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.4NG231400.1.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: 250aa    MW: 26821.2 Da    PI: 9.805
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4NG231400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB148.91.1e-4642136296
                NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyr 91 
                          r qdr++P+anvsrim+++lP +akis+ ake++q+cvsefisfvt+ea+++c+ e+rkt++++d++wa+  lGf+dy+ pl+++l++ r
  Pavir.4NG231400.1.p  42 RGQDRLMPVANVSRIMRHALPPHAKISDGAKEMIQDCVSEFISFVTGEANERCHTEHRKTVTAEDIVWAMNRLGFDDYIRPLNTFLQRMR 131
                          679*************************************************************************************** PP

                NF-YB  92 elege 96 
                          e+eg 
  Pavir.4NG231400.1.p 132 EIEGG 136
                          **985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.101.8E-4240138IPR009072Histone-fold
SuperFamilySSF471133.26E-3444139IPR009072Histone-fold
PfamPF008082.8E-2348111IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006156.9E-147593No hitNo description
PROSITE patternPS0068507894IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006156.9E-1494112No hitNo description
PRINTSPR006156.9E-14113131No 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: 250 aa     Download sequence    Send to blast
MSTDPQGPKP WAPCAMAPER AAVAKEAMST EPLVPGTEPV IRGQDRLMPV ANVSRIMRHA  60
LPPHAKISDG AKEMIQDCVS EFISFVTGEA NERCHTEHRK TVTAEDIVWA MNRLGFDDYI  120
RPLNTFLQRM REIEGGDGAG GSGSGRGSRR GSSLVALHGA QTMRPAYPDA PQGYAVRPVI  180
PRPVPVPASN AVASRFGSRY QLPGGQRSMA PYYGGAAFRA GGNRGGFYGD EASSSNEAPT  240
ARRARSRHY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_A8e-4636132197NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed primarily during seed development. {ECO:0000269|PubMed:12509518}.
UniprotTISSUE SPECIFICITY: Expressed in roots, flowers and developing siliques. Present in etiolated seedlings. {ECO:0000269|PubMed:11250072, ECO:0000269|PubMed:12509518, ECO:0000269|PubMed:17322342}.
Functional Description ? help Back to Top
Source Description
UniProtComponent of the NF-Y/HAP transcription factor complex. The NF-Y complex stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters. Plays a role in the regulation of the embryogenesis. Involved in the abscisic acid (ABA) signaling pathway. {ECO:0000269|PubMed:12509518, ECO:0000269|PubMed:17322342}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4NG231400.1.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
GenBankBT0609744e-94BT060974.1 Zea mays full-length cDNA clone ZM_BFb0079C17 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025813135.11e-114nuclear transcription factor Y subunit B-3-like
SwissprotQ84W662e-46NFYB6_ARATH; Nuclear transcription factor Y subunit B-6
TrEMBLA0A2S3HJP81e-125A0A2S3HJP8_9POAL; Uncharacterized protein
STRINGPavir.Db01322.1.p0.0(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
AT5G47670.21e-46nuclear factor Y, subunit B6
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Kim HU, et al.
    Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues.
    FEBS Open Bio, 2013. 4: p. 25-32
    [PMID:24363987]
  3. Gnesutta N,Saad D,Chaves-Sanjuan A,Mantovani R,Nardini M
    Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.
    Mol Plant, 2017. 10(4): p. 645-648
    [PMID:27871811]
  4. Li D, et al.
    MYB89 Transcription Factor Represses Seed Oil Accumulation.
    Plant Physiol., 2017. 173(2): p. 1211-1225
    [PMID:27932421]
  5. Zhao H, et al.
    The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
    Front Plant Sci, 2016. 7: p. 2045
    [PMID:28119722]
  6. Han JD, et al.
    Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program.
    Front Plant Sci, 2017. 8: p. 439
    [PMID:28421087]