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 LOC_Os04g23910.1
Common NameLOC4335427, MADS25, Os04g0304400, OSJNBa0079M09.14
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family MIKC_MADS
Protein Properties Length: 228aa    MW: 26141.7 Da    PI: 8.9467
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g23910.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF82.13.5e-26959151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      kri+n++nrqvtfskRr g++KKA EL +LCda+v +i+fs tg+ly++ss
  LOC_Os04g23910.1  9 KRIDNTMNRQVTFSKRRGGLMKKARELAILCDADVGLIVFSCTGRLYDFSS 59
                      79***********************************************96 PP
2K-box72.81e-24841701298
             K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       ++a+ +q+e++ L+++++nL +++R+llGe++++ ++++Lq L++q+e sl +iR+kK++ll e+i +l +k   +q+en +Lrkk+
  LOC_Os04g23910.1  84 SEAKFWQREVTTLRQQVQNLHHNNRQLLGEEISNFTVRDLQLLQNQVEMSLHSIRNKKDQLLAEEILKLNEKGSLVQKENSELRKKF 170
                       6789*********************************************************************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004324.9E-37160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006630.852161IPR002100Transcription factor, MADS-box
CDDcd002653.29E-41276No hitNo description
SuperFamilySSF554557.33E-32287IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004043.2E-27323IPR002100Transcription factor, MADS-box
PfamPF003192.5E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004043.2E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004043.2E-273859IPR002100Transcription factor, MADS-box
PfamPF014861.5E-2484170IPR002487Transcription factor, K-box
PROSITE profilePS5129714.37186176IPR002487Transcription 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009005anatomyroot
Sequence ? help Back to Top
Protein Sequence    Length: 228 aa     Download sequence    Send to blast
MGRGKIAIKR IDNTMNRQVT FSKRRGGLMK KARELAILCD ADVGLIVFSC TGRLYDFSSS  60
SMKSIIERYQ EAGEEHCRLL NPMSEAKFWQ REVTTLRQQV QNLHHNNRQL LGEEISNFTV  120
RDLQLLQNQV EMSLHSIRNK KDQLLAEEIL KLNEKGSLVQ KENSELRKKF NIAHQRNIEL  180
HKKLNSGEST SSEQVTRSSK DPGESSTPRD SRVCIDLELS QKEVEDE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-21176176MEF2C
5f28_B1e-21176176MEF2C
5f28_C1e-21176176MEF2C
5f28_D1e-21176176MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.542650.0callus
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329881360.0
Expression AtlasQ84NC5-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedling roots. {ECO:0000269|PubMed:14701936}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Function -- GeneRIF ? help Back to Top
  1. MADS25 is a positive regulator that controls lateral and primary root development in rice via modulation of nitrate accumulation.
    [PMID: 26258667]
  2. regulates root system development via auxin signalling
    [PMID: 29932274]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g23910.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g23910
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1029270.0AK102927.1 Oryza sativa Japonica Group cDNA clone:J033114E21, full insert sequence.
GenBankAY1776950.0AY177695.2 Oryza sativa (japonica cultivar-group) transcription factor MADS25 mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015635120.11e-167MADS-box transcription factor 25
SwissprotQ84NC51e-168MAD25_ORYSJ; MADS-box transcription factor 25
TrEMBLQ01ME41e-164Q01ME4_ORYSA; OSIGBa0092O07.6 protein
STRINGOS04T0304400-011e-166(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP61435130
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G57230.11e-79AGAMOUS-like 16
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Lee S, et al.
    Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.
    Plant Cell Physiol., 2003. 44(12): p. 1403-11
    [PMID:14701936]
  3. Puig J, et al.
    Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice.
    Gene Expr. Patterns, 2013 Jun-Jul. 13(5-6): p. 160-70
    [PMID:23466806]
  4. Yu C, et al.
    The effects of fluctuations in the nutrient supply on the expression of five members of the AGL17 clade of MADS-box genes in rice.
    PLoS ONE, 2014. 9(8): p. e105597
    [PMID:25140876]
  5. Yu C, et al.
    MADS-box transcription factor OsMADS25 regulates root development through affection of nitrate accumulation in rice.
    PLoS ONE, 2015. 10(8): p. e0135196
    [PMID:26258667]
  6. Zhang G,Xu N,Chen H,Wang G,Huang J
    OsMADS25 regulates root system development via auxin signalling in rice.
    Plant J., 2018. 95(6): p. 1004-1022
    [PMID:29932274]