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_01960.1_g00007.1

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

bHLH

Protein Properties

Length: 335aa MW: 36890.7 Da PI: 4.9455

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_01960.1_g00007.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	15.9	2.3e-05	168	208	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 ++ +iN+++ +L++llP++ +K + + L +A++Y+ Lq Rsa1.0_01960.1_g00007.1 168 KQKQTDINKKMRNLQDLLPNS-----QKDDNEALLDEAINYMTTLQ 208 333357************9.....8*************9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	10.391	158	207	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	6.2E-8	163	218	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	8.58E-5	164	212	No hit	No description
SuperFamily	SSF47459	2.62E-9	166	225	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: 335 aa Download sequence Send to blast
MVQGVPSNMD LIGRLRVVQS GGLTDQEYME LVFENGQILA KSQRSNGLSL QNQRTKSIVD 60 LYEAEYNEDF KKSVHIHDVD TSNKNLVDTQ TLKASSSKRM VVDYENRNDI VPPDEQSAVA 120 ERSVELGYES TDFTEDSEES TYQSSSLDDV RPQVPAITSK VLVKRRRKQK QTDINKKMRN 180 LQDLLPNSQK DDNEALLDEA INYMTTLQLQ VQMMAMGNRF VTPATVLPLG PHYSQMGLAT 240 GMPMGVPQLL PAPVLGAGLP LVGNSPDVLR VLNHPGLMPI QNSALFTPTE NYLPQSVPPP 300 SAALPKKIPN PTTSSNLNDA SQMGGNLSVK ESDKP

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	162	169	VKRRRKQK

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_01960.1_g00007.1

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-118	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-131	PIF6_ARATH; Transcription factor PIF6
TrEMBL	A0A0D3DV12	0.0	A0A0D3DV12_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6FJ66	0.0	A0A3P6FJ66_BRAOL; Uncharacterized protein
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-109	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]