PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT3G48160.2

Common Name

DEL1, E2FE, E2L3, ELP2, T24C20.40

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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: 403aa MW: 45460.6 Da PI: 8.2214

Description

DP-E2F-like 1

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G48160.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	74.5	1.1e-23	34	99	1	71
E2F_TDP 1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 rk+ksL+ll+++fl+l++++ ++v l+++a++L v +rRRiYDi+NVLe+++++++++kn+++wkg AT3G48160.2 34 RKQKSLGLLCTNFLALYNREGIEMVGLDDAASKL---GV--ERRRIYDIVNVLESVGVLTRRAKNQYTWKG 99 79***************999********.....****************************98 PP
2	E2F_TDP	78.2	7.7e-25	169	250	1	71
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 AT3G48160.2 169 RREKSLGLLTQNFIKLFICSEAiRIISLDDAAKLLLGDahntsIMRTKVRRLYDIANVLSSMNLIEKthtldSRKPAFKWLG 250 689*************************************999********************9999*****87 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.10	7.7E-27	30	101	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF46785	3.45E-16	33	97	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	2.8E-28	34	99	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Pfam	PF02319	2.8E-20	35	99	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Gene3D	G3DSA:1.10.10.10	2.0E-21	167	251	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	6.7E-31	169	250	IPR003316	E2F/DP family, winged-helix DNA-binding domain
SuperFamily	SSF46785	5.9E-13	171	251	IPR011991	Winged helix-turn-helix DNA-binding domain
Pfam	PF02319	5.2E-19	171	250	IPR003316	E2F/DP family, winged-helix DNA-binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0032876	Biological Process	negative regulation of DNA endoreduplication
GO:0005634	Cellular Component	nucleus
GO:0005667	Cellular Component	transcription factor complex
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000037	anatomy	shoot apex
PO:0000293	anatomy	guard cell
PO:0006340	anatomy	adult vascular leaf
PO:0009015	anatomy	portion of vascular tissue
PO:0009046	anatomy	flower
PO:0007131	developmental stage	seedling development stage

Sequence ? help Back to Top
Protein Sequence Length: 403 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 VLKDLFSHYM DAWKTWFSEV TQENPLPNTS QHR

Sequence ? help Back to Top

Protein Sequence Length: 403 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 VLKDLFSHYM DAWKTWFSEV TQENPLPNTS QHR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4yo2_A	3e-38	33	242	3	228	Transcription factor E2F8
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	AT3G48160
AtGenExpress	AT3G48160

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL 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}.
Uniprot	TISSUE 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
TAIR	E2F-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.
UniProt	Inhibitor 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
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] the atypical E2F transcription factor E2Fe/DEL1 controls the expression of the CDH1/FZR orthologous CCS52A2 gene from Arabidopsis thaliana [PMID: 18787127] DEL1 is a transcriptional repressor of the type-II cyclobutane pyrimidine dimer-photolyase DNA repair gene PHR1. [PMID: 21131907] The Arabidopsis (Arabidopsis thaliana) DEL1 gene was identified as a transcriptional target of the classical E2Fb and E2Fc transcription factors. [PMID: 21908689] Overexpression of DEL1 does not completely abolish early endoreduplication on stress. [PMID: 22535421] 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] involved in nematode feeding site generation [PMID: 23518580] Del1 Knockout Mice Developed More Severe Osteoarthritis Associated with Increased Susceptibility of Chondrocytes to Apoptosis [PMID: 27505251]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00397	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G48160.2

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

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
BioGRID	AT3G54390
IntAct	Search Q8LSZ4

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: No visible phenotype, but increased ploidy levels. {ECO:0000269\|PubMed:15649366}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G48160

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB074533	0.0	AB074533.1 Arabidopsis thaliana mRNA for E2F-like repressor E2L3, complete cds.
GenBank	BT004258	0.0	BT004258.1 Arabidopsis thaliana clone RAFL15-19-A14 (R20743) putative DP-E2F protein 1 (At3g48160) mRNA, complete cds.
GenBank	BT005524	0.0	BT005524.1 Arabidopsis thaliana clone U20743 putative DP-E2F protein 1 (At3g48160) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_190399.2	0.0	DP-E2F-like 1
Swissprot	Q8LSZ4	0.0	E2FE_ARATH; E2F transcription factor-like E2FE
TrEMBL	A0A178VE71	0.0	A0A178VE71_ARATH; E2L3
STRING	AT3G48160.2	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6304	27	43
Representative plant	OGRP2474	16	34

Link Out ? help Back to Top
Phytozome	AT3G48160.2
Entrez Gene	823971
iHOP	AT3G48160
wikigenes	AT3G48160

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] 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] 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] Vandepoele K, et al. Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell, 2002. 14(4): p. 903-16 [PMID:11971144] 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] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] 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] 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] 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] 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] Chandran D, et al. Atypical E2F transcriptional repressor DEL1 acts at the intersection of plant growth and immunity by controlling the hormone salicylic acid. Cell Host Microbe, 2014. 15(4): p. 506-13 [PMID:24721578] 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] Wang Z, et al. Del1 Knockout Mice Developed More Severe Osteoarthritis Associated with Increased Susceptibility of Chondrocytes to Apoptosis. PLoS ONE, 2016. 11(8): p. e0160684 [PMID:27505251] Heyman J,Polyn S,Eekhout T,De Veylder L Tissue-Specific Control of the Endocycle by the Anaphase Promoting Complex/Cyclosome Inhibitors UVI4 and DEL1. Plant Physiol., 2017. 175(1): p. 303-313 [PMID:28698355]