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

OBART08G00060.1

Organism

Oryza barthii

Taxonomic ID

65489

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza

Family

Protein Properties

Length: 315aa MW: 34643.1 Da PI: 7.5227

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OBART08G00060.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	40.5	4.8e-13	208	292	3	83
EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS...-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesg...rsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFk 83 k+lt+sdv++ gr+vlpkk ae+ + ++ + l + d +W++k++y ++ks++y+l eF k +gL++gD+++++ OBART08G00060.1 208 KELTKSDVGNVGRIVLPKKDAEASlpPLLQRDPLILHMDD--MvlpVTWKFKYRYwpNNKSRMYILD-SAGEFLKTHGLQAGDVIIIY 292 899****************9998844445565566666..3446*****777777777777.99*************998 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.19E-16	205	293	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.4E-20	205	300	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.44E-19	205	303	No hit	No description
SMART	SM01019	6.1E-7	206	306	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	8.557	206	308	IPR003340	B3 DNA binding domain
Pfam	PF02362	7.8E-10	208	292	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 315 aa Download sequence Send to blast
MGQMDGGDGG GGGHPYHYQA LLAAVHQQTV PFPNPFPAPS SGFADWSAST SAFTSLAAHS 60 STAPSNAVHY SFSPCYAFWT HYMLNKNAYP TSFPAPHDDH LRLANNNHPR DAPGPASSYG 120 VESFTTPSMA PNICTHMPPI EGPISAKEDK KPEILPRVVK SSDELETRNS NVEFHSETVG 180 TLPESKQGHD SRATKLLNSG EYQVILRKEL TKSDVGNVGR IVLPKKDAEA SLPPLLQRDP 240 LILHMDDMVL PVTWKFKYRY WPNNKSRMYI LDSAGEFLKT HGLQAGDVII IYKNLAPGKF 300 IIRGEKAIHQ QTTNP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	9e-30	203	294	10	101	B3 domain-containing transcription factor LEC2
6j9c_D	9e-30	203	294	10	101	B3 domain-containing transcription factor LEC2
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription regulator involved in iron deficiency response and tolerance. May regulate directly iron transporters or other transcription factors involved in iron-deficiency response. Binds specifically to the DNA sequence 5'-CATGC-3' of the IDE1 element found in the promoter of the barley iron deficiency-inducible gene IDS2. {ECO:0000269\|PubMed:18025467}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated during the early stage of iron deficiency (at protein level). {ECO:0000269\|PubMed:27137867}.

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	AK107456	0.0	AK107456.1 Oryza sativa Japonica Group cDNA clone:002-128-C10, full insert sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015648159.1	0.0	B3 domain-containing protein IDEF1 isoform X1
Swissprot	Q6Z1Z3	0.0	IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBL	A0A0D3GVE7	0.0	A0A0D3GVE7_9ORYZ; Uncharacterized protein
STRING	OBART08G00060.2	0.0	(Oryza barthii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	9e-35	B3 family protein

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] 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] Kobayashi T, et al. The spatial expression and regulation of transcription factors IDEF1 and IDEF2. Ann. Bot., 2010. 105(7): p. 1109-17 [PMID:20197292] Kobayashi T, et al. The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status. Plant J., 2012. 69(1): p. 81-91 [PMID:21880076] 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] Kobayashi T,Nishizawa NK Iron sensors and signals in response to iron deficiency. Plant Sci., 2014. 224: p. 36-43 [PMID:24908504] Kobayashi T,Nakanishi Itai R,Nishizawa NK Iron deficiency responses in rice roots. Rice (N Y), 2014. 7(1): p. 27 [PMID:26224556] Tan S, et al. CSN6, a subunit of the COP9 signalosome, is involved in early response to iron deficiency in Oryza sativa. Sci Rep, 2016. 6: p. 25485 [PMID:27137867] Kobayashi T, et al. Jasmonate signaling is activated in the very early stages of iron deficiency responses in rice roots. Plant Mol. Biol., 2016. 91(4-5): p. 533-47 [PMID:27143046]