PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G48160.1
Common NameDEL1, E2FE, E2L3, ELP2, T24C20.40
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; Arabidopsis
Family E2F/DP
Protein Properties Length: 379aa    MW: 42438.3 Da    PI: 8.5701
Description DP-E2F-like 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G48160.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1E2F_TDP74.69.9e-243499171
      E2F_TDP  1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71
                 rk+ksL+ll+++fl+l++++  ++v l+++a++L    v  +rRRiYDi+NVLe+++++++++kn+++wkg
  AT3G48160.1 34 RKQKSLGLLCTNFLALYNREGIEMVGLDDAASKL---GV--ERRRIYDIVNVLESVGVLTRRAKNQYTWKG 99
                 79*****************999************...**..****************************98 PP

2E2F_TDP78.46.9e-25169250171
      E2F_TDP   1 rkeksLrlltqkflklleksee.givtlnevakeLvse.....dvknkrRRiYDilNVLealnliek.....kekneirwkg 71 
                  r+eksL+lltq+f+kl+ +se+ +i++l+++ak L+ +      +++k+RR+YDi+NVL+++nliek     ++k++++w g
  AT3G48160.1 169 RREKSLGLLTQNFIKLFICSEAiRIISLDDAAKLLLGDahntsIMRTKVRRLYDIANVLSSMNLIEKthtldSRKPAFKWLG 250
                  689***************************************999************************9999*******87 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.107.0E-2730101IPR011991Winged helix-turn-helix DNA-binding domain
SuperFamilySSF467853.27E-163397IPR011991Winged helix-turn-helix DNA-binding domain
SMARTSM013722.8E-283499IPR003316E2F/DP family, winged-helix DNA-binding domain
PfamPF023192.6E-203599IPR003316E2F/DP family, winged-helix DNA-binding domain
Gene3DG3DSA:1.10.10.101.8E-21167251IPR011991Winged helix-turn-helix DNA-binding domain
SMARTSM013726.7E-31169250IPR003316E2F/DP family, winged-helix DNA-binding domain
PfamPF023194.7E-19171250IPR003316E2F/DP family, winged-helix DNA-binding domain
SuperFamilySSF467855.44E-13171251IPR011991Winged helix-turn-helix DNA-binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0032876Biological Processnegative regulation of DNA endoreduplication
GO:0005634Cellular Componentnucleus
GO:0005667Cellular Componenttranscription factor complex
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0006340anatomyadult vascular leaf
PO:0009015anatomyportion of vascular tissue
PO:0009046anatomyflower
PO:0007131developmental stageseedling development stage
Sequence ? help Back to Top
Protein Sequence    Length: 379 aa     Download sequence    Send to blast
MSDLSPERFK LAVTSPSSIP ESSSALQLHH SYSRKQKSLG LLCTNFLALY NREGIEMVGL  60
DDAASKLGVE RRRIYDIVNV LESVGVLTRR AKNQYTWKGF SAIPGALKEL QEEGVKDTFH  120
RFYVNENVKG SDDEDDDEES SQPHSSSQTD SSKPGSLPQS SDPSKIDNRR EKSLGLLTQN  180
FIKLFICSEA IRIISLDDAA KLLLGDAHNT SIMRTKVRRL YDIANVLSSM NLIEKTHTLD  240
SRKPAFKWLG YNGEPTFTLS SDLLQLESRK RAFGTDITNV NVKRSKSSSS SQENATERRL  300
KMKKHSTPES SYNKSFDVHE SRHGSRGGYH FGPFAPGTGT YPTAGLEDNS RRAFDVENLD  360
SDYRPSYQNQ GAYILFTSI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yo2_A1e-38332423228Transcription factor E2F8
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasAT3G48160
AtGenExpressAT3G48160
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in a cell cycle-dependent manner. Not detected during early S phase. Expressed at both the G1/S and S/G2 transitions, with a peak during G2. {ECO:0000269|PubMed:11786543, ECO:0000269|PubMed:18787127}.
UniprotTISSUE SPECIFICITY: Expressed exclusively in mitotically dividing cells. Highly expressed in young leaves and mature flowers. Lower expression in young stalk and in young and mature flowers. {ECO:0000269|PubMed:11867638, ECO:0000269|PubMed:15649366}.
Functional Description ? help Back to Top
Source Description
TAIRE2F-like protein, an inhibitor of the endocycle, preserves the mitotic state of proliferating cells by suppressing transcription of genes that are required for cells to enter the DNA endoreduplication cycle.
UniProtInhibitor of E2F-dependent activation of gene expression. Binds specifically the E2 recognition site without interacting with DP proteins and prevents transcription activation by E2F/DP heterodimers. Controls the timing of endocycle onset and inhibits endoreduplication. {ECO:0000269|PubMed:11786543, ECO:0000269|PubMed:11867638, ECO:0000269|PubMed:15649366, ECO:0000269|PubMed:18787127}.
Function -- GeneRIF ? help Back to Top
  1. DEL1 (EL3) is an important novel inhibitor of the endocycle and preserves the mitotic state of proliferating cells by suppressing transcription of genes that are required for cells to enter the DNA endoreduplication cycle.
    [PMID: 15649366]
  2. the atypical E2F transcription factor E2Fe/DEL1 controls the expression of the CDH1/FZR orthologous CCS52A2 gene from Arabidopsis thaliana
    [PMID: 18787127]
  3. DEL1 is a transcriptional repressor of the type-II cyclobutane pyrimidine dimer-photolyase DNA repair gene PHR1.
    [PMID: 21131907]
  4. The Arabidopsis (Arabidopsis thaliana) DEL1 gene was identified as a transcriptional target of the classical E2Fb and E2Fc transcription factors.
    [PMID: 21908689]
  5. Overexpression of DEL1 does not completely abolish early endoreduplication on stress.
    [PMID: 22535421]
  6. Down-regulation and over-expression of CCS52 and DEL1 in Arabidopsis affected giant cell and syncytium growth, resulting in restrained nematode development, illustrating the need for mitotic activity and endo-reduplication for feeding site maturation.
    [PMID: 22640471]
  7. involved in nematode feeding site generation
    [PMID: 23518580]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00397DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G48160.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT5G14960 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT4G11920(R)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G54390
IntActSearch Q8LSZ4
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: No visible phenotype, but increased ploidy levels. {ECO:0000269|PubMed:15649366}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G48160
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ4178360.0AJ417836.1 Arabidopsis thaliana mRNA for transcription factor E2Fe (e2Fe gene).
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_851012.10.0E2F transcription factor-like E2FE
SwissprotQ8LSZ40.0E2FE_ARATH; E2F transcription factor-like E2FE
TrEMBLD7LRJ40.0D7LRJ4_ARALL; Putative uncharacterized protein
STRINGAT3G48160.20.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Mariconti L, et al.
    The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants.
    J. Biol. Chem., 2002. 277(12): p. 9911-9
    [PMID:11786543]
  3. Kosugi S,Ohashi Y
    E2Ls, E2F-like repressors of Arabidopsis that bind to E2F sites in a monomeric form.
    J. Biol. Chem., 2002. 277(19): p. 16553-8
    [PMID:11867638]
  4. Vandepoele K, et al.
    Genome-wide analysis of core cell cycle genes in Arabidopsis.
    Plant Cell, 2002. 14(4): p. 903-16
    [PMID:11971144]
  5. Chen IP,Haehnel U,Altschmied L,Schubert I,Puchta H
    The transcriptional response of Arabidopsis to genotoxic stress - a high-density colony array study (HDCA).
    Plant J., 2003. 35(6): p. 771-86
    [PMID:12969430]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  7. Stevens R, et al.
    A CDC45 homolog in Arabidopsis is essential for meiosis, as shown by RNA interference-induced gene silencing.
    Plant Cell, 2004. 16(1): p. 99-113
    [PMID:14660803]
  8. Vlieghe K, et al.
    The DP-E2F-like gene DEL1 controls the endocycle in Arabidopsis thaliana.
    Curr. Biol., 2005. 15(1): p. 59-63
    [PMID:15649366]
  9. Demidov D,Van Damme D,Geelen D,Blattner FR,Houben A
    Identification and dynamics of two classes of aurora-like kinases in Arabidopsis and other plants.
    Plant Cell, 2005. 17(3): p. 836-48
    [PMID:15722465]
  10. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
    [PMID:18650403]
  11. Lammens T, et al.
    Atypical E2F activity restrains APC/CCCS52A2 function obligatory for endocycle onset.
    Proc. Natl. Acad. Sci. U.S.A., 2008. 105(38): p. 14721-6
    [PMID:18787127]
  12. Boudolf V, et al.
    CDKB1;1 forms a functional complex with CYCA2;3 to suppress endocycle onset.
    Plant Physiol., 2009. 150(3): p. 1482-93
    [PMID:19458112]
  13. Sozzani R, et al.
    The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis.
    Plant Mol. Biol., 2010. 72(4-5): p. 381-95
    [PMID:19937368]
  14. Boruc J, et al.
    Functional modules in the Arabidopsis core cell cycle binary protein-protein interaction network.
    Plant Cell, 2010. 22(4): p. 1264-80
    [PMID:20407024]
  15. Van Leene J, et al.
    Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana.
    Mol. Syst. Biol., 2010. 6: p. 397
    [PMID:20706207]
  16. Radziejwoski A, et al.
    Atypical E2F activity coordinates PHR1 photolyase gene transcription with endoreduplication onset.
    EMBO J., 2011. 30(2): p. 355-63
    [PMID:21131907]
  17. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  18. Berckmans B, et al.
    Light-dependent regulation of DEL1 is determined by the antagonistic action of E2Fb and E2Fc.
    Plant Physiol., 2011. 157(3): p. 1440-51
    [PMID:21908689]
  19. Claeys H,Skirycz A,Maleux K,Inz
    DELLA signaling mediates stress-induced cell differentiation in Arabidopsis leaves through modulation of anaphase-promoting complex/cyclosome activity.
    Plant Physiol., 2012. 159(2): p. 739-47
    [PMID:22535421]
  20. de Almeida Engler J, et al.
    CCS52 and DEL1 genes are key components of the endocycle in nematode-induced feeding sites.
    Plant J., 2012. 72(2): p. 185-98
    [PMID:22640471]
  21. Vieira P,Kyndt T,Gheysen G,de Almeida Engler J
    An insight into critical endocycle genes for plant-parasitic nematode feeding sites establishment.
    Plant Signal Behav, 2013. 8(6): p. e24223
    [PMID:23518580]
  22. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]