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

Sobic.003G428800.2.p

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

bHLH

Protein Properties

Length: 244aa MW: 26584.9 Da PI: 6.2452

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.003G428800.2.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	46.7	5.7e-15	71	122	1	55
CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r+ +hn+ Er RR+++N+ ++ Lr+llP a +++Kls +++ ++ +YI +Lq Sobic.003G428800.2.p 71 RKLSHNAYERDRRKQLNELYSSLRSLLPDA---DHTKLSIPTTVSRVLKYIPELQ 122 6889************************...*****************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	2.88E-16	69	138	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	13.872	70	121	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	3.0E-13	71	137	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Pfam	PF00010	3.8E-12	71	122	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.56E-10	71	125	No hit	No description
SMART	SM00353	1.7E-9	76	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: 244 aa Download sequence Send to blast
MDHQLFDDPF GSSISSLEAD IFSAGGGGQL PSPPWPDLDL DDDYDIHDLS APAANAATSS 60 GGGYGSGGSG RKLSHNAYER DRRKQLNELY SSLRSLLPDA DHTKLSIPTT VSRVLKYIPE 120 LQKQVDNLER RKKELTNANC KPGVLNTKEI VTPIVSATCL NDTEIMVQVS LHSNVAATAL 180 PLSKCIKVLE NEGLLLVSSS TYSTFENKTF YSLHLQRSQR TMKEQCPGFC DELEKIVRKK 240 AGA*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Sbi.4226	0.0	root\| shoot

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: During seeds germination, detected in embryos. In vegetative tissues under iron-sufficient, restricted almost exclusively to vascular bundles of roots and leaves, and to the root exodermis. In response to iron deficiency, accumulates in all tissues of roots and leaves. {ECO:0000269\|PubMed:21331630}.
Uniprot	TISSUE SPECIFICITY: Expressed constitutively at low levels in the roots (PubMed:16887895, PubMed:21331630). Also observed in flowers, developing seeds, embryos and vascular bundles (PubMed:21331630). {ECO:0000269\|PubMed:16887895, ECO:0000269\|PubMed:21331630}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription activator that binds to the DNA motif 5'-CACGTGG-3' in the promoter of iron (Fe) deficiency-inducible genes as well as of genes involved in iron homeostasis, thus contributing to basal tolerance to iron deficiency, iron uptake from soil and iron transport, particularly during seed maturation and germination (PubMed:16887895, PubMed:17559517, PubMed:21331630, PubMed:26224556). Promotes the accumulation of mugineic acid family phytosiderophores (MAs) (PubMed:17559517). Required for ethylene-mediated signaling during iron deficiency responses (PubMed:21112958). Improves growth and yield, especially in calcareous soil with low iron availability. Promotes iron concentration in shoots and grain (PubMed:21331630). {ECO:0000269\|PubMed:16887895, ECO:0000269\|PubMed:17559517, ECO:0000269\|PubMed:21112958, ECO:0000269\|PubMed:21331630, ECO:0000269\|PubMed:26224556}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.003G428800.2.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Strongly induced in both roots and shoots during iron (Fe) deficiency stress (PubMed:16887895, PubMed:18025467, PubMed:19737364, PubMed:21112958, PubMed:21331630, PubMed:24280375). Ethylene enhances the iron deficiency-mediated induction (PubMed:21112958). Induced by arsenate (AsV25 and AsV50); this induction is repressed by nitric oxide (NO) (PubMed:26793232). Accumulates under cadmium (Cd) stress; this induction is inhibited by the DNA methyltransferase inhibitor 5-aza-2-deoxycytidine (Aza) (PubMed:27412910). {ECO:0000269\|PubMed:16887895, ECO:0000269\|PubMed:18025467, ECO:0000269\|PubMed:19737364, ECO:0000269\|PubMed:21112958, ECO:0000269\|PubMed:21331630, ECO:0000269\|PubMed:24280375, ECO:0000269\|PubMed:26793232, ECO:0000269\|PubMed:27412910}.

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	KJ728005	0.0	KJ728005.1 Zea mays clone pUT6138 bHLH transcription factor (bHLH126) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021313618.1	1e-155	transcription factor bHLH101-like
Swissprot	Q0JFZ0	1e-106	IRO2_ORYSJ; Protein IRON-RELATED TRANSCRIPTION FACTOR 2
TrEMBL	A0A1B6Q890	1e-180	A0A1B6Q890_SORBI; Uncharacterized protein
STRING	Sb03g046090.1	1e-155	(Sorghum bicolor)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G56970.1	2e-28	bHLH family protein

Link Out ? help Back to Top
Phytozome	Sobic.003G428800.2.p

Publications ? help Back to Top
Ogo Y, et al. The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Plant J., 2007. 51(3): p. 366-77 [PMID:17559517] Kobayashi T, et al. The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. Plant J., 2009. 60(6): p. 948-61 [PMID:19737364] Wu J, et al. Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa. J. Exp. Bot., 2011. 62(2): p. 667-74 [PMID:21112958] Ogo Y, et al. OsIRO2 is responsible for iron utilization in rice and improves growth and yield in calcareous soil. Plant Mol. Biol., 2011. 75(6): p. 593-605 [PMID:21331630] Yang A,Li Y,Xu Y,Xu Y,Zhang WH A receptor-like protein RMC is involved in regulation of iron acquisition in rice. J. Exp. Bot., 2013. 64(16): p. 5009-20 [PMID:24014863] Itai RN,Ogo Y,Kobayashi T,Nakanishi H,Nishizawa NK Rice genes involved in phytosiderophore biosynthesis are synchronously regulated during the early stages of iron deficiency in roots. Rice (N Y), 2013. 6(1): p. 16 [PMID:24280375] Masuda H,Aung MS,Nishizawa NK Iron biofortification of rice using different transgenic approaches. Rice (N Y), 2013. 6(1): p. 40 [PMID:24351075] Kobayashi T,Nakanishi Itai R,Nishizawa NK Iron deficiency responses in rice roots. Rice (N Y), 2014. 7(1): p. 27 [PMID:26224556] Singh AP, et al. Nitric Oxide Alleviated Arsenic Toxicity by Modulation of Antioxidants and Thiol Metabolism in Rice (Oryza sativa L.). Front Plant Sci, 2015. 6: p. 1272 [PMID:26793232] Yang A,Zhang WH A Small GTPase, OsRab6a, is Involved in the Regulation of Iron Homeostasis in Rice. Plant Cell Physiol., 2016. 57(6): p. 1271-80 [PMID:27257291] Feng SJ, et al. Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium. Plant Cell Environ., 2016. 39(12): p. 2629-2649 [PMID:27412910]