PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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: 312aa MW: 35860 Da PI: 8.6135

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009118778.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	25.4	2.5e-08	175	215	10	55
HHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 10 rrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r R d + +++ +L++l+P++ K +K+++L k++eY+k+Lq XP_009118778.1 175 RIRDDMMSNKMRTLQQLVPNC-----HKTDKVSVLDKTIEYMKNLQ 215 666777999*********9.....6****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	12.963	165	214	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.22E-9	169	219	No hit	No description
SuperFamily	SSF47459	3.14E-12	170	223	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.1E-7	170	220	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.2E-10	175	222	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.3E-5	175	215	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: 312 aa Download sequence Send to blast
MGFHFLGQIL SPLPHRIIFS NPLSPLSLWF VNMLNNQDLM GLEWTNDVES LALKDQDISV 60 RARSGEDRIT NGLKWSDDYF YYDQADFHLQ IVPEIRKEEE NSKKDLTLVV PDEHSETGDH 120 HLHIKDYSDS SYNRRFLRNK HAKPKRRRVQ ILSDDESGDF SRKVPLVIRK SSKRRIRDDM 180 MSNKMRTLQQ LVPNCHKTDK VSVLDKTIEY MKNLQLQLQV MSIMGMNPYI PQATLNFGMH 240 NHLLRAMGIA HGLNPAKQTT LSPLIAGSNW PSPPFSHLSF PHSSNQSLFP TPASSPQCLC 300 GLVPCFPSDF FF

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	144	148	KRRRV

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_009118778.1

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_009118778.1	0.0	PREDICTED: transcription factor HFR1-like isoform X1
Swissprot	Q9FE22	1e-130	HFR1_ARATH; Transcription factor HFR1
TrEMBL	A0A397YEL7	0.0	A0A397YEL7_BRACM; Uncharacterized protein
STRING	Bo8g117510.1	0.0	(Brassica oleracea)

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-121	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]