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.J149100.2.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: 149aa    MW: 16730.3 Da    PI: 9.5199
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.J149100.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF86.12e-27959151
                       S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
             SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                       krien++nrqvtfskRr+g+ KKA E+ vLCdaev v+ifss gkly+y+s
  Pavir.J149100.2.p  9 KRIENSTNRQVTFSKRRAGLVKKAREIGVLCDAEVGVVIFSSGGKLYDYCS 59
                       79***********************************************96 PP
2K-box645.4e-2271139169
              K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskK 69 
                        yq++sgk l+++k++sl+ e++++kke++n+q e+Rhl+GedL+sL+  eL  +e++L+++ ++ R+k 
  Pavir.J149100.2.p  71 YQTNSGKILWDEKHKSLSAEIDRVKKENDNMQIELRHLKGEDLNSLQPTELIAIEEALQNGQTNLRDKL 139
                        89999999**********************************************************986 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
SuperFamilySSF554552.22E-33296IPR002100Transcription factor, MADS-box
CDDcd002652.27E-42280No hitNo description
PRINTSPR004043.2E-29323IPR002100Transcription factor, MADS-box
PfamPF003197.4E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004043.2E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004043.2E-293859IPR002100Transcription factor, MADS-box
PfamPF014866.8E-1382139IPR002487Transcription factor, K-box
PROSITE profilePS512979.6484148IPR002487Transcription 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: 149 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRAGLVK KAREIGVLCD AEVGVVIFSS GGKLYDYCSP  60
RTSLSRILEM YQTNSGKILW DEKHKSLSAE IDRVKKENDN MQIELRHLKG EDLNSLQPTE  120
LIAIEEALQN GQTNLRDKLA ILLHPLAP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-19186178Myocyte-specific enhancer factor 2B
1tqe_Q2e-19186178Myocyte-specific enhancer factor 2B
1tqe_R2e-19186178Myocyte-specific enhancer factor 2B
1tqe_S2e-19186178Myocyte-specific enhancer factor 2B
5f28_A2e-19186178MEF2C
5f28_B2e-19186178MEF2C
5f28_C2e-19186178MEF2C
5f28_D2e-19186178MEF2C
6c9l_A2e-19186178Myocyte-specific enhancer factor 2B
6c9l_B2e-19186178Myocyte-specific enhancer factor 2B
6c9l_C2e-19186178Myocyte-specific enhancer factor 2B
6c9l_D2e-19186178Myocyte-specific enhancer factor 2B
6c9l_E2e-19186178Myocyte-specific enhancer factor 2B
6c9l_F2e-19186178Myocyte-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.J149100.2.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
GenBankAJ2929611e-171AJ292961.1 Zea mays mRNA for putative MADS-domain transcription factor (m29 gene).
GenBankBT0542771e-171BT054277.1 Zea mays full-length cDNA clone ZM_BFb0210A14 mRNA, complete cds.
GenBankKJ7269301e-171KJ726930.1 Zea mays clone pUT3475 MADS transcription factor (MADS29) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808084.13e-95MADS-box transcription factor 4-like
SwissprotQ407033e-87MADS4_ORYSJ; MADS-box transcription factor 4
TrEMBLA0A3L6R8Z41e-102A0A3L6R8Z4_PANMI; MADS-box transcription factor 4-like
STRINGPavir.J33965.1.p1e-96(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G20240.11e-61MIKC_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]