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

RrC20109_p2

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

G2-like

Protein Properties

Length: 181aa MW: 19811.3 Da PI: 8.054

Description

G2-like family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC20109_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	G2-like	95.2	5e-30	26	78	2	55
G2-like 2 prlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 +rl+Wtp+LH+rFv++v++L G ++A+Pkti++lm+v+gLt+e+v+SHLQkYRl RrC20109_p2 26 ARLVWTPQLHKRFVDVVAHL-GVKNAVPKTIMQLMNVEGLTRENVASHLQKYRL 78 79****************.9*****************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51294	10.931	20	81	IPR017930	Myb domain
SuperFamily	SSF46689	1.27E-19	22	82	IPR009057	Homeodomain-like
Gene3D	G3DSA:1.10.10.60	4.6E-30	24	83	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	1.2E-23	26	78	IPR006447	Myb domain, plants
Pfam	PF00249	5.5E-9	28	77	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: 181 aa Download sequence Send to blast
IISEEDEGGD SGTEDLTTNG KTLKRARLVW TPQLHKRFVD VVAHLGVKNA VPKTIMQLMN 60 VEGLTRENVA SHLQKYRLYL KRMQGLTSEG PSSSDKLFSS TPVPPQSFQE HVGVPPPPPM 120 MQMPVYAHHM GMQGYHHQSN AHDPYHHGSG GGPANPYMMQ QNKFGSVASY PPVGGGSANE 180 N

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5lxu_A	5e-34	25	81	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}.

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_018454023.1	1e-112	PREDICTED: transcription factor LUX-like
Refseq	XP_018454028.1	1e-112	PREDICTED: transcription factor LUX-like
Swissprot	Q9SNB4	6e-97	PCL1_ARATH; Transcription factor LUX
TrEMBL	A0A0D3A8V0	1e-105	A0A0D3A8V0_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6FEQ7	1e-105	A0A3P6FEQ7_BRAOL; Uncharacterized protein
STRING	Bo1g070860.1	1e-105	(Brassica oleracea)

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	6e-90	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]