PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
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
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
1tqe_P3e-21176176Myocyte-specific enhancer factor 2B
1tqe_Q3e-21176176Myocyte-specific enhancer factor 2B
1tqe_R3e-21176176Myocyte-specific enhancer factor 2B
1tqe_S3e-21176176Myocyte-specific enhancer factor 2B
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]
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
GenBankAY1776950.0AY177695.2 Oryza sativa (japonica cultivar-group) transcription factor MADS25 mRNA, partial cds.
GenBankAK1029270.0AK102927.1 Oryza sativa Japonica Group cDNA clone:J033114E21, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015635120.11e-167PREDICTED: MADS-box transcription factor 25
SwissprotQ84NC51e-169MAD25_ORYSJ; MADS-box transcription factor 25
TrEMBLQ01ME41e-166Q01ME4_ORYSA;
STRINGLOC_Os04g23910.11e-166(Oryza sativa Japonica Group)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP1617761
MonocotsOGMP61435130
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. 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]
  2. 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]