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

Pavir.6NG003500.1.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

Protein Properties

Length: 360aa MW: 38728.3 Da PI: 6.4585

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6NG003500.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	42.4	1.2e-13	254	340	3	85
EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkld 85 k+lt+sdv + gr+vlpkk ae+ +++ + l++ d +W++k+++ ++ks++y+l+ eFvk +gL++gD ++++ + Pavir.6NG003500.1.p 254 KELTKSDVANVGRIVLPKKDAEASlpPLVQGDPLILQMDDmVLPVTWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDALIIYKN 340 899****************99999666666666777774455***99888888888888.99**************9933 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.7E-20	251	348	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	9.4E-7	252	352	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	7.06E-15	252	340	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS50863	8.628	252	354	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.6E-10	254	344	IPR003340	B3 DNA binding domain
CDD	cd10017	2.09E-19	254	352	No hit	No description

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: 360 aa Download sequence Send to blast
MGQMGSPDGD GRGGGGGSHP HHQYHYQALL AAVQNPTQGL HPFPLPFHVG PPAAGPAADA 60 AASTHNAAPH SQHSRGFADW SASSSAFASV SPQPAPATTN APPFPYNLSQ SYALWSHYML 120 SKNAMPYSSY PAPHEDNPRS LRHTHIPPDK DSGSTYSMET AGSASSLGFD SFTTMSLGPN 180 ICAHMSPMEA SLPAKEAENS EDLPTVVRNS DDMDTINSEE VHLDTAATLP ESKPSHESCT 240 MKFNSGEYQV VLRKELTKSD VANVGRIVLP KKDAEASLPP LVQGDPLILQ MDDMVLPVTW 300 KFKYRFWPNN KSRMYILEAA GEFVKTHGLQ AGDALIIYKN SVPGKFIIRA EKAIQQTNP*

Sequence ? help Back to Top

Protein Sequence Length: 360 aa Download sequence Send to blast

MGQMGSPDGD GRGGGGGSHP HHQYHYQALL AAVQNPTQGL HPFPLPFHVG PPAAGPAADA  60
AASTHNAAPH SQHSRGFADW SASSSAFASV SPQPAPATTN APPFPYNLSQ SYALWSHYML  120
SKNAMPYSSY PAPHEDNPRS LRHTHIPPDK DSGSTYSMET AGSASSLGFD SFTTMSLGPN  180
ICAHMSPMEA SLPAKEAENS EDLPTVVRNS DDMDTINSEE VHLDTAATLP ESKPSHESCT  240
MKFNSGEYQV VLRKELTKSD VANVGRIVLP KKDAEASLPP LVQGDPLILQ MDDMVLPVTW  300
KFKYRFWPNN KSRMYILEAA GEFVKTHGLQ AGDALIIYKN SVPGKFIIRA EKAIQQTNP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	3e-31	243	340	4	101	B3 domain-containing transcription factor LEC2
6j9c_D	3e-31	243	340	4	101	B3 domain-containing transcription factor LEC2
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.6559	0.0	callus\| leaf\| root\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots. {ECO:0000269\|PubMed:18025467}.

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	Pavir.6NG003500.1.p

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	BT038952	0.0	BT038952.1 Zea mays full-length cDNA clone ZM_BFb0345D11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025822621.1	0.0	B3 domain-containing protein IDEF1-like isoform X2
Swissprot	Q6Z1Z3	1e-118	IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBL	A0A2T7D291	0.0	A0A2T7D291_9POAL; Uncharacterized protein
STRING	Pavir.Fb00027.1.p	0.0	(Panicum virgatum)

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	2e-32	B3 family protein

Link Out ? help Back to Top
Phytozome	Pavir.6NG003500.1.p

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]