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

XP_009116882.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 352aa MW: 39486.9 Da PI: 4.9699

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009116882.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	12.9	0.00021	175	225	5	55
HHHHHHHHH.....HHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 5 hnerErrRR.....driNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 n+ +rRR ++iN+++ +L++llP++ +K + + L +A++Y+ Lq XP_009116882.1 175 SNILVKRRRkqketNDINKKMRNLQDLLPNS-----QKEDNEALLDEAINYMTTLQ 225 5566666662222257************9.....799999********9998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	1.4E-8	173	235	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.41E-5	173	229	No hit	No description
SuperFamily	SSF47459	1.44E-9	175	243	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	10.036	175	224	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: 352 aa Download sequence Send to blast
MQMMFVLTKL IYCCCRLTDQ EYMELVFENG QILAKSQRSN GFSMHNQRTK SIVDLYEAEY 60 NEDFKKTIHG ADTSDKNLVD TQVVPEPLVV AAYETNMLMN QLNLIQSLKA SSSKRMVVDY 120 ENRKDIVPPD EQSVVAERSV ELGYDSTDFT EDSEESTYQS SSLDDVRPQV PARTSNILVK 180 RRRKQKETND INKKMRNLQD LLPNSQKEDN EALLDEAINY MTTLQHQVQM MTMGKRFVTP 240 ATMLPLGPQY SQMGLATGMQ MGVPQLLPAP VLGAGLPLVN TQADVLRVLN HPVLMPIQNS 300 APFTPMQNYL PQYVPPACAA FPNLIPNSTT SSNLDDARTH GGNLSGKESD KP

Sequence ? help Back to Top

Protein Sequence Length: 352 aa Download sequence Send to blast

MQMMFVLTKL IYCCCRLTDQ EYMELVFENG QILAKSQRSN GFSMHNQRTK SIVDLYEAEY  60
NEDFKKTIHG ADTSDKNLVD TQVVPEPLVV AAYETNMLMN QLNLIQSLKA SSSKRMVVDY  120
ENRKDIVPPD EQSVVAERSV ELGYDSTDFT EDSEESTYQS SSLDDVRPQV PARTSNILVK  180
RRRKQKETND INKKMRNLQD LLPNSQKEDN EALLDEAINY MTTLQHQVQM MTMGKRFVTP  240
ATMLPLGPQY SQMGLATGMQ MGVPQLLPAP VLGAGLPLVN TQADVLRVLN HPVLMPIQNS  300
APFTPMQNYL PQYVPPACAA FPNLIPNSTT SSNLDDARTH GGNLSGKESD KP

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	178	185	VKRRRKQK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.24337	4e-48	root\| silique

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009116882.1

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	0.0	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_018509580.1	0.0	PREDICTED: transcription factor PIF6 isoform X1
Swissprot	Q8L5W7	1e-151	PIF6_ARATH; Transcription factor PIF6
TrEMBL	A0A3P5YPE0	0.0	A0A3P5YPE0_BRACM; Uncharacterized protein
STRING	Bra007660.1-P	0.0	(Brassica rapa)

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-142	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]