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

Rsa1.0_00010.1_g00026.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 410aa MW: 45702.1 Da PI: 4.4331

Description

E2F/DP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00010.1_g00026.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	85.5	4.2e-27	118	183	1	71
E2F_TDP 1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 r+++sL llt+kf++l++++e+gi++ln++a++L +v ++RRiYDi+NVLe+++liek+ kn+i+wkg Rsa1.0_00010.1_g00026.1 118 RYDSSLALLTKKFINLIKQAEDGILDLNKAADTL---EV--QKRRIYDITNVLEGIGLIEKTLKNRIKWKG 183 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	1.3E-28	115	185	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF46785	2.45E-17	118	181	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	3.4E-34	118	183	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Pfam	PF02319	3.8E-24	120	183	IPR003316	E2F/DP family, winged-helix DNA-binding domain
CDD	cd14660	1.81E-44	194	300	No hit	No description
SuperFamily	SSF144074	1.15E-31	195	300	No hit	No description
Pfam	PF16421	9.3E-32	199	298	IPR032198	E2F transcription factor, CC-MB domain

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: 410 aa Download sequence Send to blast
MSDPHQQPER NQPYNRQHHP SVASMKPPLV APGEYHRFDA AETHGGGGGP DQVSEEIVIK 60 SSLKRKTDLV DEPIEFNTGV LQTPVPGKGG KAKKSSRSYV KSNAGSPGNN LAQAGACRYD 120 SSLALLTKKF INLIKQAEDG ILDLNKAADT LEVQKRRIYD ITNVLEGIGL IEKTLKNRIK 180 WKGLDVSNPG ETMENIANLQ DELQNLAFEE AKLDDQIRES QERLTSLSED ENNKRLLFVT 240 EDDIKNLPCF QNSTLIAVKA PHGTTLEVPD PDEAGGYPQR RYRIILRSTM GPIDVYLVSQ 300 FEETFEDIPN ADEPSNVPST SGLPDNQDVS MPMKEDITVK NMETQEVDDT HRVSSDVESH 360 DFVDGIMKIV PPDLDMDVDY WLRSEVGEVS ITDMWPNECI LDPVTFFALI

Sequence ? help Back to Top

Protein Sequence Length: 410 aa Download sequence Send to blast

MSDPHQQPER NQPYNRQHHP SVASMKPPLV APGEYHRFDA AETHGGGGGP DQVSEEIVIK  60
SSLKRKTDLV DEPIEFNTGV LQTPVPGKGG KAKKSSRSYV KSNAGSPGNN LAQAGACRYD  120
SSLALLTKKF INLIKQAEDG ILDLNKAADT LEVQKRRIYD ITNVLEGIGL IEKTLKNRIK  180
WKGLDVSNPG ETMENIANLQ DELQNLAFEE AKLDDQIRES QERLTSLSED ENNKRLLFVT  240
EDDIKNLPCF QNSTLIAVKA PHGTTLEVPD PDEAGGYPQR RYRIILRSTM GPIDVYLVSQ  300
FEETFEDIPN ADEPSNVPST SGLPDNQDVS MPMKEDITVK NMETQEVDDT HRVSSDVESH  360
DFVDGIMKIV PPDLDMDVDY WLRSEVGEVS ITDMWPNECI LDPVTFFALI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1cf7_A	2e-23	117	184	6	74	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00010.1_g00026.1

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	AF400000	0.0	AF400000.1 Thlaspi caerulescens E2F-related transcription factor 1 (E2F1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018443113.1	0.0	PREDICTED: transcription factor E2FB-like
Refseq	XP_018445774.1	0.0	PREDICTED: transcription factor E2FB-like
Swissprot	Q9FV71	0.0	E2FB_ARATH; Transcription factor E2FB
TrEMBL	A0A397XKS4	0.0	A0A397XKS4_BRACM; Uncharacterized protein
STRING	Bra002398.1-P	0.0	(Brassica rapa)

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
AT5G22220.3	0.0	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]