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.2NG581100.1.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: 254aa    MW: 28626.5 Da    PI: 9.5441
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2NG581100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF98.92e-311059251
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         rienk+nrqvtfskRrng+lKKA+E+SvLCdaeva+i+fs++g+lyeyss
  Pavir.2NG581100.1.p 10 RIENKINRQVTFSKRRNGLLKKAHEISVLCDAEVALIVFSTKGRLYEYSS 59
                         8***********************************************96 PP
2K-box95.77.2e-32861721298
                K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                          a+++++  e+ +Lk +++ Lq++qR+llGe+L+sL++keLqqLeqqL++slk+iRs+Kn+l++ +i+elqkkek+l ++n  L+k +
  Pavir.2NG581100.1.p  86 ADQANWGDEYGRLKTKLDALQKSQRQLLGEQLDSLTIKELQQLEQQLDSSLKHIRSRKNQLMFYSISELQKKEKSLTDQNGVLQKLM 172
                          67899***************************************************************************9998755 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.0E-38160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.156161IPR002100Transcription factor, MADS-box
CDDcd002652.65E-42274No hitNo description
SuperFamilySSF554551.26E-32284IPR002100Transcription factor, MADS-box
PRINTSPR004047.6E-31323IPR002100Transcription factor, MADS-box
PfamPF003196.6E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004047.6E-312338IPR002100Transcription factor, MADS-box
PRINTSPR004047.6E-313859IPR002100Transcription factor, MADS-box
PfamPF014863.5E-2987171IPR002487Transcription factor, K-box
PROSITE profilePS5129715.92688179IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010154Biological Processfruit 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: 254 aa     Download sequence    Send to blast
MGRGPVQLRR IENKINRQVT FSKRRNGLLK KAHEISVLCD AEVALIVFST KGRLYEYSSH  60
ESMEGILERY QRYSFEERAV LDPSIADQAN WGDEYGRLKT KLDALQKSQR QLLGEQLDSL  120
TIKELQQLEQ QLDSSLKHIR SRKNQLMFYS ISELQKKEKS LTDQNGVLQK LMEAEKEKNN  180
ALMNAHLREQ QNGASTSLPS PPLSTVPDSL PTLNIGPCQP RGGTVGESEP EPSPAQVNSG  240
KLPPWMLRSV SNR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-21174173Myocyte-specific enhancer factor 2B
1tqe_Q2e-21174173Myocyte-specific enhancer factor 2B
1tqe_R2e-21174173Myocyte-specific enhancer factor 2B
1tqe_S2e-21174173Myocyte-specific enhancer factor 2B
6c9l_A2e-21174173Myocyte-specific enhancer factor 2B
6c9l_B2e-21174173Myocyte-specific enhancer factor 2B
6c9l_C2e-21174173Myocyte-specific enhancer factor 2B
6c9l_D2e-21174173Myocyte-specific enhancer factor 2B
6c9l_E2e-21174173Myocyte-specific enhancer factor 2B
6c9l_F2e-21174173Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.177940.0leaf| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Not expressed at early stages of plant development. First detected in leaves 4 weeks after germination, and expression levels are increased when the plant reaches the reproductive stage. {ECO:0000269|PubMed:15299121}.
UniprotTISSUE SPECIFICITY: Widely expressed. Transcripts accumulate to higher levels in organs that retain meristematic characteristics: in the apical meristem and in the meristematic leaf primordia formed on its flank; in the developing panicle at the early stage of rachis-branch primordia differentiation; in the procambium of the rachis branches and in all floral organ primordia. {ECO:0000269|PubMed:10814814}.
UniprotTISSUE SPECIFICITY: Widely expressed. Transcripts accumulate to higher levels in organs that retain meristematic characteristics: in the apical meristem and in the meristematic leaf primordia formed on its flank; in the developing panicle at the early stage of rachis-branch primordia differentiation; in the procambium of the rachis branches and in all floral organ primordia. {ECO:0000269|PubMed:11971906, ECO:0000269|PubMed:15299121}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
UniProtProbable transcription factor that may promote floral transition phase and differentiation program of the vegetative shoot. {ECO:0000269|PubMed:11971906, ECO:0000269|PubMed:15299121}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.2NG581100.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025800406.11e-174MADS-box transcription factor 18-like
SwissprotA2YNI21e-138MAD18_ORYSI; MADS-box transcription factor 18
SwissprotQ0D4T41e-138MAD18_ORYSJ; MADS-box transcription factor 18
TrEMBLA0A1L5YFA10.0A0A1L5YFA1_PANVG; APL3
STRINGPavir.Ba00457.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP115137113
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G69120.11e-68MIKC_MADS family protein
Publications ? help Back to Top
  1. Jia H, et al.
    Characterization and transcriptional profiles of two rice MADS-box genes.
    Plant Sci., 2000. 155(2): p. 115-122
    [PMID:10814814]
  2. Chen C, et al.
    Adapting rice anther culture to gene transformation and RNA interference.
    Sci. China, C, Life Sci., 2006. 49(5): p. 414-28
    [PMID:17172048]
  3. Yoshida H, et al.
    superwoman1-cleistogamy, a hopeful allele for gene containment in GM rice.
    Plant Biotechnol. J., 2007. 5(6): p. 835-46
    [PMID:17764519]
  4. Yao SG,Ohmori S,Kimizu M,Yoshida H
    Unequal genetic redundancy of rice PISTILLATA orthologs, OsMADS2 and OsMADS4, in lodicule and stamen development.
    Plant Cell Physiol., 2008. 49(5): p. 853-7
    [PMID:18378529]
  5. 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]
  6. 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]
  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. Wang H, et al.
    OsMADS32 interacts with PI-like proteins and regulates rice flower development.
    J Integr Plant Biol, 2015. 57(5): p. 504-13
    [PMID:25081486]
  9. Lombardo F, et al.
    The superwoman1-cleistogamy2 mutant is a novel resource for gene containment in rice.
    Plant Biotechnol. J., 2017. 15(1): p. 97-106
    [PMID:27336225]