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.6NG327900.3.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 M-type_MADS
Protein Properties Length: 107aa    MW: 12260.1 Da    PI: 10.9222
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG327900.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.63.4e-283988251
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         rie+ + rqv fskRr g++KKA+ELSvLCda+va+i+fs+ g+lye++s
  Pavir.6NG327900.3.p 39 RIEDRTSRQVRFSKRRSGLFKKAYELSVLCDAQVALIVFSPAGRLYEFAS 88
                         8***********************************************86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006630.3053090IPR002100Transcription factor, MADS-box
SMARTSM004326.8E-353089IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.96E-273290IPR002100Transcription factor, MADS-box
CDDcd002657.68E-323287No hitNo description
PRINTSPR004044.8E-293252IPR002100Transcription factor, MADS-box
PfamPF003193.1E-273986IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-295267IPR002100Transcription factor, MADS-box
PRINTSPR004044.8E-296788IPR002100Transcription factor, MADS-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 107 aa     Download sequence    Send to blast
MEEREEATTA RRAELQLLQQ LDKEEIKGKR KRGRVELRRI EDRTSRQVRF SKRRSGLFKK  60
AYELSVLCDA QVALIVFSPA GRLYEFASSG SRIRSSSHLS ALYLIS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1n6j_A2e-183289259Myocyte-specific enhancer factor 2B
1n6j_B2e-183289259Myocyte-specific enhancer factor 2B
1tqe_P2e-183289360Myocyte-specific enhancer factor 2B
1tqe_Q2e-183289360Myocyte-specific enhancer factor 2B
1tqe_R2e-183289360Myocyte-specific enhancer factor 2B
1tqe_S2e-183289360Myocyte-specific enhancer factor 2B
6c9l_A2e-183289360Myocyte-specific enhancer factor 2B
6c9l_B2e-183289360Myocyte-specific enhancer factor 2B
6c9l_C2e-183289360Myocyte-specific enhancer factor 2B
6c9l_D2e-183289360Myocyte-specific enhancer factor 2B
6c9l_E2e-183289360Myocyte-specific enhancer factor 2B
6c9l_F2e-183289360Myocyte-specific enhancer factor 2B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG327900.3.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
GenBankAK2429808e-66AK242980.1 Oryza sativa Japonica Group cDNA, clone: J090094F15, full insert sequence.
GenBankAP0055298e-66AP005529.3 Oryza sativa Japonica Group genomic DNA, chromosome 8, PAC clone:P0702E04.
GenBankAP0149648e-66AP014964.1 Oryza sativa Japonica Group DNA, chromosome 8, cultivar: Nipponbare, complete sequence.
GenBankAY1777018e-66AY177701.1 Oryza sativa (japonica cultivar-group) transcription factor MADS37 mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025820080.14e-39MADS-box transcription factor 51-like isoform X1
RefseqXP_025820081.14e-39MADS-box transcription factor 51-like isoform X1
SwissprotP0C5B22e-27MAD56_ORYSJ; MADS-box transcription factor 56
TrEMBLA0A3L6PT547e-49A0A3L6PT54_PANMI; MADS-box transcription factor 56-like
STRINGPavir.J26790.1.p3e-58(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G11880.16e-24AGAMOUS-like 14
Publications ? help Back to Top
  1. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  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. Bai Z, et al.
    The impact and origin of copy number variations in the Oryza species.
    BMC Genomics, 2016. 17: p. 261
    [PMID:27025496]
  4. Shibaya T, et al.
    Hd18, Encoding Histone Acetylase Related to Arabidopsis FLOWERING LOCUS D, is Involved in the Control of Flowering Time in Rice.
    Plant Cell Physiol., 2016. 57(9): p. 1828-38
    [PMID:27318280]
  5. Han Z,Zhang B,Zhao H,Ayaad M,Xing Y
    Genome-Wide Association Studies Reveal that Diverse Heading Date Genes Respond to Short and Long Day Lengths between Indica and Japonica Rice.
    Front Plant Sci, 2016. 7: p. 1270
    [PMID:27621738]