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

Carubv10003027m

Common Name

CARUB_v10003027mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

E2F/DP

Protein Properties

Length: 472aa MW: 51722.2 Da PI: 4.4799

Description

E2F/DP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10003027m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	E2F_TDP	86.1	2.7e-27	132	197	1	71
E2F_TDP 1 rkeksLrlltqkflkllekseegivtlnevakeLvsedvknkrRRiYDilNVLealnliekkekneirwkg 71 r+++sL+llt+kf++l++++e+gi++ln++a++L +v ++RRiYDi+NVLe+++liek+ kn+i+wkg Carubv10003027m 132 RYDSSLGLLTKKFINLIKQAEDGILDLNKAAETL---EV--QKRRIYDITNVLEGIGLIEKTLKNRIQWKG 197 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	5.0E-29	129	199	IPR011991	Winged helix-turn-helix DNA-binding domain
SuperFamily	SSF46785	1.9E-17	132	195	IPR011991	Winged helix-turn-helix DNA-binding domain
SMART	SM01372	8.5E-35	132	197	IPR003316	E2F/DP family, winged-helix DNA-binding domain
Pfam	PF02319	2.0E-24	134	197	IPR003316	E2F/DP family, winged-helix DNA-binding domain
CDD	cd14660	3.53E-44	208	314	No hit	No description
SuperFamily	SSF144074	5.23E-32	210	314	No hit	No description
Pfam	PF16421	1.4E-31	213	312	IPR032198	E2F transcription factor, CC-MB domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008284	Biological Process	positive regulation of cell proliferation
GO:0009733	Biological Process	response to auxin
GO:0010090	Biological Process	trichome morphogenesis
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0051302	Biological Process	regulation of cell division
GO:0051446	Biological Process	positive regulation of meiotic cell cycle
GO:0005634	Cellular Component	nucleus
GO:0005667	Cellular Component	transcription factor complex
GO:0005737	Cellular Component	cytoplasm
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 472 aa Download sequence Send to blast
MSDEPEKFPP SKRQQQHPSL SSMKPPLVAP GEYHRFDSAE TRLAGGAAAA ADHLVSDSIV 60 IKSTLKRKTD AVNQIVEANE LSTGVLQTPV SGKGGKAKKT SRSAKSNKSG TQASGSNAGS 120 PGNNFAQAGT CRYDSSLGLL TKKFINLIKQ AEDGILDLNK AAETLEVQKR RIYDITNVLE 180 GIGLIEKTLK NRIQWKGLDV SKPGETIESI ANLQDEVHNL TVEEAKLDDQ IRDSQERLTS 240 LSEDENNKRL LFVTEDDIKN LPCFQNKTLI AVKAPHGTTL EVPDPDEAGG YSQRRYRMIL 300 RSTMGPIDVY LVSQFEESFE DIPHTDEPSK VPDEPSKVPD GPSNLPSTSG LPENHDVATP 360 MEEDSTERNM ETQELDDTQR VYSEIESHDF VDGIMKIVPP DLDMGVDYWL RSEVGEVSIT 420 DLWPDESGPD WNHLGSFDQN HAEPSNTTLE QPQTPSSPTP EDSTATRSTG S*

Sequence ? help Back to Top

Protein Sequence Length: 472 aa Download sequence Send to blast

MSDEPEKFPP SKRQQQHPSL SSMKPPLVAP GEYHRFDSAE TRLAGGAAAA ADHLVSDSIV  60
IKSTLKRKTD AVNQIVEANE LSTGVLQTPV SGKGGKAKKT SRSAKSNKSG TQASGSNAGS  120
PGNNFAQAGT CRYDSSLGLL TKKFINLIKQ AEDGILDLNK AAETLEVQKR RIYDITNVLE  180
GIGLIEKTLK NRIQWKGLDV SKPGETIESI ANLQDEVHNL TVEEAKLDDQ IRDSQERLTS  240
LSEDENNKRL LFVTEDDIKN LPCFQNKTLI AVKAPHGTTL EVPDPDEAGG YSQRRYRMIL  300
RSTMGPIDVY LVSQFEESFE DIPHTDEPSK VPDEPSKVPD GPSNLPSTSG LPENHDVATP  360
MEEDSTERNM ETQELDDTQR VYSEIESHDF VDGIMKIVPP DLDMGVDYWL RSEVGEVSIT  420
DLWPDESGPD WNHLGSFDQN HAEPSNTTLE QPQTPSSPTP EDSTATRSTG S*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1cf7_A	5e-24	132	198	7	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	Carubv10003027m

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	AF242580	0.0	AF242580.1 Arabidopsis thaliana E2F transcription factor-1 E2F1 mRNA, complete cds.
GenBank	AJ294533	0.0	AJ294533.1 Arabidopsis thaliana mRNA for E2F-related protein (e2Fb gene).
GenBank	AY136479	0.0	AY136479.1 Arabidopsis thaliana expressed protein (At5g22220) mRNA, complete cds.
GenBank	BT006610	0.0	BT006610.1 Arabidopsis thaliana At5g22220 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006289493.1	0.0	transcription factor E2FB
Swissprot	Q9FV71	0.0	E2FB_ARATH; Transcription factor E2FB
TrEMBL	R0FJU8	0.0	R0FJU8_9BRAS; Uncharacterized protein
STRING	XP_006289493.1	0.0	(Capsella rubella)

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	0.0	E2F transcription factor 1

Link Out ? help Back to Top
Phytozome	Carubv10003027m
Entrez Gene	17883604

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]