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.6NG073900.1.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 NF-YB
Protein Properties Length: 243aa    MW: 24518.1 Da    PI: 5.9554
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG073900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB174.41.1e-5450145297
                NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyr 91 
                          +e drflPianvsrimk+ lPanakisk+aketvqecvsefisfvt+easdkcqrekrktingddllwa++tlGfe yv plk yl++yr
  Pavir.6NG073900.1.p  50 KELDRFLPIANVSRIMKRSLPANAKISKEAKETVQECVSEFISFVTGEASDKCQREKRKTINGDDLLWAMTTLGFEAYVGPLKSYLNRYR 139
                          789*************************************************************************************** PP

                NF-YB  92 elegek 97 
                          e+egek
  Pavir.6NG073900.1.p 140 EAEGEK 145
                          ***997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.102.1E-5047155IPR009072Histone-fold
SuperFamilySSF471133.73E-3853156IPR009072Histone-fold
PfamPF008085.9E-2755119IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006153.2E-1883101No hitNo description
PROSITE patternPS00685086102IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006153.2E-18102120No hitNo description
PRINTSPR006153.2E-18121139No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 243 aa     Download sequence    Send to blast
MKSRKGYGGQ QGHLLSPVGS PPSDNESGAA AAAGCGSSAG YAGGGDSPAK ELDRFLPIAN  60
VSRIMKRSLP ANAKISKEAK ETVQECVSEF ISFVTGEASD KCQREKRKTI NGDDLLWAMT  120
TLGFEAYVGP LKSYLNRYRE AEGEKAAVGG ARHGDGAADD APLGACAVAA PGDRAGHHDA  180
AGGSADVGLM MGVGGGFGAG GGTAYGGDGP KVVEFDGEEA ENGRGMQRGF GGSGHLHGAV  240
QW*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4g91_B8e-4550140292Transcription factor HapC (Eurofung)
4g92_B8e-4550140292Transcription factor HapC (Eurofung)
5g49_A1e-4444140197NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.184134e-76root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, nodes, leaf blades, leaf sheaths and young panicles. {ECO:0000269|PubMed:20566706}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of flowering time under long day (LD) conditions. Functions as repressor of flowering, independently of HD1 and GHD7. Controls flowering time by negatively regulating the expression of EHD1 and HD3A (PubMed:20566706, PubMed:21148627). Regulates plant height by promoting cell elongation in the internodes (PubMed:20566706). Component of the NF-Y/HAP transcription factor complex (By similarity). {ECO:0000250, ECO:0000269|PubMed:20566706, ECO:0000269|PubMed:21148627}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG073900.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Circadian-regulation under long day (LD) conditions. Expression increases in the middle of daytime, peaks around the end of the light period and gradually decreases during the dark period and beginning of daylight. {ECO:0000269|PubMed:26542958}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB1246521e-150AB124652.1 Oryza sativa Japonica Group Hd5 gene for imperfect Hd5 protein, complete cds, cultivar:Hayamasari.
GenBankAB6932011e-150AB693201.1 Oryza sativa Japonica Group Hd5 gene for heading date 5, complete cds, cultivar: Kitaibuki.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004972725.11e-102nuclear transcription factor Y subunit B-11
SwissprotQ0J7P45e-76HD5_ORYSJ; Nuclear transcription factor Y subunit B-11
TrEMBLA0A3L6PMD71e-118A0A3L6PMD7_PANMI; Uncharacterized protein
STRINGPavir.Fb00481.1.p1e-142(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20138331
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G14540.13e-55nuclear factor Y, subunit B3
Publications ? help Back to Top
  1. Yan WH, et al.
    A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice.
    Mol Plant, 2011. 4(2): p. 319-30
    [PMID:21148627]
  2. Dai X, et al.
    LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon).
    J Integr Plant Biol, 2012. 54(10): p. 790-9
    [PMID:22963226]
  3. Kim SK, et al.
    OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice.
    Planta, 2016. 243(3): p. 563-76
    [PMID:26542958]