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 Pavir.4KG313000.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family MIKC_MADS
Protein Properties Length: 227aa    MW: 25992.8 Da    PI: 8.8681
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG313000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF92.71.8e-29959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krien + rqvtfskRrng+lKKA+ELSvLCdaeva++++s++gklye++s
  Pavir.4KG313000.1.p  9 KRIENPTSRQVTFSKRRNGLLKKAFELSVLCDAEVALVVISPRGKLYEFAS 59
                         79***********************************************86 PP
2K-box71.62.4e-2478171699
                K-box   6 gksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLr 95 
                          ++++++++ e+ + +++ L k++e L+  +R+llGe+Le++s++eL++Le +Leksl  iR +K++ll eq+++l++ke  l+++n++Lr
  Pavir.4KG313000.1.p  78 SSKTAQQDIEQVKADAEGLAKKLEALEAYKRKLLGEKLEECSIEELHSLEVKLEKSLHCIRGRKTQLLEEQVNKLKEKEMTLRKNNEELR 167
                          334788999********************************************************************************* PP

                K-box  96 kkle 99 
                          +k +
  Pavir.4KG313000.1.p 168 EKCK 171
                          *976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004327.0E-39160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006631.076161IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-30323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.92E-32381IPR002100Transcription factor, MADS-box
CDDcd002657.43E-42375No hitNo description
PfamPF003191.6E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004046.2E-303859IPR002100Transcription factor, MADS-box
PfamPF014864.2E-2582171IPR002487Transcription factor, K-box
PROSITE profilePS5129713.64286176IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000060Biological Processprotein import into nucleus, translocation
GO:0009409Biological Processresponse to cold
GO:0009739Biological Processresponse to gibberellin
GO:0009911Biological Processpositive regulation of flower development
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008134Molecular Functiontranscription factor binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 227 aa     Download sequence    Send to blast
MVRGKTQMKR IENPTSRQVT FSKRRNGLLK KAFELSVLCD AEVALVVISP RGKLYEFASA  60
SVQKTIERYR TYTKDNVSSK TAQQDIEQVK ADAEGLAKKL EALEAYKRKL LGEKLEECSI  120
EELHSLEVKL EKSLHCIRGR KTQLLEEQVN KLKEKEMTLR KNNEELREKC KNQPPLPLTP  180
ARPVITVEDD RPEQNDDDRM DVETELYLGL PGRDPRRNEV AEVRSG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-18172172MEF2C
5f28_B2e-18172172MEF2C
5f28_C2e-18172172MEF2C
5f28_D2e-18172172MEF2C
6byy_A2e-18173173MEF2 CHIMERA
6byy_B2e-18173173MEF2 CHIMERA
6byy_C2e-18173173MEF2 CHIMERA
6byy_D2e-18173173MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.34880.0leaf| root
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Low expression in the young panicle continues to decline as the organ mature. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
UniprotTISSUE SPECIFICITY: Expressed in mature leaves and at low levels in roots and young panicles. {ECO:0000269|PubMed:15144377, ECO:0000269|PubMed:17166135}.
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00076ChIP-chipTransfer from AT2G45660Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4KG313000.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9607740.0EU960774.1 Zea mays clone 228490 MADS-box transcription factor 56 mRNA, complete cds.
GenBankEU9625040.0EU962504.1 Zea mays clone 243238 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025797677.11e-150MADS-box transcription factor 50-like
RefseqXP_025797678.11e-150MADS-box transcription factor 50-like
RefseqXP_025797679.11e-150MADS-box transcription factor 50-like
SwissprotQ9XJ601e-122MAD50_ORYSJ; MADS-box transcription factor 50
TrEMBLA0A1L5YF981e-161A0A1L5YF98_PANVG; SL1
STRINGGRMZM2G171365_P011e-125(Zea mays)
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
AT2G45660.18e-75AGAMOUS-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]