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

GRMZM2G405699_P01

Organism

Zea mays

Taxonomic ID

4577

Taxonomic Lineage

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

Family

Protein Properties

Length: 316aa MW: 34378.2 Da PI: 6.3879

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GRMZM2G405699_P01	genome	MaizeSequence	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	37.1	5.8e-12	236	316	3	79
EE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-E CS B3 3 kvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDf 79 k+lt+sdv +sgr+vlpkk ae+ +++ + l++ d W++k+++ ++ks++y+l+ eFvk +gL++gD+ GRMZM2G405699_P01 236 KELTKSDVANSGRIVLPKKDAEAGlpPLVQGDPLILQMDDmVLPIIWKFKYRFwpNNKSRMYILE-AAGEFVKTHGLQAGDT 316 899****************88899666666656676664445***99888888888888.99***********6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd10017	1.83E-16	233	316	No hit	No description
SuperFamily	SSF101936	5.1E-13	233	316	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.9E-17	233	316	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS50863	8.698	234	316	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.1E-8	236	316	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:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 316 aa Download sequence Send to blast
MGQMGGPDGD GPHHQYHYQA LLAAVQNPSQ GLHVPLHAGA GAPAAGPGPR PGADADASST 60 HNANATPHSQ PPRAFTDWSA SNSAFAAQPA PATTNTPFHY NLSQSYALWT HYMLNKNVSY 120 STYSTPHEPL RHTHIPDKYS GCAFSLGFDS FTTMSLGPNI CANMTPMERS ISAKEPENSE 180 DLPTVVRSSD EMDTRNSGDV RRDTVDTLPE SKQSHESCAS VSNKFDSGEY QVILRKELTK 240 SDVANSGRIV LPKKDAEAGL PPLVQGDPLI LQMDDMVLPI IWKFKYRFWP NNKSRMYILE 300 AAGEFVKTHG LQAGDT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9c_A	2e-28	225	315	4	94	B3 domain-containing transcription factor LEC2
6j9c_D	2e-28	225	315	4	94	B3 domain-containing transcription factor LEC2
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Zm.98484	0.0	ovary\| shoot

Expression -- Microarray ? help Back to Top
Source	ID
Expression Atlas	GRMZM2G405699

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	GRMZM2G405699_P01

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	EU971515	0.0	EU971515.1 Zea mays clone 366455 mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_020395340.1	0.0	B3 domain-containing protein IDEF1 isoform X1
Swissprot	Q6Z1Z3	4e-99	IDEF1_ORYSJ; B3 domain-containing protein IDEF1
TrEMBL	A0A1D6LDA6	0.0	A0A1D6LDA6_MAIZE; Putative B3 DNA binding domain family protein
STRING	GRMZM2G405699_P01	0.0	(Zea mays)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP11346	28	31
Representative plant	OGRP788	17	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G28300.1	4e-28	B3 family protein

Link Out ? help Back to Top
Phytozome	GRMZM2G405699_P01

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]