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

Carubv10019130m

Common Name

CARUB_v10019130mg

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: 258aa MW: 29406.1 Da PI: 8.4206

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10019130m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	49.1	1e-15	75	127	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 ++ +hn+ Er RR++iNs f++Lr++lP + +skKls e+ + +YI +Lq Carubv10019130m 75 KKLNHNASERDRRKKINSLFSTLRSCLPAsN---HSKKLSIPETISRSLKYIPELQ 127 6789***********************55...9999*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.589	74	126	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.6E-15	75	140	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.8E-13	75	127	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.50E-14	75	131	No hit	No description
SuperFamily	SSF47459	1.7E-17	75	144	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.2E-12	80	132	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010106	Biological Process	cellular response to iron ion starvation
GO:0055072	Biological Process	iron ion homeostasis
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 258 aa Download sequence Send to blast
MCSLIPSPLF QNFGWPSRGK YESYYGAGEN INNGPFLDFP VPQTYGVTHH HQNSLQGVSV 60 SSEGNKIDNN QVVVKKLNHN ASERDRRKKI NSLFSTLRSC LPASNHSKKL SIPETISRSL 120 KYIPELQQQV KNLIQKKEEL LVRVSGQRDF KHYDKQQQKA IASYLSTVSA TRLGESEVMV 180 QISSSKIHNF SISNVLSGLE EDGFALVDVS SSRSHGERLF YTLHLQMENM DDYYKINCEE 240 LSERMLYLYE KYEKSLD*

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10019130m

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	-

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	XP_006292870.1	0.0	transcription factor ORG2
Swissprot	Q9M1K1	1e-153	ORG2_ARATH; Transcription factor ORG2
TrEMBL	R0HP72	0.0	R0HP72_9BRAS; Uncharacterized protein
STRING	XP_006292870.1	0.0	(Capsella rubella)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM482	28	153

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G56970.1	1e-155	bHLH family protein

Link Out ? help Back to Top
Phytozome	Carubv10019130m
Entrez Gene	17886806

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] 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] 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]