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 ONIVA08G24560.1
Organism
Oryza nivara
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
Family MIKC_MADS
Protein Properties Length: 279aa    MW: 32233.1 Da    PI: 9.9307
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA08G24560.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.51.3e-313383151
                     S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
           SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                     krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s
  ONIVA08G24560.1 33 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 83
                     79***********************************************96 PP
2K-box86.74.7e-291082068100
            K-box   8 sleeakaeslqqelakLkkeienLqreqRh......llGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLr 95 
                      + e+++ + +++e+ kLk+++enLqr+qR+      llGedL+sL +keL++Le+qL++slk++R++++++l++q+ elq+ke++++e+n++Lr
  ONIVA08G24560.1 108 NRESEQLKASRNEYLKLKARVENLQRTQRQliawinLLGEDLDSLGIKELESLEKQLDSSLKHVRTTRTKHLVDQLTELQRKEQMVSEANRCLR 201
                      467888999********************733333368******************************************************** PP

            K-box  96 kklee 100
                      +klee
  ONIVA08G24560.1 202 RKLEE 206
                      **987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.3E-412584IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.3892585IPR002100Transcription factor, MADS-box
SuperFamilySSF554557.33E-3426113IPR002100Transcription factor, MADS-box
CDDcd002651.08E-4426101No hitNo description
PROSITE patternPS0035002781IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-322747IPR002100Transcription factor, MADS-box
PfamPF003192.8E-263481IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-324762IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-326283IPR002100Transcription factor, MADS-box
PfamPF014861.2E-21110204IPR002487Transcription factor, K-box
PROSITE profilePS5129714.606114210IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0001708Biological Processcell fate specification
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010093Biological Processspecification of floral organ identity
GO:0048481Biological Processplant ovule development
GO:0048833Biological Processspecification of floral organ number
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 279 aa     Download sequence    Send to blast
MAEKKKKKKK PQSLLVLTNW RSIGMGRGRV ELKRIENKIN RQVTFAKRRN GLLKKAYELS  60
VLCDAEVALI IFSNRGKLYE FCSTQSMTKT LEKYQKCSYA GPETAVQNRE SEQLKASRNE  120
YLKLKARVEN LQRTQRQLIA WINLLGEDLD SLGIKELESL EKQLDSSLKH VRTTRTKHLV  180
DQLTELQRKE QMVSEANRCL RRKLEESNHV RGQQVWEQGC NLIGYERQPE VQQPLHGGNG  240
FFHPLDAAGE PTLQIGYPAE HHEAMNSACM NTYMPPWLP
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A2e-26992061103Developmental protein SEPALLATA 3
4ox0_B2e-26992061103Developmental protein SEPALLATA 3
4ox0_C2e-26992061103Developmental protein SEPALLATA 3
4ox0_D2e-26992061103Developmental protein SEPALLATA 3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1210EKKKKKKKP
239KKKKKKK
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
UniProtProbable transcription factor. May be involved in the control of flowering time. {ECO:0000269|PubMed:9339904, ECO:0000269|Ref.10}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00605ChIP-seqTransfer from AT1G24260Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1002630.0AK100263.1 Oryza sativa Japonica Group cDNA clone:J023063L04, full insert sequence.
GenBankAY5519210.0AY551921.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS216 mRNA, complete cds.
GenBankFJ7509340.0FJ750934.1 Oryza sativa clone KCS054B01 MADS-box transcription factor 7 mRNA, complete cds.
GenBankOSU319940.0U31994.1 Oryza sativa MADS box protein OsMADS45 mRNA, complete cds.
GenBankOSU788910.0U78891.2 Oryza sativa MADS box protein (MADS7) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015648762.10.0MADS-box transcription factor 7
SwissprotP0C5B00.0MADS7_ORYSI; MADS-box transcription factor 7
SwissprotQ0J4660.0MADS7_ORYSJ; MADS-box transcription factor 7
TrEMBLA0A0E0IF020.0A0A0E0IF02_ORYNI; Uncharacterized protein
STRINGONIVA08G24560.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP34833469
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.11e-89MIKC_MADS family protein
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. Shitsukawa N, et al.
    Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat.
    Plant Cell, 2007. 19(6): p. 1723-37
    [PMID:17586655]
  3. Bai X,Wang Q,Chu C
    Excision of a selective marker in transgenic rice using a novel Cre/loxP system controlled by a floral specific promoter.
    Transgenic Res., 2008. 17(6): p. 1035-43
    [PMID:18437520]
  4. Qu L, et al.
    Expression pattern and functional analysis of a MADS-box gene M79 from rice.
    Sci. China, C, Life Sci., 2001. 44(2): p. 161-9
    [PMID:18726433]
  5. Cui R, et al.
    Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa).
    Plant J., 2010. 61(5): p. 767-81
    [PMID:20003164]
  6. Li H, et al.
    The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice.
    Cell Res., 2010. 20(3): p. 299-313
    [PMID:20038961]
  7. 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]
  8. Tang X, et al.
    Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis.
    Plant Physiol., 2010. 154(4): p. 1855-70
    [PMID:20959420]
  9. Wang SS,Wang CS,Tseng TH,Hou YL,Chen KY
    High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice.
    Theor. Appl. Genet., 2011. 122(8): p. 1489-96
    [PMID:21327937]
  10. Li H, et al.
    Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate.
    Plant Cell, 2011. 23(7): p. 2536-52
    [PMID:21784949]
  11. Yoshida H
    Is the lodicule a petal: molecular evidence?
    Plant Sci., 2012. 184: p. 121-8
    [PMID:22284716]
  12. Duan Y, et al.
    Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.).
    Plant Mol. Biol., 2012. 80(4-5): p. 429-42
    [PMID:22933119]
  13. Wong CE,Singh MB,Bhalla PL
    Novel members of the AGAMOUS LIKE 6 subfamily of MIKCC-type MADS-box genes in soybean.
    BMC Plant Biol., 2013. 13: p. 105
    [PMID:23870482]
  14. Hu Z,Ding X,Hu S,Sun Y,Xia L
    Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.
    Biotechnol. Lett., 2013. 35(12): p. 2177-83
    [PMID:23974493]
  15. Bai X, et al.
    Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice.
    Sci Rep, 2016. 6: p. 19022
    [PMID:26744119]
  16. Dreni L,Zhang D
    Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes.
    J. Exp. Bot., 2016. 67(6): p. 1625-38
    [PMID:26956504]