PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.3434s0008.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family NF-YB
Protein Properties Length: 235aa    MW: 25601.5 Da    PI: 6.5144
Description NF-YB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.3434s0008.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NF-YB171.68.7e-5455150297
                NF-YB   2 reqdrflPianvsrimkkvlPanakiskdaketvqecvsefisfvtseasdkcqrekrktingddllwalatlGfedyveplkvylkkyr 91 
                          reqd+++Pianv+rim+k lP++akis+daket+qecvse+isfvt+ea+++cqre+rkti+++d+lwa+++lGf++yv+pl++y+++yr
  Cagra.3434s0008.1.p  55 REQDQYMPIANVIRIMRKNLPSHAKISDDAKETIQECVSEYISFVTGEANERCQREQRKTITAEDILWAMSKLGFDNYVDPLTLYINRYR 144
                          89**************************************************************************************** PP

                NF-YB  92 elegek 97 
                          e+e+++
  Cagra.3434s0008.1.p 145 EIETDR 150
                          ***997 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.20.105.4E-4947156IPR009072Histone-fold
SuperFamilySSF471134.5E-3757156IPR009072Histone-fold
PfamPF008083.0E-2660124IPR003958Transcription factor CBF/NF-Y/archaeal histone domain
PRINTSPR006151.1E-1688106No hitNo description
PROSITE patternPS00685091107IPR003956Transcription factor, NFYB/HAP3, conserved site
PRINTSPR006151.1E-16107125No hitNo description
PRINTSPR006151.1E-16126144No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0009785Biological Processblue light signaling pathway
GO:0010262Biological Processsomatic embryogenesis
GO:0045723Biological Processpositive regulation of fatty acid biosynthetic process
GO:0045893Biological Processpositive regulation 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: 235 aa     Download sequence    Send to blast
MERGAPFPHY QLPKPNSGLN LDQLTNANPM TSSVAVAGSS DKNKGQQQQQ PCMAREQDQY  60
MPIANVIRIM RKNLPSHAKI SDDAKETIQE CVSEYISFVT GEANERCQRE QRKTITAEDI  120
LWAMSKLGFD NYVDPLTLYI NRYREIETDR GSALRGEASS LRQAYGGNGI GFHGPPHGLP  180
PPGPYGYGMV DQSMVMGGGR YYQNGSGQDG SGSGGGSSSS INGMSVYDPY VQYK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5g49_A3e-5754145697NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6
Search in ModeBase
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. Acts as a central regulator of the embryogenesis. Required for the speciation of cotyledon identity and the completion of embryo maturation. Controls seed storage protein genes through the regulation of FUS3 and ABI3. Involved in the blue light (BL) and abscisic acid (ABA) signaling pathways. {ECO:0000269|PubMed:12578989, ECO:0000269|PubMed:15695450, ECO:0000269|PubMed:17322342, ECO:0000269|PubMed:9657152}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.3434s0008.1.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
GenBankAB4934740.0AB493474.1 Arabidopsis thaliana At1g21970 mRNA for hypothetical protein, partial cds, clone: RAAt1g21970.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006303559.11e-138nuclear transcription factor Y subunit B-9
SwissprotQ9SFD81e-137NFYB9_ARATH; Nuclear transcription factor Y subunit B-9
TrEMBLR0GKL21e-136R0GKL2_9BRAS; Uncharacterized protein
STRINGCagra.3434s0008.1.p1e-174(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM80422640
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G21970.11e-114NF-YB family protein
Publications ? help Back to Top
  1. Yang C, et al.
    VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis.
    Curr. Biol., 2013. 23(14): p. 1324-9
    [PMID:23810531]
  2. Guo F, et al.
    Induced expression of AtLEC1 and AtLEC2 differentially promotes somatic embryogenesis in transgenic tobacco plants.
    PLoS ONE, 2013. 8(8): p. e71714
    [PMID:23951228]
  3. 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]
  4. 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]
  5. Garcês HM,Koenig D,Townsley BT,Kim M,Sinha NR
    Truncation of LEAFY COTYLEDON1 protein is required for asexual reproduction in Kalanchoë daigremontiana.
    Plant Physiol., 2014. 165(1): p. 196-206
    [PMID:24664206]
  6. Rikiishi K,Maekawa M
    Seed maturation regulators are related to the control of seed dormancy in wheat (Triticum aestivum L.).
    PLoS ONE, 2014. 9(9): p. e107618
    [PMID:25211528]
  7. Yamamoto A, et al.
    Cell-by-cell developmental transition from embryo to post-germination phase revealed by heterochronic gene expression and ER-body formation in Arabidopsis leafy cotyledon mutants.
    Plant Cell Physiol., 2014. 55(12): p. 2112-25
    [PMID:25282558]
  8. Shen Y,Devic M,Lepiniec L,Zhou DX
    Chromodomain, Helicase and DNA-binding CHD1 protein, CHR5, are involved in establishing active chromatin state of seed maturation genes.
    Plant Biotechnol. J., 2015. 13(6): p. 811-20
    [PMID:25581843]
  9. Yoshii M,Yamamoto A,Kagaya Y,Takeda S,Hattori T
    The Arabidopsis transcription factor NAI1 is required for enhancing the active histone mark but not for removing the repressive mark on PYK10, a seedling-specific gene upon embryonic-to-postgerminative developmental phase transition.
    Plant Signal Behav, 2015. 10(12): p. e1105418
    [PMID:26479492]
  10. Huang M,Hu Y,Liu X,Li Y,Hou X
    Arabidopsis LEAFY COTYLEDON1 Mediates Postembryonic Development via Interacting with PHYTOCHROME-INTERACTING FACTOR4.
    Plant Cell, 2015. 27(11): p. 3099-111
    [PMID:26566918]
  11. Huang M,Hu Y,Liu X,Li Y,Hou X
    Arabidopsis LEAFY COTYLEDON1 controls cell fate determination during post-embryonic development.
    Front Plant Sci, 2015. 6: p. 955
    [PMID:26579186]
  12. Schneider A, et al.
    Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos.
    Plant J., 2016. 85(2): p. 305-19
    [PMID:26678037]
  13. Baud S, et al.
    Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed.
    Plant Physiol., 2016. 171(2): p. 1099-112
    [PMID:27208266]
  14. Fatihi A, et al.
    Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds.
    Plant Sci., 2016. 250: p. 198-204
    [PMID:27457996]
  15. Zhao H, et al.
    The Arabidopsis thaliana Nuclear Factor Y Transcription Factors.
    Front Plant Sci, 2016. 7: p. 2045
    [PMID:28119722]
  16. 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]
  17. Pelletier JM, et al.
    LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development.
    Proc. Natl. Acad. Sci. U.S.A., 2017. 114(32): p. E6710-E6719
    [PMID:28739919]
  18. Horstman A, et al.
    The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis.
    Plant Physiol., 2017. 175(2): p. 848-857
    [PMID:28830937]
  19. Tao Z, et al.
    Embryonic epigenetic reprogramming by a pioneer transcription factor in plants.
    Nature, 2017. 551(7678): p. 124-128
    [PMID:29072296]
  20. Hanano A,Almousally I,Shaban M,Murphy DJ
    Arabidopsis plants exposed to dioxin result in a WRINKLED seed phenotype due to 20S proteasomal degradation of WRI1.
    J. Exp. Bot., 2018. 69(7): p. 1781-1794
    [PMID:29394403]
  21. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619
    [PMID:29475938]
  22. Boulard C, et al.
    LEC1 (NF-YB9) directly interacts with LEC2 to control gene expression in seed.
    Biochim Biophys Acta Gene Regul Mech, 2018. 1861(5): p. 443-450
    [PMID:29580949]