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

Carubv10023654m

Common Name

CARUB_v10023654mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

bHLH

Protein Properties

Length: 321aa MW: 35910 Da PI: 4.3075

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10023654m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	34.5	3.7e-11	136	179	7	55
HHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 7 erErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 + ErrRR r+++++ Lr+l+P+ +K++Ka+i+ Av Y+++Lq Carubv10023654m 136 ISERRRRGRMKDKLYALRSLVPNI-----TKMDKASIVGDAVLYVQELQ 179 67*******************7.....7****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	6.67E-16	128	194	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	15.193	129	178	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	5.6E-16	131	198	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	6.31E-12	131	181	No hit	No description
SMART	SM00353	3.1E-14	135	184	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	9.8E-9	136	179	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0034756	Biological Process	regulation of iron ion transport
GO:0071281	Biological Process	cellular response to iron ion
GO:0071369	Biological Process	cellular response to ethylene stimulus
GO:0071732	Biological Process	cellular response to nitric oxide
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 321 aa Download sequence Send to blast
MDERVNALSN MNDLELHDFL VDPNFDQFIN LIRGDHHQTI DENPVLDFDL GPLQSSPCFI 60 DENQFIPTPV DDLFDELPDL DSNVAESFRS FDGESVRAGG GEEEEEDYND GDDSSATTTN 120 NDGSRKTKTD RSRTLISERR RRGRMKDKLY ALRSLVPNIT KMDKASIVGD AVLYVQELQS 180 QAKKLKSDIA GLEASLNSTG GYQEPALDAQ KTQPFRSINP PVSKQIIQMD VIQVEEKGFY 240 VRLMCNKGEG VAPSLYKSLE SLTSFQVQNS NLSSPSPDRY LLTYTLDGTC FEQSLNLPNL 300 KLWITGSLLN QGFEFIKPFT *

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10023654m

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	BT026446	0.0	BT026446.1 Arabidopsis thaliana At2g28160 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006294616.1	0.0	transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
Swissprot	Q0V7X4	0.0	FIT_ARATH; Transcription factor FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR
TrEMBL	R0HDB5	0.0	R0HDB5_9BRAS; Uncharacterized protein
STRING	XP_006294616.1	0.0	(Capsella rubella)

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	0.0	FER-like regulator of iron uptake

Link Out ? help Back to Top
Phytozome	Carubv10023654m
Entrez Gene	17889967

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]