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_03378.1_g00005.1

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

G2-like

Protein Properties

Length: 250aa MW: 26758.2 Da PI: 4.4115

Description

G2-like family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_03378.1_g00005.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	G2-like	95.7	3.6e-30	151	204	1	55
G2-like 1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 +prl+Wtp+LH+rFv++v++L G ++A+Pkti++lm+v+gLt+e+v+SHLQkYRl Rsa1.0_03378.1_g00005.1 151 RPRLVWTPQLHKRFVDVVAHL-GVKNAVPKTIMQLMNVEGLTRENVASHLQKYRL 204 59*****************.9*****************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	10.643	146	207	IPR017930	Myb domain
SuperFamily	SSF46689	1.08E-19	148	208	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	2.6E-30	150	209	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	1.6E-23	152	204	IPR006447	Myb domain, plants
Pfam	PF00249	9.7E-9	154	203	IPR001005	SANT/Myb domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 250 aa Download sequence Send to blast
MGEEVRMSDY DVSGDGDRVL EWEMGLPSDD DLTSLSYSLI PPNLAMAFSI TPEKSRTIED 60 VNRASETTFS SLRSGGSSGL NTSSSNNNNN NSVAAEEEDE EEEDRVGSSS PGSDSKKQKT 120 SGDGVDLSPS AAAAEEGDSG TEDPTGKTLK RPRLVWTPQL HKRFVDVVAH LGVKNAVPKT 180 IMQLMNVEGL TRENVASHLQ KYRLYLKRMQ GLTTEGPSSS DKLFSSTPVP PQSFQELGGG 240 NGNGQGNVSA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5lxu_A	2e-36	151	207	1	57	Transcription factor LUX
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that is essential for the generation of the circadian clock oscillation. Is necessary for activation of CCA1 and LHY expression. Is coregulated with TOC1 and seems to be repressed by CCA1 and LHY by direct binding of these proteins to the evening element in the LUX promoter. Directly regulates the expression of PRR9, a major component of the morning transcriptional feedback circuit, by binding specific sites on PRR9 promoter. Binds to its own promoter, inducing a negative auto-regulatory feedback loop within the core clock. Binds to ELF3 and associates with ELF4 in a diurnal complex which is required for the expression of the growth-promoting transcription factors PIF4 and PIF5 and subsequent hypocotyl growth in the early evening. {ECO:0000269\|PubMed:16006522, ECO:0000269\|PubMed:16164597, ECO:0000269\|PubMed:21236673, ECO:0000269\|PubMed:21753751, ECO:0000269\|PubMed:22311777}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_03378.1_g00005.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian oscillation with peaks at subjective dusk. {ECO:0000269\|PubMed:16006522, ECO:0000269\|PubMed:16164597, ECO:0000269\|PubMed:17132630, ECO:0000269\|PubMed:21753751}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018440641.1	0.0	PREDICTED: transcription factor LUX
Swissprot	Q9SNB4	1e-136	PCL1_ARATH; Transcription factor LUX
TrEMBL	M4DNW6	1e-140	M4DNW6_BRARP; Uncharacterized protein
STRING	Bra018204.1-P	1e-141	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4055	27	58

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G46640.2	1e-105	G2-like family protein

Publications ? help Back to Top
Higham CF,Husmeier D A Bayesian approach for parameter estimation in the extended clock gene circuit of Arabidopsis thaliana. BMC Bioinformatics, 2013. 14 Suppl 10: p. S3 [PMID:24267177]