development. {ECO:0000269|PubMed:18334668}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc01g060310.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2401931e-150Solanum lycopersicum strain Heinz 1706 chromosome 1 clone hba-152e17 map 1, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004229069.14e-60agamous-like MADS-box protein AGL62
SwissprotQ9FKK22e-30AGL62_ARATH; Agamous-like MADS-box protein AGL62
TrEMBLA0A3Q7EFF62e-59A0A3Q7EFF6_SOLLC; Uncharacterized protein
STRINGSolyc01g060310.1.13e-99(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA1846024
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60440.17e-33AGAMOUS-like 62
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. Xu W, et al.
    Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds.
    Plant Cell, 2016. 28(6): p. 1343-60
    [PMID:27233529]
  3. Figueiredo DD,Batista RA,Roszak PJ,Köhler C
    Auxin production couples endosperm development to fertilization.
    Nat Plants, 2015. 1: p. 15184
    [PMID:27251719]
  4. Figueiredo DD,Batista RA,Roszak PJ,Hennig L,Köhler C
    Auxin production in the endosperm drives seed coat development in Arabidopsis.
    Elife, 2017.
    [PMID:27848912]
  5. Fiume E,Coen O,Xu W,Lepiniec L,Magnani E
    Growth of the Arabidopsis sub-epidermal integument cell layers might require an endosperm signal.
    Plant Signal Behav, 2017. 12(8): p. e1339000
    [PMID:28613109]
  6. Zhang S, et al.
    FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development.
    Plant Physiol., 2018. 177(1): p. 285-299
    [PMID:29523711]