PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pavir.5KG676500.1.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: 210aa    MW: 24140.6 Da    PI: 7.7051
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG676500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF93.78.6e-30959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krien++nrqvtfskRrngilKKA E+SvLCdaev v+ifss gkly+++s
  Pavir.5KG676500.1.p  9 KRIENSTNRQVTFSKRRNGILKKAREISVLCDAEVGVVIFSSAGKLYDFCS 59
                         79***********************************************96 PP
2K-box73.18.4e-2571167197
                K-box   1 yqkssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqee 90 
                          yq++sgk l+++k++sl+ e++++kke++++q e+Rhl+GedL+sL+ keL  +e++L+++l++  +k +e++  ++++ ++ e+e++  
  Pavir.5KG676500.1.p  71 YQTNSGKILWDEKHKSLSAEIDRIKKENDTMQIELRHLKGEDLNSLQPKELIMIEEALDNGLTNLNEKLMEHWELHVRNNKMLEDENKLL 160
                          89999999********************************************************************************** PP

                K-box  91 nkaLrkk 97 
                            +L+++
  Pavir.5KG676500.1.p 161 AFKLHQQ 167
                          ***9997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.333161IPR002100Transcription factor, MADS-box
SMARTSM004329.3E-43160IPR002100Transcription factor, MADS-box
CDDcd002655.42E-45280No hitNo description
SuperFamilySSF554558.89E-35296IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-30323IPR002100Transcription factor, MADS-box
PfamPF003191.5E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-302338IPR002100Transcription factor, MADS-box
PRINTSPR004041.6E-303859IPR002100Transcription factor, MADS-box
PfamPF014866.4E-1482164IPR002487Transcription factor, K-box
PROSITE profilePS5129712.31684170IPR002487Transcription 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: 210 aa     Download sequence    Send to blast
MGRGKIEIKR IENSTNRQVT FSKRRNGILK KAREISVLCD AEVGVVIFSS AGKLYDFCSP  60
KTSLSKILEK YQTNSGKILW DEKHKSLSAE IDRIKKENDT MQIELRHLKG EDLNSLQPKE  120
LIMIEEALDN GLTNLNEKLM EHWELHVRNN KMLEDENKLL AFKLHQQDIA LSGSMRDLEL  180
GYHPDRDFAA QMPITFRVQP SHPNLQENN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A2e-19186178MEF2C
5f28_B2e-19186178MEF2C
5f28_C2e-19186178MEF2C
5f28_D2e-19186178MEF2C
6byy_A2e-19175173MEF2 CHIMERA
6byy_B2e-19175173MEF2 CHIMERA
6byy_C2e-19175173MEF2 CHIMERA
6byy_D2e-19175173MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.144150.0callus| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in lodicules and stamens from early to late stage of flower development. {ECO:0000269|PubMed:10945340, ECO:0000269|Ref.1}.
UniprotTISSUE SPECIFICITY: Highly expressed in anthers and carpels. Expressed in pollen, tapetum and stigma. {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 (whorl 2). {ECO:0000269|PubMed:14704206}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5KG676500.1.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
GenBankAJ2929590.0AJ292959.1 Zea mays mRNA for putative MADS-domain transcription factor (m16 gene).
GenBankBT0648490.0BT064849.1 Zea mays full-length cDNA clone ZM_BFb0210M20 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025816957.11e-153MADS-box transcription factor 2
SwissprotQ407021e-148MADS2_ORYSJ; MADS-box transcription factor 2
TrEMBLA0A2S3HPC71e-152A0A2S3HPC7_9POAL; Uncharacterized protein
TrEMBLA0A2T7DDM51e-151A0A2T7DDM5_9POAL; Uncharacterized protein
TrEMBLA0A3L6RIC41e-152A0A3L6RIC4_PANMI; MADS-box transcription factor 2
STRINGPavir.Ea03625.1.p1e-153(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
AT5G20240.14e-75MIKC_MADS family protein
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]