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

RrC23113_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

bHLH

Protein Properties

Length: 156aa MW: 17538.2 Da PI: 4.4044

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC23113_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	17.5	7.3e-06	131	153	7	29
HHHHHHHHHHHHHHHHHHCTSCC CS HLH 7 erErrRRdriNsafeeLrellPk 29 + Er+RR r+++++ Lr l+P+ RrC23113_p1 131 ISERKRRGRMKDKLYALRALVPN 153 78********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	1.74E-6	118	155	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.8E-5	123	154	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	10.15	124	156	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	3.09E-5	126	156	No hit	No description

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: 156 aa Download sequence Send to blast
MEGTVNVLSN LSDIELHNFL VDPNFDQFIN LIRGDDQSNK NPSLDFDLGG PFQNSPSFVD 60 ENHFIPTHVD DLFDELPDLD SNVAESFRSL DAESVKAGGD DDYNDCEDSS ATTTHTDGSR 120 KTRTDRSKTL ISERKRRGRM KDKLYALRAL VPNITK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor. Essential protein involved in iron uptake responses. Regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. Confers enhanced iron mobilization responses at low iron supply. {ECO:0000269\|PubMed:15539473, ECO:0000269\|PubMed:15556641, ECO:0000269\|PubMed:16117851}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: In roots by iron deficiency. Repressed by cytokinins. Induced by cold, UV, ethylene (ACC), jasmonic acid (JA), flagellin, and salicylic acid (SA) treatments. {ECO:0000269\|PubMed:12679534, ECO:0000269\|PubMed:15531708, ECO:0000269\|PubMed:15539473, ECO:0000269\|PubMed:15556641, ECO:0000269\|PubMed:18397377}.

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	AC240985	0.0	AC240985.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB008O16, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018475151.1	1e-110	PREDICTED: transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR-like
Swissprot	Q0V7X4	1e-82	FIT_ARATH; Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
TrEMBL	A0A078H179	7e-98	A0A078H179_BRANA; BnaC03g46920D protein
TrEMBL	A0A0D3B7A7	7e-98	A0A0D3B7A7_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6AUB9	8e-98	A0A3P6AUB9_BRAOL; Uncharacterized protein
STRING	Bo3g040310.1	1e-98	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4187	28	57

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G28160.1	5e-85	FER-like regulator of iron uptake

Publications ? help Back to Top
Schmid NB, et al. Feruloyl-CoA 6'-Hydroxylase1-dependent coumarins mediate iron acquisition from alkaline substrates in Arabidopsis. Plant Physiol., 2014. 164(1): p. 160-72 [PMID:24246380] Doustaly F, et al. Uranium perturbs signaling and iron uptake response in Arabidopsis thaliana roots. Metallomics, 2014. 6(4): p. 809-21 [PMID:24549117] Le CT, et al. ZINC FINGER OF ARABIDOPSIS THALIANA12 (ZAT12) Interacts with FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT) Linking Iron Deficiency and Oxidative Stress Responses. Plant Physiol., 2016. 170(1): p. 540-57 [PMID:26556796] Yang L, et al. Carbon Monoxide Interacts with Auxin and Nitric Oxide to Cope with Iron Deficiency in Arabidopsis. Front Plant Sci, 2016. 7: p. 112 [PMID:27014280] Zhou C, et al. Paenibacillus polymyxa BFKC01 enhances plant iron absorption via improved root systems and activated iron acquisition mechanisms. Plant Physiol. Biochem., 2016. 105: p. 162-173 [PMID:27105423] Mai HJ,Pateyron S,Bauer P Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks. BMC Plant Biol., 2016. 16(1): p. 211 [PMID:27716045] Zhou C, et al. Exogenous Melatonin Improves Plant Iron Deficiency Tolerance via Increased Accumulation of Polyamine-Mediated Nitric Oxide. Int J Mol Sci, 2017. [PMID:27792144] Ezer D, et al. The G-Box Transcriptional Regulatory Code in Arabidopsis. Plant Physiol., 2017. 175(2): p. 628-640 [PMID:28864470] Naranjo-Arcos MA, et al. Dissection of iron signaling and iron accumulation by overexpression of subgroup Ib bHLH039 protein. Sci Rep, 2017. 7(1): p. 10911 [PMID:28883478] 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] Cui Y, et al. Four IVa bHLH Transcription Factors Are Novel Interactors of FIT and Mediate JA Inhibition of Iron Uptake in Arabidopsis. Mol Plant, 2018. 11(9): p. 1166-1183 [PMID:29960107]