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

Rsa1.0_02882.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 251aa MW: 28436.1 Da PI: 6.0989

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_02882.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	51.3	2.1e-16	70	122	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 ++ +hn+ Er RR++iNs f+ Lr++lP + +skKls +++ + +YI +Lq Rsa1.0_02882.1_g00001.1 70 KKLNHNASERDRRKKINSLFSSLRSCLPAsD---QSKKLSIPQTVSRSLKYIPELQ 122 6789***********************66...*****************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.704	69	121	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	1.0E-13	70	122	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	5.23E-16	70	139	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.14E-13	70	122	No hit	No description
Gene3D	G3DSA:4.10.280.10	7.1E-14	70	136	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	1.3E-11	75	127	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: 251 aa Download sequence Send to blast
MCALVPPVFP NFGWPSTGEY ESYYLAGENL DDFTFLDFPA QETYGVEHHQ EIQELLGVSV 60 ASEGNGVVTK KLNHNASERD RRKKINSLFS SLRSCLPASD QSKKLSIPQT VSRSLKYIPE 120 LQGEVKKLIK KKEELLVRVS SQRDIEHYVE PQPKAVTRYV ATISATRLGD NEVMVQISSS 180 KIHNFSISNV LSGLEEDGFV LVDVSSSRSH GERLFYTLHL QMGNIDNHNL TCEELNQRML 240 YLYEECGNSF R

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_02882.1_g00001.1

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	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018458568.1	0.0	PREDICTED: transcription factor ORG3-like
Swissprot	Q9M1K1	1e-135	ORG2_ARATH; Transcription factor ORG2
TrEMBL	A0A397ZPU9	1e-171	A0A397ZPU9_BRACM; Uncharacterized protein
STRING	Bra014657.1-P	1e-170	(Brassica rapa)

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
AT3G56980.1	1e-126	bHLH family protein

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]