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 ONIVA03G01420.2
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: 359aa    MW: 40236.1 Da    PI: 10.4096
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA03G01420.2genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.97.5e-3095145151
                      S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
           SRF-TF   1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 
                      krien + rqvtfskRrng+lKKA+ELSvLCdaeva+i+fs++gklye++s
  ONIVA03G01420.2  95 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALIVFSPRGKLYEFAS 145
                      79***********************************************86 PP
2K-box69.79.5e-24207300699
            K-box   6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                      g+++ +++ e+ + +++ L k++e L++ +R+llGe+L+++s++eL++Le +Le+sl +iR +K++ll eq+ +l++ke +l+++n++Lr+k +
  ONIVA03G01420.2 207 GNKTVQQDIEQVKADADGLAKKLEALETYKRKLLGEKLDECSIEELHSLEVKLERSLISIRGRKTKLLEEQVAKLREKEMKLRKDNEELREKCK 300
                      4557788899*********************************************************************************976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004329.8E-4187146IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.73587147IPR002100Transcription factor, MADS-box
PROSITE patternPS00350089143IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-3089109IPR002100Transcription factor, MADS-box
SuperFamilySSF554558.11E-2989150IPR002100Transcription factor, MADS-box
CDDcd002653.17E-3689149No hitNo description
PfamPF003194.6E-2796143IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-30109124IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-30124145IPR002100Transcription factor, MADS-box
PfamPF014864.7E-24212300IPR002487Transcription factor, K-box
PROSITE profilePS5129713.413215305IPR002487Transcription 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
Sequence ? help Back to Top
Protein Sequence    Length: 359 aa     Download sequence    Send to blast
MTIKNGNATA RTPPVAVCLC LPLPRGGVAT TRTKGNGNTR RDQKGKPRRR GRGEKGEGVG  60
EKEERASSLG YGQTLQRLHH HSLPFLMVRG KTQMKRIENP TSRQVTFSKR RNGLLKKAFE  120
LSVLCDAEVA LIVFSPRGKL YEFASASCRL NSHTTSIKKL VVRLARYVTP KSIYIIKGST  180
SEDVTSALTP LKKTIERYRT YTKENIGNKT VQQDIEQVKA DADGLAKKLE ALETYKRKLL  240
GEKLDECSIE ELHSLEVKLE RSLISIRGRK TKLLEEQVAK LREKEMKLRK DNEELREKCK  300
NQPPLSAPLT VRAEDENPDR NINTTNDNMD VETELFIGLP GRSRSSGGAA EDSQAMPHS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-1787188188MEF2C
5f28_B1e-1787188188MEF2C
5f28_C1e-1787188188MEF2C
5f28_D1e-1787188188MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor active in flowering time control. May control internode elongation and promote floral transition phase. May act upstream of the floral regulators MADS1, MADS14, MADS15 and MADS18 in the floral induction pathway. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCT8300370.0CT830037.1 Oryza sativa (indica cultivar-group) cDNA clone:OSIGCSA030D10, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015630979.11e-155MADS-box transcription factor 50
RefseqXP_025880188.11e-155MADS-box transcription factor 50
SwissprotQ9XJ601e-157MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBLA0A0E0GG170.0A0A0E0GG17_ORYNI; Uncharacterized protein
STRINGONIVA03G01420.20.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP14133379
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45660.11e-62AGAMOUS-like 20
Publications ? help Back to Top
  1. Thomson MJ,Edwards JD,Septiningsih EM,Harrington SE,McCouch SR
    Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL.
    Genetics, 2006. 172(4): p. 2501-14
    [PMID:16452146]
  2. Park SJ, et al.
    Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod.
    Plant J., 2008. 56(6): p. 1018-29
    [PMID:18774969]
  3. Lee S,Jeong DH,An G
    A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses.
    Plant Signal Behav, 2008. 3(7): p. 471-4
    [PMID:19704489]
  4. Maas LF,McClung A,McCouch S
    Dissection of a QTL reveals an adaptive, interacting gene complex associated with transgressive variation for flowering time in rice.
    Theor. Appl. Genet., 2010. 120(5): p. 895-908
    [PMID:19949767]
  5. Sun C, et al.
    The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice.
    Plant Cell, 2012. 24(8): p. 3235-47
    [PMID:22892321]
  6. Choi SC, et al.
    Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3.
    Plant Physiol., 2014. 164(3): p. 1326-37
    [PMID:24420930]
  7. Núñez-López L,Aguirre-Cruz A,Barrera-Figueroa BE,Peña-Castro JM
    Improvement of enzymatic saccharification yield in Arabidopsis thaliana by ectopic expression of the rice SUB1A-1 transcription factor.
    PeerJ, 2015. 3: p. e817
    [PMID:25780769]
  8. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
    [PMID:25855537]
  9. Liu X, et al.
    Brassinosteroid (BR) biosynthetic gene lhdd10 controls late heading and plant height in rice (Oryza sativa L.).
    Plant Cell Rep., 2016. 35(2): p. 357-68
    [PMID:26518431]
  10. Hwang YH, et al.
    Functional conservation of rice OsNF-YB/YC and Arabidopsis AtNF-YB/YC proteins in the regulation of flowering time.
    Plant Cell Rep., 2016. 35(4): p. 857-65
    [PMID:26754793]
  11. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
    [PMID:27318280]
  12. Alter P, et al.
    Flowering Time-Regulated Genes in Maize Include the Transcription Factor ZmMADS1.
    Plant Physiol., 2016. 172(1): p. 389-404
    [PMID:27457125]