PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os07g41370.1
Common NameLOC4343851, MADS18, MADS2, MADS28, Os07g0605200, OsJ_25046, OSJNBb0040H10.26
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: 250aa    MW: 28284.8 Da    PI: 9.2925
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os07g41370.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF98.62.6e-311059251
                      ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      rienk+nrqvtfskRrng+lKKA+E+SvLCda+va+i+fs++gklye+ss
  LOC_Os07g41370.1 10 RIENKINRQVTFSKRRNGLLKKAHEISVLCDADVALIVFSTKGKLYEFSS 59
                      8***********************************************96 PP
2K-box92.29.2e-31841721098
             K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                       +++++e++  e+  Lk++++ Lq++qR+llGe+L++L++keLqqLe+qLe slk+iRskKn+ll+e+i+elqkkek+l+++n+ L+k +
  LOC_Os07g41370.1  84 NTEDQENWGDEYGILKSKLDALQKSQRQLLGEQLDTLTIKELQQLEHQLEYSLKHIRSKKNQLLFESISELQKKEKSLKNQNNVLQKLM 172
                       467789*****************************************************************************998755 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.085161IPR002100Transcription factor, MADS-box
SMARTSM004327.3E-39160IPR002100Transcription factor, MADS-box
CDDcd002657.80E-43274No hitNo description
SuperFamilySSF554551.16E-33291IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-30323IPR002100Transcription factor, MADS-box
PfamPF003192.2E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-303859IPR002100Transcription factor, MADS-box
PfamPF014868.7E-2885171IPR002487Transcription factor, K-box
PROSITE profilePS5129716.19388179IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009908Biological Processflower development
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010154Biological Processfruit development
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 250 aa     Download sequence    Send to blast
MGRGPVQLRR IENKINRQVT FSKRRNGLLK KAHEISVLCD ADVALIVFST KGKLYEFSSH  60
SSMEGILERY QRYSFDERAV LEPNTEDQEN WGDEYGILKS KLDALQKSQR QLLGEQLDTL  120
TIKELQQLEH QLEYSLKHIR SKKNQLLFES ISELQKKEKS LKNQNNVLQK LMETEKEKNN  180
AIINTNREEQ NGATPSTSSP TPVTAPDPIP TTNNSQSQPR GSGESEAQPS PAQAGNSKLP  240
PWMLRTSHT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6byy_A9e-21174173MEF2 CHIMERA
6byy_B9e-21174173MEF2 CHIMERA
6byy_C9e-21174173MEF2 CHIMERA
6byy_D9e-21174173MEF2 CHIMERA
6bz1_A1e-20174173MEF2 CHIMERA
6bz1_B1e-20174173MEF2 CHIMERA
6bz1_C1e-20174173MEF2 CHIMERA
6bz1_D1e-20174173MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.45730.0flower| panicle| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329747220.0
Expression AtlasQ0D4T4-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Not expressed at early stages of plant development. First detected in leaves 4 weeks after germination, and expression levels are increased when the plant reaches the reproductive stage. {ECO:0000269|PubMed:15299121}.
UniprotTISSUE SPECIFICITY: Widely expressed. Transcripts accumulate to higher levels in organs that retain meristematic characteristics: in the apical meristem and in the meristematic leaf primordia formed on its flank; in the developing panicle at the early stage of rachis-branch primordia differentiation; in the procambium of the rachis branches and in all floral organ primordia. {ECO:0000269|PubMed:10814814}.
UniprotTISSUE SPECIFICITY: Widely expressed. Transcripts accumulate to higher levels in organs that retain meristematic characteristics: in the apical meristem and in the meristematic leaf primordia formed on its flank; in the developing panicle at the early stage of rachis-branch primordia differentiation; in the procambium of the rachis branches and in all floral organ primordia. {ECO:0000269|PubMed:11971906, ECO:0000269|PubMed:15299121}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
UniProtProbable transcription factor that may promote floral transition phase and differentiation program of the vegetative shoot. {ECO:0000269|PubMed:11971906, ECO:0000269|PubMed:15299121}.
Function -- GeneRIF ? help Back to Top
  1. These data implicate the developmentally late spatially restricted accumulation of OsMADS2 transcripts in the differentiating lodicule to control growth of these regions.
    [PMID: 17409064]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os07g41370.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
IntActSearch Q0D4T4
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs07g41370
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ0116750.0AJ011675.1 Oryza sativa mRNA for MADS-box protein.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015647484.10.0MADS-box transcription factor 18 isoform X2
SwissprotA2YNI20.0MAD18_ORYSI; MADS-box transcription factor 18
SwissprotQ0D4T40.0MAD18_ORYSJ; MADS-box transcription factor 18
TrEMBLA0A0E0QAY80.0A0A0E0QAY8_ORYRU; Uncharacterized protein
STRINGOS07T0605200-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP115137113
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60910.11e-80AGAMOUS-like 8
Publications ? help Back to Top
  1. Moon YH, et al.
    Determination of the motif responsible for interaction between the rice APETALA1/AGAMOUS-LIKE9 family proteins using a yeast two-hybrid system.
    Plant Physiol., 1999. 120(4): p. 1193-204
    [PMID:10444103]
  2. Jia H, et al.
    Characterization and transcriptional profiles of two rice MADS-box genes.
    Plant Sci., 2000. 155(2): p. 115-122
    [PMID:10814814]
  3. Masiero S, et al.
    Ternary complex formation between MADS-box transcription factors and the histone fold protein NF-YB.
    J. Biol. Chem., 2002. 277(29): p. 26429-35
    [PMID:11971906]
  4. Cooper B, et al.
    A network of rice genes associated with stress response and seed development.
    Proc. Natl. Acad. Sci. U.S.A., 2003. 100(8): p. 4945-50
    [PMID:12684538]
  5. Fornara F, et al.
    Functional characterization of OsMADS18, a member of the AP1/SQUA subfamily of MADS box genes.
    Plant Physiol., 2004. 135(4): p. 2207-19
    [PMID:15299121]
  6. Chen C, et al.
    Adapting rice anther culture to gene transformation and RNA interference.
    Sci. China, C, Life Sci., 2006. 49(5): p. 414-28
    [PMID:17172048]
  7. Yadav SR,Prasad K,Vijayraghavan U
    Divergent regulatory OsMADS2 functions control size, shape and differentiation of the highly derived rice floret second-whorl organ.
    Genetics, 2007. 176(1): p. 283-94
    [PMID:17409064]
  8. Yoshida H, et al.
    superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice.
    Plant Biotechnol. J., 2007. 5(6): p. 835-46
    [PMID:17764519]
  9. Yao SG,Ohmori S,Kimizu M,Yoshida H
    Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development.
    Plant Cell Physiol., 2008. 49(5): p. 853-7
    [PMID:18378529]
  10. Seok HY, et al.
    Rice ternary MADS protein complexes containing class B MADS heterodimer.
    Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604
    [PMID:20888318]
  11. Kobayashi K, et al.
    Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene.
    Plant Cell, 2012. 24(5): p. 1848-59
    [PMID:22570445]
  12. Wei X, et al.
    Fine mapping of BH1, a gene controlling lemma and palea development in rice.
    Plant Cell Rep., 2013. 32(9): p. 1455-63
    [PMID:23689259]
  13. Wang H, et al.
    OsMADS32 interacts with PI-like proteins and regulates rice flower development.
    J Integr Plant Biol, 2015. 57(5): p. 504-13
    [PMID:25081486]
  14. Lombardo F, et al.
    The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice.
    Plant Biotechnol. J., 2017. 15(1): p. 97-106
    [PMID:27336225]