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

GSBRNA2T00097758001

Common Name

GSBRNA2T00097758001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 272aa MW: 29807.9 Da PI: 8.6065

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00097758001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	26.6	1.1e-08	112	143	4	37
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS- CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskK 37 h+ Er+RR++i +++ eL++llP+++ ++ K GSBRNA2T00097758001 112 VHKLSERKRRNEISKKLCELQDLLPNCY--KDDK 143 6999**********************74..4444 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00083	2.50E-7	106	144	No hit	No description
SuperFamily	SSF47459	6.54E-8	106	144	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	9.782	108	169	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.1E-8	111	143	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	2.5E-6	112	143	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 272 aa Download sequence Send to blast
MVIFSSLLHI LDLYETEYDE GFKKNIKNLG GSQVVPNVEV ITAPPDEQSI AVGRSAELYF 60 ASSSMLSGGT SRDLKLLFFK KEKSDDGSDD GKTRVTATTR KTVAKKKRST EVHKLSERKR 120 RNEISKKLCE LQDLLPNCYK DDKMMSMGNG IIPSTSTMLA MGHYSPTGLR MHMGEAATTT 180 SVPQFLPMNL QGTGFSRINE ASSQMLSNFL NHHTGLIPNS PIFSPLESCS HQFVVPSCFP 240 GTHSTSFTPF SKSAPTSNLE DAMQFKGSNG Y*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	105	120	KKRSTEVHKLSERKRR

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Etiolated seedlings. {ECO:0000269\|PubMed:12826627}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor. Involved in responses to transient and long-term shade. Required for the light-mediated inhibition of hypocotyl elongation. Necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. Seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00097758001

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Expressed with a circadian rhythm showing peaks during the light period. Up-regulated by simulated shade in light-grown plants, in a phytochrome-dependent manner; low red/far-red ratio (R/FR) light, but repressed by a high R/FR light. Rapidly down-regulated after seedling deetiolation. {ECO:0000269\|PubMed:14668869, ECO:0000269\|PubMed:16565297, ECO:0000269\|PubMed:16891401}.

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	AC232491	0.0	AC232491.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB049N04, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013740663.1	1e-152	transcription factor PIL1
Swissprot	Q8L5W8	1e-105	PIL1_ARATH; Transcription factor PIL1
TrEMBL	A0A078ILN4	0.0	A0A078ILN4_BRANA; BnaC03g72400D protein
STRING	Bo3g039450.1	1e-173	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13937	17	25

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G46970.1	1e-90	phytochrome interacting factor 3-like 1

Publications ? help Back to Top
Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Luo Q, et al. COP1 and phyB Physically Interact with PIL1 to Regulate Its Stability and Photomorphogenic Development in Arabidopsis. Plant Cell, 2014. 26(6): p. 2441-2456 [PMID:24951480] Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] Kasulin L, et al. A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina. Mol. Ecol., 2017. 26(13): p. 3389-3404 [PMID:28316114]