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

AT1G47870.1

Common Name

ATE2F2, ATE2FC, E2F2, E2FC, T2E6.2

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: 396aa MW: 44487.9 Da PI: 5.8097

Description

E2F/DP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G47870.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	85	5.8e-27	155	220	1	71
E2F_TDP 1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 r+++sL+llt+kf+kl++++e+g+++ln +a L +v ++RRiYDi+NVLe+++liek+ kn+irwkg AT1G47870.1 155 RYDSSLGLLTKKFVKLIQEAEDGTLDLNYCAVVL---EV--QKRRIYDITNVLEGIGLIEKTTKNHIRWKG 220 6899****************************...99..**************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:1.10.10.10	1.0E-27	153	222	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	1.2E-32	155	220	IPR003316	E2F/DP family, winged-helix DNA-binding domain
SuperFamily	SSF46785	6.53E-17	155	218	IPR011991	Winged helix-turn-helix DNA-binding domain
Pfam	PF02319	1.8E-24	157	220	IPR003316	E2F/DP family, winged-helix DNA-binding domain
CDD	cd14660	3.61E-41	231	336	No hit	No description
SuperFamily	SSF144074	4.18E-29	231	335	No hit	No description
Pfam	PF16421	7.9E-26	236	333	IPR032198	E2F transcription factor, CC-MB domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0000902	Biological Process	cell morphogenesis
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0042023	Biological Process	DNA endoreduplication
GO:0051782	Biological Process	negative regulation of cell division
GO:0005667	Cellular Component	transcription factor complex
GO:0005730	Cellular Component	nucleolus
GO:0005737	Cellular Component	cytoplasm
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding
GO:0046982	Molecular Function	protein heterodimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000025	anatomy	root tip
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000282	anatomy	trichome
PO:0000293	anatomy	guard cell
PO:0006079	anatomy	shoot system meristem
PO:0006085	anatomy	root meristem
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 396 aa Download sequence Send to blast
MAATSNSGED PTLSYHHRSP FRFELLQSIS SSDPRYSSLT PSSTNRPFSV SQSLPNSQLS 60 PLISPHWDDS YSQITQKVQK SRKNHRIQLG SIANMSGGES IDIAKVIVKQ ESSPQNVKRV 120 YNKSKGGTKL LKAGKRMANG EVQNGGLNGA SINCRYDSSL GLLTKKFVKL IQEAEDGTLD 180 LNYCAVVLEV QKRRIYDITN VLEGIGLIEK TTKNHIRWKG ADNLGQKDLG DQISRLKSEV 240 ESMQSEESRL DDLIRERQEA LRSLEEDDYC RRYMFMTEED ITSLPRFQNQ TLLAIKAPTA 300 SYIEVPDPDE MSFPQQYRMV IRSRMGPIDV YLLSKYKGDS AETSDKLGNE SDQKAPVGVD 360 TPSLKIVTSD TDLKADYWFE SDAEVSLTDL WSNFNS

Sequence ? help Back to Top

Protein Sequence Length: 396 aa Download sequence Send to blast

MAATSNSGED PTLSYHHRSP FRFELLQSIS SSDPRYSSLT PSSTNRPFSV SQSLPNSQLS  60
PLISPHWDDS YSQITQKVQK SRKNHRIQLG SIANMSGGES IDIAKVIVKQ ESSPQNVKRV  120
YNKSKGGTKL LKAGKRMANG EVQNGGLNGA SINCRYDSSL GLLTKKFVKL IQEAEDGTLD  180
LNYCAVVLEV QKRRIYDITN VLEGIGLIEK TTKNHIRWKG ADNLGQKDLG DQISRLKSEV  240
ESMQSEESRL DDLIRERQEA LRSLEEDDYC RRYMFMTEED ITSLPRFQNQ TLLAIKAPTA  300
SYIEVPDPDE MSFPQQYRMV IRSRMGPIDV YLLSKYKGDS AETSDKLGNE SDQKAPVGVD  360
TPSLKIVTSD TDLKADYWFE SDAEVSLTDL WSNFNS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1cf7_A	2e-23	155	221	7	74	PROTEIN (TRANSCRIPTION FACTOR E2F-4)
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	261741_at	0.0
Expression Atlas	AT1G47870	-
AtGenExpress	AT1G47870	-
ATTED-II	AT1G47870	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in a cell cycle-dependent manner. Not detected at the G1/S transition, but increases during the progression into S phase and peaks after the passage into G2. {ECO:0000269\|PubMed:11669580, ECO:0000269\|PubMed:11786543, ECO:0000269\|PubMed:12468727}.
Uniprot	TISSUE SPECIFICITY: Expressed in meristematic areas, vascular tissues, apical part of the roots, cotyledons, upper region of the hypocotyls, trichomes, young flower buds and pollen grains. {ECO:0000269\|PubMed:12468727, ECO:0000269\|PubMed:16920782}.

Functional Description ? help Back to Top
Source	Description
TAIR	Member of the E2F transcription factors, (cell cycle genes), key components of the cyclin D/retinoblastoma/E2F pathway. AtE2Fc is regulated by a balance between gene expression and ubiquitin-proteasome proteolysis. AtE2Fc might play a role in cell division and during the transition from skotomorphogenesis to photomorphogenesis. E2Fc has been shown to interact with DPB in its nonphosphorylated form; when E2Fc is phosphorylated, the formation of the E2Fc/DPB heterodimer is lost.
UniProt	Involved in transcriptional repression. May act by repressing E2F-regulated genes in mature differentiated cells, but is not an antagonist of E2FA. Restricts cell division and is involved in the coordination between cell proliferation and endoreduplication during development. May play a role during the transition from skotomorphogenesis to photomorphogenesis. Regulated by phosphorylation-dependent proteolysis via the protein-ubiquitin ligase SCF(SKP2A) complex. {ECO:0000269\|PubMed:11786543, ECO:0000269\|PubMed:11891240, ECO:0000269\|PubMed:12468727, ECO:0000269\|PubMed:16920782, ECO:0000269\|PubMed:19662336}.

Function -- GeneRIF ? help Back to Top
The interaction of E2FC with DPB is a key factor in controlling the balance between cell proliferation and the switch to the endocycle program. [PMID: 16920782] E2Fc induction led primarily to gene downregulation, and appears to function outside the CYCD3-RBR pathway, does not have a direct effect on cell cycle genes, and promoter analysis suggests a distinct binding site preference. [PMID: 19662336] The Arabidopsis (Arabidopsis thaliana) DEL1 gene was identified as a transcriptional target of the classical E2Fb and E2Fc transcription factors. [PMID: 21908689]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00190	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G47870.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by light. {ECO:0000269\|PubMed:12468727, ECO:0000269\|PubMed:18424613}.

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G37640(R)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9FV70

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G47870

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF242581	0.0	AF242581.1 Arabidopsis thaliana E2F transcription factor-2 E2F2 mRNA, complete cds.
GenBank	AJ417834	0.0	AJ417834.1 Arabidopsis thaliana mRNA for transcription factor E2Fc (e2Fc gene).
GenBank	AY045636	0.0	AY045636.1 Arabidopsis thaliana At1g47870/T2E6_2 mRNA, complete cds.
GenBank	AY058231	0.0	AY058231.1 Arabidopsis thaliana At1g47870/T2E6_2 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_175222.1	0.0	winged-helix DNA-binding transcription factor family protein
Swissprot	Q9FV70	0.0	E2FC_ARATH; Transcription factor E2FC
TrEMBL	A0A178WB46	0.0	A0A178WB46_ARATH; E2FC
STRING	AT1G47870.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM808	28	121
Representative plant	OGRP1225	17	49

Link Out ? help Back to Top
Phytozome	AT1G47870.1
Entrez Gene	841202
iHOP	AT1G47870
wikigenes	AT1G47870

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] de Jager SM,Menges M,Bauer UM,Murra JA Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol. Biol., 2001. 47(4): p. 555-68 [PMID:11669580] 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 Interaction of the Arabidopsis E2F and DP proteins confers their concomitant nuclear translocation and transactivation. Plant Physiol., 2002. 128(3): p. 833-43 [PMID:11891240] Vandepoele K, et al. Genome-wide analysis of core cell cycle genes in Arabidopsis. Plant Cell, 2002. 14(4): p. 903-16 [PMID:11971144] del Pozo JC,Boniotti MB,Gutierrez C Arabidopsis E2Fc functions in cell division and is degraded by the ubiquitin-SCF(AtSKP2) pathway in response to light. Plant Cell, 2002. 14(12): p. 3057-71 [PMID:12468727] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Koroleva OA,Tomlinson ML,Leader D,Shaw P,Doonan JH High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions. Plant J., 2005. 41(1): p. 162-74 [PMID:15610358] del Pozo JC,Diaz-Trivino S,Cisneros N,Gutierrez C The balance between cell division and endoreplication depends on E2FC-DPB, transcription factors regulated by the ubiquitin-SCFSKP2A pathway in Arabidopsis. Plant Cell, 2006. 18(9): p. 2224-35 [PMID:16920782] Jurado S, et al. SKP2A, an F-box protein that regulates cell division, is degraded via the ubiquitin pathway. Plant J., 2008. 53(5): p. 828-41 [PMID:18036202] L Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis. Plant Cell, 2008. 20(4): p. 947-68 [PMID:18424613] de Jager SM, et al. Dissecting regulatory pathways of G1/S control in Arabidopsis: common and distinct targets of CYCD3;1, E2Fa and E2Fc. Plant Mol. Biol., 2009. 71(4-5): p. 345-65 [PMID:19662336] 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] Jurado S, et al. The Arabidopsis cell cycle F-box protein SKP2A binds to auxin. Plant Cell, 2010. 22(12): p. 3891-904 [PMID:21139066] Heckmann S, et al. The E2F transcription factor family regulates CENH3 expression in Arabidopsis thaliana. Plant J., 2011. 68(4): p. 646-56 [PMID:21771121] 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] Hirano H,Shinmyo A,Sekine M Both negative and positive G1 cell cycle regulators undergo proteasome-dependent degradation during sucrose starvation in Arabidopsis. Plant Signal Behav, 2011. 6(9): p. 1394-6 [PMID:22019639] Gaudinier A, et al. Enhanced Y1H assays for Arabidopsis. Nat. Methods, 2011. 8(12): p. 1053-5 [PMID:22037706] Cruz-Ram A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division. Cell, 2012. 150(5): p. 1002-15 [PMID:22921914] 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] Kobayashi K, et al. Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J., 2015. 34(15): p. 1992-2007 [PMID:26069325] Li B, et al. Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. Plant Cell, 2018. 30(1): p. 178-195 [PMID:29317470] Huntley R, et al. The maize retinoblastoma protein homologue ZmRb-1 is regulated during leaf development and displays conserved interactions with G1/S regulators and plant cyclin D (CycD) proteins. Plant Mol. Biol., 1998. 37(1): p. 155-69 [PMID:9620273]