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.9NG097100.1.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: 250aa    MW: 28225.2 Da    PI: 6.8821
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG097100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF87.85.9e-281059251
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         rienk+ rqvtf+kRrng+lKKA+ELS+LCdaeva+++fs+ g+ly +ss
  Pavir.9NG097100.1.p 10 RIENKISRQVTFAKRRNGLLKKAYELSILCDAEVALVLFSHAGRLYQFSS 59
                         9***********************************************96 PP
2K-box95.86.9e-32831749100
                K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                           ++ ++++ +qe+ kLk ++e Lq++qR+llGedL +L+  eL+qLe+q++k lk+iRs+K+++ll+++ +l++ke++lq++n  L++kl
  Pavir.9NG097100.1.p  83 PSSDEMQNHYQEYVKLKTRVEVLQHSQRNLLGEDLAPLTTSELEQLESQVDKTLKQIRSRKTQVLLDELCDLKRKEHMLQDANIVLKRKL 172
                          567889***********************************************************************************9 PP

                K-box  99 ee 100
                          +e
  Pavir.9NG097100.1.p 173 DE 174
                          86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.02161IPR002100Transcription factor, MADS-box
SMARTSM004322.9E-36160IPR002100Transcription factor, MADS-box
SuperFamilySSF554554.06E-30282IPR002100Transcription factor, MADS-box
CDDcd002652.92E-41279No hitNo description
PRINTSPR004045.0E-29323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.2E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004045.0E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004045.0E-293859IPR002100Transcription factor, MADS-box
PfamPF014866.4E-2885172IPR002487Transcription factor, K-box
PROSITE profilePS5129715.02788178IPR002487Transcription 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: 250 aa     Download sequence    Send to blast
MGRGKVVLQR IENKISRQVT FAKRRNGLLK KAYELSILCD AEVALVLFSH AGRLYQFSSS  60
SNLLKTLERY QRYIYASADA AVPSSDEMQN HYQEYVKLKT RVEVLQHSQR NLLGEDLAPL  120
TTSELEQLES QVDKTLKQIR SRKTQVLLDE LCDLKRKEHM LQDANIVLKR KLDEVEAEAP  180
PPLQPQLPWQ GGSGDDAMVS DGPPQPEHFF QALESNPSLQ PTFHTMDMNQ HPVPAPGGCY  240
PPAWSAWMA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A2e-24751721101Developmental protein SEPALLATA 3
4ox0_B2e-24751721101Developmental protein SEPALLATA 3
4ox0_C2e-24751721101Developmental protein SEPALLATA 3
4ox0_D2e-24751721101Developmental protein SEPALLATA 3
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaves and at low levels in roots and spikelets (rice flower). {ECO:0000269|Ref.7}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9NG097100.1.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
GenBankJN6616140.0JN661614.1 Panicum miliaceum panicle phytomer 2-like protein (PAP2) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025796987.11e-171MADS-box transcription factor 34-like
RefseqXP_025796988.11e-171MADS-box transcription factor 34-like
SwissprotQ6Q9H61e-122MAD34_ORYSJ; MADS-box transcription factor 34
TrEMBLA0A2S3IHY41e-170A0A2S3IHY4_9POAL; Uncharacterized protein
TrEMBLA0A2T7C0Y01e-170A0A2T7C0Y0_9POAL; Uncharacterized protein
STRINGPavir.Ia00529.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP136182630
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G02310.12e-82MIKC_MADS family protein
Publications ? help Back to Top
  1. Kobayashi K,Maekawa M,Miyao A,Hirochika H,Kyozuka J
    PANICLE PHYTOMER2 (PAP2), encoding a SEPALLATA subfamily MADS-box protein, positively controls spikelet meristem identity in rice.
    Plant Cell Physiol., 2010. 51(1): p. 47-57
    [PMID:19933267]
  2. Gao X, et al.
    The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development.
    Plant Physiol., 2010. 153(2): p. 728-40
    [PMID:20395452]
  3. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]
  4. Lin X, et al.
    The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas.
    New Phytol., 2014. 202(2): p. 689-702
    [PMID:24372518]
  5. Conrad LJ, et al.
    The polycomb group gene EMF2B is essential for maintenance of floral meristem determinacy in rice.
    Plant J., 2014. 80(5): p. 883-94
    [PMID:25279942]
  6. Liu M,Li H,Su Y,Li W,Shi C
    G1/ELE Functions in the Development of Rice Lemmas in Addition to Determining Identities of Empty Glumes.
    Front Plant Sci, 2016. 7: p. 1006
    [PMID:27462334]