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; Camelineae; Arabidopsis

Family

bHLH

Protein Properties

Length: 234aa MW: 25487.9 Da PI: 8.8356

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G54680.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	36.8	7.2e-12	75	122	4	54
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksL 54 ++ rE++RRdr+N++f eL +l + + +K +Ka+iL Av+ + +L AT5G54680.1 75 SKACREKQRRDRLNDKFMELGAILEPG---NPPKTDKAAILVDAVRMVTQL 122 5678********************8...78************99988 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	9.95E-14	62	137	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	4.02E-10	69	127	No hit	No description
PROSITE profile	PS50888	13.497	71	122	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.7E-13	74	144	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.6E-9	75	122	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.3E-9	77	128	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd14686	0.00513	137	169	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 234 aa Download sequence Send to blast
MVSPENANWI CDLIDADYGS FTIQGPGFSW PVQQPIGVSS NSSAGVDGSA GNSEASKEPG 60 SKKRGRCESS SATSSKACRE KQRRDRLNDK FMELGAILEP GNPPKTDKAA ILVDAVRMVT 120 QLRGEAQKLK DSNSSLQDKI KELKTEKNEL RDEKQRLKTE KEKLEQQLKA MNAPQPSFFP 180 APPMMPTAFA SAQGQAPGNK MVPIISYPGV AMWQFMPPAS VDTSQDHVLR PPVA

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.9639	0.0	bud\| flower\| leaf\| root\| seed\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145359245	0.0
Genevisible	248171_at	0.0
Expression Atlas	AT5G54680	-
AtGenExpress	AT5G54680	-
ATTED-II	AT5G54680	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Widely expressed throughout development, mostly in vasculatures. {ECO:0000269\|PubMed:17028341}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor. Plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. May regulate gene expression in response to metal homeostasis changes. {ECO:0000269\|PubMed:17028341}.

Function -- GeneRIF ? help Back to Top
bHLH104 and ILR3 play pivotal roles in the regulation of Fe deficiency responses. [PMID: 25794933] The AMV CP-ILR3 interaction may down-regulate a host factor, NEET, leading to the activation of plant hormone responses to obtain a hormonal equilibrium state, where infection remains at a level that does not affect plant viability. [PMID: 26929142] The transcription factor IAA-LEUCINE RESISTANT3 (ILR3) regulates iron deficiency response, aliphatic glucosinolate (GLS) biosynthesis and pathogen response. [PMID: 29882068]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G54680.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9FH37

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Plants are more sensitive to IAA conjugates. {ECO:0000269\|PubMed:17028341}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G54680

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF488629	0.0	AF488629.1 Arabidopsis thaliana clone bHLH105 putative bHLH transcription factor mRNA, complete cds.
GenBank	AY054585	0.0	AY054585.1 Arabidopsis thaliana Unknown protein (At5g54680; K5F14.2) mRNA, complete cds.
GenBank	BT002189	0.0	BT002189.1 Arabidopsis thaliana Unknown protein (At5g54680) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_200279.1	1e-173	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Refseq	XP_020888968.1	1e-173	transcription factor ILR3
Swissprot	Q9FH37	1e-174	ILR3_ARATH; Transcription factor ILR3
TrEMBL	A0A178UAU8	1e-171	A0A178UAU8_ARATH; ILR3
TrEMBL	D7MUC3	1e-171	D7MUC3_ARALL; Uncharacterized protein
STRING	AT5G54680.1	1e-172	(Arabidopsis thaliana)
STRING	fgenesh2_kg.8__1365__AT5G54680.1	1e-172	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM1437	28	90
Representative plant	OGRP755	17	66

Link Out ? help Back to Top
Phytozome	AT5G54680.1
Entrez Gene	835557
iHOP	AT5G54680
wikigenes	AT5G54680

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Rampey RA, et al. An Arabidopsis basic helix-loop-helix leucine zipper protein modulates metal homeostasis and auxin conjugate responsiveness. Genetics, 2006. 174(4): p. 1841-57 [PMID:17028341] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Jaspers P, et al. Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors. Plant J., 2009. 60(2): p. 268-79 [PMID:19548978] Long TA, et al. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell, 2010. 22(7): p. 2219-36 [PMID:20675571] Meinke DW A survey of dominant mutations in Arabidopsis thaliana. Trends Plant Sci., 2013. 18(2): p. 84-91 [PMID:22995285] Selote D,Samira R,Matthiadis A,Gillikin JW,Long TA Iron-binding E3 ligase mediates iron response in plants by targeting basic helix-loop-helix transcription factors. Plant Physiol., 2015. 167(1): p. 273-86 [PMID:25452667] Zhang J, et al. The bHLH transcription factor bHLH104 interacts with IAA-LEUCINE RESISTANT3 and modulates iron homeostasis in Arabidopsis. Plant Cell, 2015. 27(3): p. 787-805 [PMID:25794933] Li X,Zhang H,Ai Q,Liang G,Yu D Two bHLH Transcription Factors, bHLH34 and bHLH104, Regulate Iron Homeostasis in Arabidopsis thaliana. Plant Physiol., 2016. 170(4): p. 2478-93 [PMID:26921305] Aparicio F,Pallás V The coat protein of Alfalfa mosaic virus interacts and interferes with the transcriptional activity of the bHLH transcription factor ILR3 promoting salicylic acid-dependent defence signalling response. Mol. Plant Pathol., 2017. 18(2): p. 173-186 [PMID:26929142] Liang G,Zhang H,Li X,Ai Q,Yu D bHLH transcription factor bHLH115 regulates iron homeostasis in Arabidopsis thaliana. J. Exp. Bot., 2017. 68(7): p. 1743-1755 [PMID:28369511] Ezer D, et al. The G-Box Transcriptional Regulatory Code in Arabidopsis. Plant Physiol., 2017. 175(2): p. 628-640 [PMID:28864470] Li B, et al. Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. Plant Cell, 2018. 30(1): p. 178-195 [PMID:29317470] Min JH, et al. Arabidopsis Basic Helix-Loop-Helix 34 (bHLH34) Is Involved in Glucose Signaling through Binding to a GAGA Cis-Element. Front Plant Sci, 2017. 8: p. 2100 [PMID:29321786] Samira R, et al. The bHLH transcription factor ILR3 modulates multiple stress responses in Arabidopsis. Plant Mol. Biol., 2018. 97(4-5): p. 297-309 [PMID:29882068]