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 Solyc12g088080.1.1
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: 98aa    MW: 11295.2 Da    PI: 10.5885
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc12g088080.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF871.1e-271058250
                        ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
              SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                        ri+n++ rqvtfskRrng+lKKA+EL +LCdaev viifsst kly+y+
  Solyc12g088080.1.1 10 RIDNSTSRQVTFSKRRNGLLKKAKELAILCDAEVGVIIFSSTSKLYDYA 58
                        8***********************************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.81161IPR002100Transcription factor, MADS-box
SMARTSM004322.5E-37160IPR002100Transcription factor, MADS-box
CDDcd002655.71E-36262No hitNo description
SuperFamilySSF554557.19E-28271IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-28323IPR002100Transcription factor, MADS-box
PfamPF003192.3E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-282338IPR002100Transcription factor, MADS-box
PRINTSPR004044.7E-283859IPR002100Transcription 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: 98 aa     Download sequence    Send to blast
MGRGKILIRR IDNSTSRQVT FSKRRNGLLK KAKELAILCD AEVGVIIFSS TSKLYDYANT  60
RFSPPISHTF FACQMLELQF IFNFLEKNFL RVFSFVY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-18160160MEF2C
5f28_B2e-18160160MEF2C
5f28_C2e-18160160MEF2C
5f28_D2e-18160160MEF2C
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Specifically expressed in roots, mostly in lateral roots (LR) primordia, young emerging LRs, apex and base of LRs, apex of the primary root, and in the stele. Barely detectable in shoots. {ECO:0000269|PubMed:12837945, ECO:0000269|PubMed:16021502, ECO:0000269|PubMed:17148611, ECO:0000269|PubMed:9430595}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. Required for root plasticity in response to nitrate, NO(3)(-). Promotes lateral root growth in a NRT1.1-dependent manner. {ECO:0000269|PubMed:15667327, ECO:0000269|PubMed:17148611, ECO:0000269|PubMed:9430595}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc12g088080.1.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by nitrate in root cell culture, (PubMed:9430595, PubMed:17148611). In roots, seems induced by nitrogen (N) deprivation (e.g. nitrate free medium) but rapidly repressed by N re-supply (e.g. nitrate, glutamine and ammonium) (PubMed:16021502). Slight repression in shoots during nitrogen (N) deprivation. {ECO:0000269|PubMed:16021502, ECO:0000269|PubMed:17148611, ECO:0000269|PubMed:9430595}.
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_004252725.14e-35MADS-box transcription factor 23-like isoform X1
RefseqXP_010314595.13e-35MADS-box transcription factor 23-like isoform X2
RefseqXP_015060173.14e-35MADS-box transcription factor 23-like
SwissprotQ9SI387e-32ANR1_ARATH; MADS-box transcription factor ANR1
TrEMBLA0A2P6PQN21e-34A0A2P6PQN2_ROSCH; Putative transcription factor MADS-type1 family
STRINGSolyc12g088080.1.12e-65(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
AT2G14210.13e-34AGAMOUS-like 44
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. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  3. Yan Y,Wang H,Hamera S,Chen X,Fang R
    miR444a has multiple functions in the rice nitrate-signaling pathway.
    Plant J., 2014. 78(1): p. 44-55
    [PMID:24460537]
  4. Lei L, et al.
    Nitrogen use efficiency is regulated by interacting proteins relevant to development in wheat.
    Plant Biotechnol. J., 2018. 16(6): p. 1214-1226
    [PMID:29193541]
  5. Sun CH, et al.
    Chrysanthemum MADS-box transcription factor CmANR1 modulates lateral root development via homo-/heterodimerization to influence auxin accumulation in Arabidopsis.
    Plant Sci., 2018. 266: p. 27-36
    [PMID:29241564]