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

RrC2707_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

E2F/DP

Protein Properties

Length: 308aa MW: 34267.8 Da PI: 4.4992

Description

E2F/DP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC2707_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	76.3	3e-24	59	117	7	70
E2F_TDP 7 rlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwk 70 +llt+kf++l++++e+gi++ln++a++L +v ++RRiYDi+NVLe+++liek+ kn+i+w+ RrC2707_p1 59 GLLTKKFINLIKQAEDGILDLNKAADTL---EV--QKRRIYDITNVLEGIGLIEKTLKNRIQWN 117 689***********************...99..**************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01372	8.8E-26	53	118	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Pfam	PF02319	8.2E-22	59	117	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Gene3D	G3DSA:1.10.10.10	8.4E-24	59	116	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF46785	1.09E-15	59	116	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF144074	1.07E-10	115	142	No hit	No description
Pfam	PF16421	6.2E-13	121	196	IPR032198	E2F transcription factor, CC-MB domain
SuperFamily	SSF144074	1.07E-10	179	198	No hit	No description

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

Sequence ? help Back to Top
Protein Sequence Length: 308 aa Download sequence Send to blast
MLDLESMLTD MVNQNEPSEL NAGVLQTPIS GKGGKAKKSS RSVKYNKIGT QASAGFNAGL 60 LTKKFINLIK QAEDGILDLN KAADTLEVQK RRIYDITNVL EGIGLIEKTL KNRIQWNIDL 120 NKTLIAVKAP HGTTLEVPDP DEVCLSAHKR NAQHTLCNCF SIFITYPSIN QAGGYPQRRY 180 RIILRSTMGP IDVYLVSQFE ERFEDIPDVD DPSNVPSTSG IPENQDVAVP MGEDSTIKNM 240 ETQEVDDTKR VYSDMESHDF VDGIMKIVPP DLDTDVDYWL RSEVGEVSIT DMWPNECILN 300 SVTSSALI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1cf7_A	5e-21	49	116	3	71	PROTEIN (TRANSCRIPTION FACTOR E2F-4)
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The binding of retinoblastoma-related proteins represses transactivation. Involved in the control of cell-cycle progression from G1 to S phase and from G2 to M phase. Stimulates cell proliferation and delays differentiation. Represses cell enlargement and endoreduplication in auxin-free conditions. {ECO:0000269\|PubMed:11669580, ECO:0000269\|PubMed:11786543, ECO:0000269\|PubMed:11862494, ECO:0000269\|PubMed:11891240, ECO:0000269\|PubMed:12913157, ECO:0000269\|PubMed:16055635, ECO:0000269\|PubMed:16514015}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated by light and by auxin. May be up-regulated by E2FA. {ECO:0000269\|PubMed:16055635, ECO:0000269\|PubMed:16514015, ECO:0000269\|PubMed:18424613}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JN942988	1e-150	JN942988.1 Brassica juncea E2F transcription factor (E2Fb) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013622097.1	1e-140	PREDICTED: transcription factor E2FB-like
Refseq	XP_013682231.1	1e-140	transcription factor E2FB
Swissprot	Q9FV71	1e-92	E2FB_ARATH; Transcription factor E2FB
TrEMBL	A0A0D3B298	1e-137	A0A0D3B298_BRAOL; Uncharacterized protein
STRING	Bo3g015790.1	1e-138	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM808	28	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G22220.2	3e-84	E2F transcription factor 1

Publications ? help Back to Top
Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] Wu M,Liu L,Hijazi H,Chan C A multi-layer inference approach to reconstruct condition-specific genes and their regulation. Bioinformatics, 2013. 29(12): p. 1541-52 [PMID:23610368] Kobayashi K, et al. Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J., 2015. 34(15): p. 1992-2007 [PMID:26069325]