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.J149100.1.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: 216aa    MW: 25070.5 Da    PI: 7.7615
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.J149100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF85.14.1e-27959151
                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       krien++nrqvtfskRr+g+ KKA E+ vLCdaev v+ifss gkly+y+s
  Pavir.J149100.1.p  9 KRIENSTNRQVTFSKRRAGLVKKAREIGVLCDAEVGVVIFSSGGKLYDYCS 59
                       79***********************************************96 PP
2K-box64.83e-2271160190
              K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqee 90 
                        yq++sgk l+++k++sl+ e++++kke++n+q e+Rhl+GedL+sL+  eL  +e++L+++ ++ R+k +++++++ ++ ++ e+e++  
  Pavir.J149100.1.p  71 YQTNSGKILWDEKHKSLSAEIDRVKKENDNMQIELRHLKGEDLNSLQPTELIAIEEALQNGQTNLRDKLMDHWRMHKRNGKMLEDEHKML 160
                        89999999************************************************************9999999999999998887655 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.8E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006632.043161IPR002100Transcription factor, MADS-box
SuperFamilySSF554555.89E-33295IPR002100Transcription factor, MADS-box
CDDcd002651.40E-42280No hitNo description
PRINTSPR004047.1E-29323IPR002100Transcription factor, MADS-box
PfamPF003191.5E-241057IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004047.1E-293859IPR002100Transcription factor, MADS-box
PfamPF014867.5E-1582164IPR002487Transcription factor, K-box
PROSITE profilePS5129712.16984170IPR002487Transcription 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: 216 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRAGLVK KAREIGVLCD AEVGVVIFSS GGKLYDYCSP  60
RTSLSRILEM YQTNSGKILW DEKHKSLSAE IDRVKKENDN MQIELRHLKG EDLNSLQPTE  120
LIAIEEALQN GQTNLRDKLM DHWRMHKRNG KMLEDEHKML SFRMAYQHQQ DVELSGGMRE  180
LEIGYHQVQH DRDFTSQMPF TFRVQPSHPN LQEDE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-18171169Myocyte-specific enhancer factor 2B
1tqe_Q2e-18171169Myocyte-specific enhancer factor 2B
1tqe_R2e-18171169Myocyte-specific enhancer factor 2B
1tqe_S2e-18171169Myocyte-specific enhancer factor 2B
6c9l_A2e-18171169Myocyte-specific enhancer factor 2B
6c9l_B2e-18171169Myocyte-specific enhancer factor 2B
6c9l_C2e-18171169Myocyte-specific enhancer factor 2B
6c9l_D2e-18171169Myocyte-specific enhancer factor 2B
6c9l_E2e-18171169Myocyte-specific enhancer factor 2B
6c9l_F2e-18171169Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.224780.0leaf
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in lodicules, at intermediate levels in stamens, and weakly in carpels. Expressed in pollen. {ECO:0000269|PubMed:10394955, ECO:0000269|PubMed:12905025, ECO:0000269|Ref.1}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the development of floral organs. B-class protein required for normal development of lodicules and stamens (whorls 2 and 3). May function as a heterodimer with MADS16. {ECO:0000269|PubMed:9869408}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.J149100.1.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
GenBankBT0542770.0BT054277.1 Zea mays full-length cDNA clone ZM_BFb0210A14 mRNA, complete cds.
GenBankKJ7269300.0KJ726930.1 Zea mays clone pUT3475 MADS transcription factor (MADS29) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808084.11e-158MADS-box transcription factor 4-like
SwissprotQ407031e-133MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBLA0A2S3HBW31e-157A0A2S3HBW3_9POAL; Uncharacterized protein
TrEMBLA0A2T7EDL91e-157A0A2T7EDL9_9POAL; Uncharacterized protein
STRINGPavir.J33965.1.p1e-161(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP34343877
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G20240.12e-72MIKC_MADS family protein
Publications ? help Back to Top
  1. Ronai Z, et al.
    Transcription factor binding study by capillary zone electrophoretic mobility shift assay.
    Electrophoresis, 2003. 24(1-2): p. 96-100
    [PMID:12652578]
  2. 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]
  3. Kang HG,An G
    Morphological alterations by ectopic expression of the rice OsMADS4 gene in tobacco plants.
    Plant Cell Rep., 2005. 24(2): p. 120-6
    [PMID:15703945]
  4. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]