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

RrC170_p12

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

bHLH

Protein Properties

Length: 320aa MW: 35639 Da PI: 4.9328

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC170_p12	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	16.2	2e-05	153	193	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 ++ +iN+++ L++llP+a +K + + L +A++Y+ Lq RrC170_p12 153 KQKQTNINKRMRDLQDLLPNA-----QKDDNEALLNEAINYMTTLQ 193 233358************9.....8*************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	4.5E-9	142	204	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	7.31E-6	142	197	No hit	No description
PROSITE profile	PS50888	10.245	143	192	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	5.1E-10	150	214	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010017	Biological Process	red or far-red light signaling pathway
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 320 aa Download sequence Send to blast
MNHVAFTLTD QEYMELVFEN GQILAKSQRS NGLSLQNQRT KSIVDLYEAE YNEDFKKSVH 60 IHDVGTSNKN LIDTQTLKAS SSKRMVVDYE NRNDIVPPDE QSAVAERSVE LDYESTDFTE 120 DSEESTYQSS SLDDLRSQVP ARTSKVLVKR RRKQKQTNIN KRMRDLQDLL PNAQKDDNEA 180 LLNEAINYMT TLQLQVQMMT MGNRFVTPAT MLPLAPHYSQ MGLATGMQMG VPQLLPAPVI 240 GAGFPLVGNS PDVLRVLNHP GLMPIQNSAL FTPTENYVPQ FVPPACAAFP NQIPNSTTSS 300 NLNDARTDGG NLSGKESDKP

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	147	154	VKRRRKQK

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	AC172877	1e-128	AC172877.1 Brassica rapa subsp. oleifera cultivar Inbred line 'Chiifu' clone KBrH042F19, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018493597.1	0.0	PREDICTED: LOW QUALITY PROTEIN: transcription factor PIF6
Swissprot	Q8L5W7	1e-130	PIF6_ARATH; Transcription factor PIF6
TrEMBL	A0A0D3DV12	0.0	A0A0D3DV12_BRAOL; Uncharacterized protein
TrEMBL	A0A3P5YPE0	0.0	A0A3P5YPE0_BRACM; Uncharacterized protein
TrEMBL	A0A3P6FJ66	0.0	A0A3P6FJ66_BRAOL; Uncharacterized protein
STRING	Bra007660.1-P	0.0	(Brassica rapa)
STRING	Bo02373s010.1	0.0	(Brassica oleracea)
STRING	Bo8g097630.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM13423	14	25

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G62090.2	1e-120	phytochrome interacting factor 3-like 2

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] 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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Adams E,Diaz C,Hong JP,Shin R 14-3-3 proteins participate in light signaling through association with PHYTOCHROME INTERACTING FACTORs. Int J Mol Sci, 2014. 15(12): p. 22801-14 [PMID:25501334] Galvão VC,Collani S,Horrer D,Schmid M Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana. Plant J., 2015. 84(5): p. 949-62 [PMID:26466761] Gomez EJ,Gerhardt K,Judd J,Tabor JJ,Suh J Light-Activated Nuclear Translocation of Adeno-Associated Virus Nanoparticles Using Phytochrome B for Enhanced, Tunable, and Spatially Programmable Gene Delivery. ACS Nano, 2016. 10(1): p. 225-37 [PMID:26618393] Ochoa-Fernandez R, et al. Optogenetics in Plants: Red/Far-Red Light Control of Gene Expression. Methods Mol. Biol., 2016. 1408: p. 125-39 [PMID:26965120] Gangl R,Tenhaken R Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark. Front Plant Sci, 2016. 7: p. 1115 [PMID:27507985] Paik I,Kathare PK,Kim JI,Huq E Expanding Roles of PIFs in Signal Integration from Multiple Processes. Mol Plant, 2017. 10(8): p. 1035-1046 [PMID:28711729]