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

OB08G10110.1

Common Name

LOC102704633

Organism

Oryza brachyantha

Taxonomic ID

4533

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: 364aa MW: 40311.9 Da PI: 7.5816

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OB08G10110.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	42.8	9.1e-14	257	350	3	93
EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS.SEE..E CS B3 3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr.sefelv 93 k+lt+sdv++ gr+vlpkk ae+ + ++ ++ l + d +W++k++y ++ks++y+l eF k +gL++gD+++++ ++ +++++ OB08G10110.1 257 KELTKSDVGNVGRIVLPKKDAEASlpPLLQRDPMILHMDDmVLPVTWKFKYRYwpNNKSRMYILD-SAGEFLKTHGLQAGDVIIIY--KNlASGKFM 350 899****************99988555567777777775555*****777777777777.99**************99..555666444 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	2.2E-21	254	356	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.7E-16	254	343	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.86E-20	254	352	No hit	No description
SMART	SM01019	2.7E-7	255	355	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	8.91	255	357	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-10	257	350	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: 364 aa Download sequence Send to blast
MGQMDGGGDG GGYPYHYQAL LAAVHQQTVP FPNPFPAPSS GTEAPLHNHS HNHNHNHNHN 60 HNHNHNHNHN HNHNHNHNAA PHPHTPTPRG FADWSASTSA FTSLAAHSSP APSNAVHYSF 120 SPCYAFWAHY MVNKNAYPSF PAPHEEPPHQ LRLANSHPRD ASGPASSFGV ESFNSASMAP 180 NICNHMPPIE GPISANEDKK PEILPRVIKS SDELETRNSG VELHCETVGA LPESKQSHES 240 RATKLLNSGE YQVILRKELT KSDVGNVGRI VLPKKDAEAS LPPLLQRDPM ILHMDDMVLP 300 VTWKFKYRYW PNNKSRMYIL DSAGEFLKTH GLQAGDVIII YKNLASGKFM IRGEKAIHQQ 360 TTNS

Sequence ? help Back to Top

Protein Sequence Length: 364 aa Download sequence Send to blast

MGQMDGGGDG GGYPYHYQAL LAAVHQQTVP FPNPFPAPSS GTEAPLHNHS HNHNHNHNHN  60
HNHNHNHNHN HNHNHNHNAA PHPHTPTPRG FADWSASTSA FTSLAAHSSP APSNAVHYSF  120
SPCYAFWAHY MVNKNAYPSF PAPHEEPPHQ LRLANSHPRD ASGPASSFGV ESFNSASMAP  180
NICNHMPPIE GPISANEDKK PEILPRVIKS SDELETRNSG VELHCETVGA LPESKQSHES  240
RATKLLNSGE YQVILRKELT KSDVGNVGRI VLPKKDAEAS LPPLLQRDPM ILHMDDMVLP  300
VTWKFKYRYW PNNKSRMYIL DSAGEFLKTH GLQAGDVIII YKNLASGKFM IRGEKAIHQQ  360
TTNS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	2e-29	252	343	10	101	B3 domain-containing transcription factor LEC2
6j9c_D	2e-29	252	343	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	OB08G10110.1

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_006659013.1	0.0	PREDICTED: B3 domain-containing protein IDEF1-like
Swissprot	Q6Z1Z3	0.0	IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBL	J3MPI2	0.0	J3MPI2_ORYBR; Uncharacterized protein
STRING	OB08G10110.1	0.0	(Oryza brachyantha)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP11346	28	31

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	8e-35	B3 family protein

Link Out ? help Back to Top
Entrez Gene	102704633

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]