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.2KG001200.2.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: 247aa    MW: 28233.1 Da    PI: 9.5097
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2KG001200.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.99.7e-32959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krienk+nrqvtfskRrng+lKKA+E+SvLCdaevavi+fs++gklyey++
  Pavir.2KG001200.2.p  9 KRIENKINRQVTFSKRRNGLLKKANEISVLCDAEVAVIVFSPKGKLYEYAT 59
                         79***********************************************86 PP
2K-box85.98.2e-2982163889
                K-box   8 sleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqe 89 
                          s+e + + ++++e++kLk++i ++q+ ++hl+GedLesL+lkeLqqLeqqLe+slk+iRs+K++ l e+ + lqk   + q+
  Pavir.2KG001200.2.p  82 SAEPESEVNWCHEYRKLKAKIGTIQKCHKHLMGEDLESLNLKELQQLEQQLESSLKHIRSRKERSLQEENKALQKELADRQK 163
                          555667789*****************************************************************98777665 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006632.842161IPR002100Transcription factor, MADS-box
SMARTSM004322.2E-42160IPR002100Transcription factor, MADS-box
CDDcd002657.31E-42276No hitNo description
SuperFamilySSF554551.7E-34291IPR002100Transcription factor, MADS-box
PRINTSPR004042.4E-31323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.2E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004042.4E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004042.4E-313859IPR002100Transcription factor, MADS-box
PfamPF014864.5E-2287162IPR002487Transcription factor, K-box
PROSITE profilePS5129713.28188179IPR002487Transcription 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: 247 aa     Download sequence    Send to blast
MGRGKVQLKR IENKINRQVT FSKRRNGLLK KANEISVLCD AEVAVIVFSP KGKLYEYATD  60
DRMDKILERY ECYSYAEKAL ISAEPESEVN WCHEYRKLKA KIGTIQKCHK HLMGEDLESL  120
NLKELQQLEQ QLESSLKHIR SRKERSLQEE NKALQKELAD RQKAAASRPQ VQWDPHTQAQ  180
TSSSSSSFLM RQDQQPLQPP QNIWYPPVTG ERGEEAAAVA QRQPGQAQPQ LRIGSLPPWM  240
TSHLNA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6byy_A6e-23174173MEF2 CHIMERA
6byy_B6e-23174173MEF2 CHIMERA
6byy_C6e-23174173MEF2 CHIMERA
6byy_D6e-23174173MEF2 CHIMERA
6bz1_A6e-23174173MEF2 CHIMERA
6bz1_B6e-23174173MEF2 CHIMERA
6bz1_C6e-23174173MEF2 CHIMERA
6bz1_D6e-23174173MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.159100.0stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the floral meristem at very early stage of the spikelet (rice flower) development. Expressed in lemmas, paleas and lodicules from early to late stage of flower development. {ECO:0000269|PubMed:10945340}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.2KG001200.2.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9598850.0EU959885.1 Zea mays clone 220235 mRNA sequence.
GenBankEU9630610.0EU963061.1 Zea mays clone 257029 MADS-box transcription factor 15 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001105333.21e-128zea apetala homolog 1
SwissprotQ6Q9I21e-112MAD15_ORYSJ; MADS-box transcription factor 15
TrEMBLB6TDJ61e-132B6TDJ6_MAIZE; MADS-box transcription factor 15
STRINGTraes_2DL_903A29CBA.11e-115(Triticum aestivum)
STRINGGRMZM2G148693_P021e-115(Zea mays)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G69120.18e-59MIKC_MADS family protein
Publications ? help Back to Top
  1. Cai Q, et al.
    [PAEs in composts of municipal sludge and rice straw].
    Ying Yong Sheng Tai Xue Bao, 2003. 14(11): p. 1993-6
    [PMID:14997664]
  2. Wang K, et al.
    DEP and AFO regulate reproductive habit in rice.
    PLoS Genet., 2010. 6(1): p. e1000818
    [PMID:20107517]
  3. 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]
  4. Ramanujam R,Yishi X,Liu H,Naqvi NI
    Structure-function analysis of Rgs1 in Magnaporthe oryzae: role of DEP domains in subcellular targeting.
    PLoS ONE, 2012. 7(7): p. e41084
    [PMID:22927898]
  5. Ang TN,Ngoh GC,Chua AS,Lee MG
    Elucidation of the effect of ionic liquid pretreatment on rice husk via structural analyses.
    Biotechnol Biofuels, 2012. 5(1): p. 67
    [PMID:22958710]
  6. Zhang G,Huang K,Jiang X,Huang D,Yang Y
    Acetylation of rice straw for thermoplastic applications.
    Carbohydr Polym, 2013. 96(1): p. 218-26
    [PMID:23688473]
  7. 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]
  8. Hu S, et al.
    A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7.
    Rice (N Y), 2013. 6(1): p. 24
    [PMID:24280027]
  9. Ji Y, et al.
    A comprehensive assessment of human exposure to phthalates from environmental media and food in Tianjin, China.
    J. Hazard. Mater., 2014. 279: p. 133-40
    [PMID:25051237]
  10. Huang Y, et al.
    Phthalates in Commercial Chinese Rice Wines: Concentrations and the Cumulative Risk Assessment to Adult Males in Shanghai.
    Biomed. Environ. Sci., 2014. 27(10): p. 819-23
    [PMID:25341819]
  11. Tamaki S, et al.
    FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice.
    Proc. Natl. Acad. Sci. U.S.A., 2015. 112(8): p. E901-10
    [PMID:25675495]
  12. Wu F, et al.
    The ABCs of flower development: mutational analysis of AP1/FUL-like genes in rice provides evidence for a homeotic (A)-function in grasses.
    Plant J., 2017. 89(2): p. 310-324
    [PMID:27689766]