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.1NG219300.1.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: 225aa    MW: 25240.2 Da    PI: 8.0787
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1NG219300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF76.71.7e-241056248
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEE CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklye 48
                         rien   rqvtf+kRr+g+lKKA ELSvLCda + +iifs +gkly+
  Pavir.1NG219300.1.p 10 RIENPVHRQVTFCKRRAGLLKKARELSVLCDAHIGIIIFSAHGKLYD 56
                         8********************************************97 PP
2K-box45.92.4e-16921741899
                K-box  18 qqelakLkkeienLqreqRhllGedLe.sLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
                          +qe   L++ei+ Lq+ +R + G+  +  ++++eL+ Le+ Le  + +iRs K+++++++i+ l+ ke +l+ +n+ L++k+ 
  Pavir.1NG219300.1.p  92 KQETVVLQQEINLLQKGLRYIYGNRANeHMNVEELNALERYLEIWMYNIRSAKMQIMIQEIQALKSKEGMLKAANEVLQEKIV 174
                          789999*****************998626***************************************************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.352161IPR002100Transcription factor, MADS-box
SMARTSM004328.1E-35160IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.49E-27176IPR002100Transcription factor, MADS-box
CDDcd002651.49E-39278No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-26323IPR002100Transcription factor, MADS-box
PfamPF003193.4E-231055IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-262338IPR002100Transcription factor, MADS-box
PRINTSPR004044.3E-263859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129710.6188179IPR002487Transcription factor, K-box
PfamPF014865.7E-2191173IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0048364Biological Processroot development
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: 225 aa     Download sequence    Send to blast
MARGKVQLRR IENPVHRQVT FCKRRAGLLK KARELSVLCD AHIGIIIFSA HGKLYDLATT  60
GTMEELIERY KTASGEAALQ SDGGGGHRMD PKQETVVLQQ EINLLQKGLR YIYGNRANEH  120
MNVEELNALE RYLEIWMYNI RSAKMQIMIQ EIQALKSKEG MLKAANEVLQ EKIVEQSGLL  180
DVGMMVAAQQ NGHFTVPLIE EITNPLTILS GYSNCRGSEM GYSF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A5e-16170169MEF2C
5f28_B5e-16170169MEF2C
5f28_C5e-16170169MEF2C
5f28_D5e-16170169MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.336680.0leaf| root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves and spikelets (rice flower). {ECO:0000269|Ref.7}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.1NG219300.1.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
GenBankAB0033260.0AB003326.1 Oryza sativa Japonica Group mRNA for MADS box-like protein, complete cds, clone:R3786.
GenBankAK0691220.0AK069122.1 Oryza sativa Japonica Group cDNA clone:J023004P21, full insert sequence.
GenBankAY5519250.0AY551925.1 Oryza sativa (japonica cultivar-group) MADS-box protein RMADS220 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004972486.11e-159MADS-box transcription factor 26
SwissprotA2YQK91e-147MAD26_ORYSI; MADS-box transcription factor 26
SwissprotQ0J8G81e-147MAD26_ORYSJ; MADS-box transcription factor 26
TrEMBLK3YJK01e-158K3YJK0_SETIT; Uncharacterized protein
STRINGSi014419m1e-159(Setaria italica)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP149136112
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G71692.18e-63AGAMOUS-like 12
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. Lee S, et al.
    Further characterization of a rice AGL12 group MADS-box gene, OsMADS26.
    Plant Physiol., 2008. 147(1): p. 156-68
    [PMID:18354041]
  3. Khong GN, et al.
    OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice.
    Plant Physiol., 2015. 169(4): p. 2935-49
    [PMID:26424158]