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

AT3G56970.1

Common Name

BHLH038, bHLH38, EN8, F24I3.50, ORG2

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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: 253aa MW: 28714.2 Da PI: 5.7006

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G56970.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	52.4	9.4e-17	72	124	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 ++ +hn+ Er RR++iN+ f+ Lr++lP + +skKls e++ k +YI +Lq AT3G56970.1 72 KKLNHNASERDRRKKINTLFSSLRSCLPAsD---QSKKLSIPETVSKSLKYIPELQ 124 6789***********************66...*****************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.964	71	123	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	6.24E-15	72	128	No hit	No description
Gene3D	G3DSA:4.10.280.10	9.4E-16	72	137	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	5.3E-14	72	124	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	6.54E-17	72	139	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.4E-12	77	129	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006357	Biological Process	regulation of transcription from RNA polymerase II promoter
GO:0010106	Biological Process	cellular response to iron ion starvation
GO:0055072	Biological Process	iron ion homeostasis
GO:0090575	Cellular Component	RNA polymerase II transcription factor complex
GO:0000977	Molecular Function	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 253 aa Download sequence Send to blast
MCALVPSFFT NFGWPSTNQY ESYYGAGDNL NNGTFLELTV PQTYEVTHHQ NSLGVSVSSE 60 GNEIDNNPVV VKKLNHNASE RDRRKKINTL FSSLRSCLPA SDQSKKLSIP ETVSKSLKYI 120 PELQQQVKRL IQKKEEILVR VSGQRDFELY DKQQPKAVAS YLSTVSATRL GDNEVMVQVS 180 SSKIHNFSIS NVLGGIEEDG FVLVDVSSSR SQGERLFYTL HLQVENMDDY KINCEELSER 240 MLYLYEKCEN SFN

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145339595	0.0
Expression Atlas	AT3G56970	-
AtGenExpress	AT3G56970	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Roots. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of the basic helix-loop-helix transcription factor family protein.

Function -- GeneRIF ? help Back to Top
AtbHLH38 and AtbHLH39 are induced under iron deficiency. They are involved in the iron deficiency induced synthesis and excretion of riboflavin or vitamin B2. [AtbHLH38] [PMID: 17260143]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G56970.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by OBP3, auxin and salicylic acid (SA). Repressed by jasmonic acid (JA), UV LIGHT, and heat treatments. Up regulated by iron deficiency in roots and leaves, as well as by nickel, high zinc or high copper treatments. Repressed by high iron, low copper and low zinc treatments. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:12887587, ECO:0000269\|PubMed:17516080}.

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

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT1G07640 (A), AT3G55370 (A)

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q9M1K1

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G56970

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF488576	0.0	AF488576.1 Arabidopsis thaliana clone bHLH038 putative bHLH transcription factor mRNA, complete cds.
GenBank	AK221542	0.0	AK221542.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL07-73-C01.
GenBank	BT026419	0.0	BT026419.1 Arabidopsis thaliana At3g56970 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191256.1	0.0	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Swissprot	Q9M1K1	0.0	ORG2_ARATH; Transcription factor ORG2
TrEMBL	A0A178VHQ5	0.0	A0A178VHQ5_ARATH; ORG2
STRING	AT3G56970.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM482	28	153
Representative plant	OGRP2826	11	29

Link Out ? help Back to Top
Phytozome	AT3G56970.1
Entrez Gene	824864
iHOP	AT3G56970
wikigenes	AT3G56970

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] Kang HG,Foley RC,Oñate-Sánchez L,Lin C,Singh KB Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid. Plant J., 2003. 35(3): p. 362-72 [PMID:12887587] 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] 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] Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J., 2004. 38(2): p. 366-79 [PMID:15078338] Fujita Y, et al. AREB1 Is a transcription activator of novel ABRE-dependent ABA signaling that enhances drought stress tolerance in Arabidopsis. Plant Cell, 2005. 17(12): p. 3470-88 [PMID:16284313] Yoine M,Ohto MA,Onai K,Mita S,Nakamura K The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay causes pleiotropic phenotypic changes and altered sugar signalling in Arabidopsis. Plant J., 2006. 47(1): p. 49-62 [PMID:16740149] Tran LS, et al. Co-expression of the stress-inducible zinc finger homeodomain ZFHD1 and NAC transcription factors enhances expression of the ERD1 gene in Arabidopsis. Plant J., 2007. 49(1): p. 46-63 [PMID:17233795] Vorwieger A, et al. Iron assimilation and transcription factor controlled synthesis of riboflavin in plants. Planta, 2007. 226(1): p. 147-58 [PMID:17260143] Wang HY, et al. Iron deficiency-mediated stress regulation of four subgroup Ib BHLH genes in Arabidopsis thaliana. Planta, 2007. 226(4): p. 897-908 [PMID:17516080] Yuan Y, et al. FIT interacts with AtbHLH38 and AtbHLH39 in regulating iron uptake gene expression for iron homeostasis in Arabidopsis. Cell Res., 2008. 18(3): p. 385-97 [PMID:18268542] 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] Ivanov R,Brumbarova T,Bauer P Fitting into the harsh reality: regulation of iron-deficiency responses in dicotyledonous plants. Mol Plant, 2012. 5(1): p. 27-42 [PMID:21873619] Wang N, et al. Requirement and functional redundancy of Ib subgroup bHLH proteins for iron deficiency responses and uptake in Arabidopsis thaliana. Mol Plant, 2013. 6(2): p. 503-13 [PMID:22983953] Sivitz AB,Hermand V,Curie C,Vert G Arabidopsis bHLH100 and bHLH101 control iron homeostasis via a FIT-independent pathway. PLoS ONE, 2012. 7(9): p. e44843 [PMID:22984573] Matsuoka K, et al. Gibberellin-induced expression of Fe uptake-related genes in Arabidopsis. Plant Cell Physiol., 2014. 55(1): p. 87-98 [PMID:24192296] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] 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] Shen C, et al. Involvement of endogenous salicylic acid in iron-deficiency responses in Arabidopsis. J. Exp. Bot., 2016. 67(14): p. 4179-93 [PMID:27208542] 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] Kailasam S,Wang Y,Lo JC,Chang HF,Yeh KC S-Nitrosoglutathione works downstream of nitric oxide to mediate iron-deficiency signaling in Arabidopsis. Plant J., 2018. 94(1): p. 157-168 [PMID:29396986] Kurt F,Filiz E Genome-wide and comparative analysis of bHLH38, bHLH39, bHLH100 and bHLH101 genes in Arabidopsis, tomato, rice, soybean and maize: insights into iron (Fe) homeostasis. Biometals, 2018. 31(4): p. 489-504 [PMID:29546482]