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_013584111.1

Organism

Brassica oleracea

Taxonomic ID

3712

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: 282aa MW: 31912.6 Da PI: 6.5855

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013584111.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	20.3	9.8e-07	133	173	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 rrR d + +++ +L++llP++ K + +++L kA+ Y+k+Lq XP_013584111.1 133 RRRNDMLSNKMRKLQKLLPNC-----HKEDTVSVLDKAIVYMKDLQ 173 666666799*********9.....699**************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	11.687	123	172	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	2.88E-10	132	181	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.71E-8	132	177	No hit	No description
Gene3D	G3DSA:4.10.280.10	3.4E-9	133	180	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009642	Biological Process	response to light intensity
GO:0009738	Biological Process	abscisic acid-activated signaling pathway
GO:0010218	Biological Process	response to far red light
GO:0005634	Cellular Component	nucleus
GO:0005829	Cellular Component	cytosol
GO:0003712	Molecular Function	transcription cofactor activity
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 282 aa Download sequence Send to blast
MELGWNNDVG SLAVKDRGIS ERARSDKERL ITGLKSSYGY VDHDQTYIQF QTVPEIHREE 60 ENSEKDLTLA VPDEHSETGD HHDHQIYDFS DNXYYLRNKH VKPKRSRIEI FSDDESEGFT 120 REVPTVTSKG FKRRRNDMLS NKMRKLQKLL PNCHKEDTVS VLDKAIVYMK DLQLQLQVMS 180 IMGMNPYFAQ ATINFGMHND LVTAMAIAQG INLVNQTTSS PLIPASNSPL PPFINLSIPH 240 TSNQSLFPTT ALPASSTQCL CGLVPXFPSF LDFSSHTMVG RL

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
UniProt	Atypical bHLH transcription factor that regulates photomorphogenesis through modulation of phytochrome (e.g. PHYA) and cryptochrome signalings (Ref.4, PubMed:11090209, PubMed:10995393, PubMed:19482971). Suppresses the transcriptional regulation activity of PIF4 by forming non-DNA-binding heterodimer. {ECO:0000269\|PubMed:10995393, ECO:0000269\|PubMed:11090209, ECO:0000269\|PubMed:19482971, ECO:0000269\|Ref.4}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013584111.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Twofold induction by far-red light and 14-fold suppression by red light.

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_013584111.1	0.0	PREDICTED: LOW QUALITY PROTEIN: transcription factor HFR1
Swissprot	Q9FE22	1e-132	HFR1_ARATH; Transcription factor HFR1
TrEMBL	A0A3P6EV42	0.0	A0A3P6EV42_BRAOL; Uncharacterized protein
STRING	Bra033315.1-P	1e-141	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM14015	16	24

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G02340.1	1e-134	bHLH family protein

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] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Bou-Torrent J, et al. Plant proximity perception dynamically modulates hormone levels and sensitivity in Arabidopsis. J. Exp. Bot., 2014. 65(11): p. 2937-47 [PMID:24609653] 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] 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] Sheerin DJ, et al. Light-activated phytochrome A and B interact with members of the SPA family to promote photomorphogenesis in Arabidopsis by reorganizing the COP1/SPA complex. Plant Cell, 2015. 27(1): p. 189-201 [PMID:25627066] Karumuri S,Bandopadhyay R In silico analysis of the structure and interaction of COP1 protein of Arabidopsis thaliana. Indian J. Biochem. Biophys., 2014. 51(5): p. 343-9 [PMID:25630103] Tan CM, et al. Arabidopsis HFR1 is a potential nuclear substrate regulated by the Xanthomonas type III effector XopD(Xcc8004). PLoS ONE, 2015. 10(2): p. e0117067 [PMID:25647296] Singh SP,Singh SP,Pandey T,Singh RR,Sawant SV A novel male sterility-fertility restoration system in plants for hybrid seed production. Sci Rep, 2015. 5: p. 11274 [PMID:26073981] Bou-Torrent J, et al. Regulation of Carotenoid Biosynthesis by Shade Relies on Specific Subsets of Antagonistic Transcription Factors and Cofactors. Plant Physiol., 2015. 169(3): p. 1584-94 [PMID:26082398] Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance. New Phytol., 2016. 211(3): p. 967-79 [PMID:27105120] Hayes S, et al. UV-B Perceived by the UVR8 Photoreceptor Inhibits Plant Thermomorphogenesis. Curr. Biol., 2017. 27(1): p. 120-127 [PMID:27989670] 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] Xu X, et al. Reciprocal proteasome-mediated degradation of PIFs and HFR1 underlies photomorphogenic development in Arabidopsis. Development, 2017. 144(10): p. 1831-1840 [PMID:28420710] Woloszynska M, et al. The Elongator complex regulates hypocotyl growth in darkness and during photomorphogenesis. J. Cell. Sci., 2019. [PMID:28720596] Yan J, et al. Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis. Plant Cell, 2017. 29(12): p. 3012-3029 [PMID:29114014] Singh M,Gupta A,Singh D,Khurana JP,Laxmi A Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth. Sci Rep, 2017. 7(1): p. 16101 [PMID:29170398] Li R, et al. Nitric oxide promotes light-initiated seed germination by repressing PIF1 expression and stabilizing HFR1. Plant Physiol. Biochem., 2018. 123: p. 204-212 [PMID:29248678]