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

Bradi2g58390.1.p

Common Name

BRADI_2g58390, LOC100840416

Organism

Brachypodium distachyon

Taxonomic ID

15368

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium

Family

Protein Properties

Length: 699aa MW: 74130.6 Da PI: 7.9023

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Bradi2g58390.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	60.9	2.2e-19	541	635	2	94
EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS B3 2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 +kvl++sdv+++gr+vlpkk ae+h ++k++ ++ + +ed ++r+W++++++ ++ks++y+l+ ++ +Fv++n+L+egDf+v++ ++ + Bradi2g58390.1.p 541 QKVLKQSDVGSLGRIVLPKKEAETHlpELKTRDGISIPMEDiGTSRVWNMRYRFwpNNKSRMYLLE-NTGDFVRSNELQEGDFIVIY--SDVK 630 79***********************999*******7778***99777777777777.*****************9..5555 PP E..EE CS B3 90 felvv 94 +++++ Bradi2g58390.1.p 631 GRYLI 635 55555 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	9.8E-27	530	632	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10015	1.21E-34	538	638	No hit	No description
SuperFamily	SSF101936	3.53E-22	539	634	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	2.9E-18	540	641	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.08	540	641	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.5E-16	541	633	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009657	Biological Process	plastid organization
GO:0009733	Biological Process	response to auxin
GO:0009737	Biological Process	response to abscisic acid
GO:0009793	Biological Process	embryo development ending in seed dormancy
GO:0031930	Biological Process	mitochondria-nucleus signaling pathway
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0005829	Cellular Component	cytosol
GO:0001076	Molecular Function	transcription factor activity, RNA polymerase II transcription factor binding
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 699 aa Download sequence Send to blast
MDASAGSPPP PHSQQKHGGG AWPGKAPAGE IPPGEDDFLF ADDTFPSLPD FPCLSSPSSS 60 TFSSSSSSNS SSAFTAAATR GGGEQHAAAE DGIDALADLD QLLDFASLSV PSWEDEPLFP 120 DDVGMMLEDA DAMSDDHKPP ARHAADAGCR AAGKAAAAAS GGGEGFVASG GGAAEDLPRF 180 FMEWLTNNRD CISAEDLRSI RLKRSTIEAA AARLGGGRQG TMQLLKLILT WVQNHHLQKK 240 RLRVDASMEM DASPAGPHGS HHHHHQLPSP GANPGYEFPA AAPEGTSWTM PYQQAAFTPP 300 SAYGGETQTA IYPNTTSTTT AATGPYPFQQ SCSTSSVVVS SQPFSPPAAA TDMQTAPMSG 360 SAGSGNNSVP LVWPQQYAFP GGAPTGNSYP MLQPFAPGFA MPMCPQRAAG GTEPSATKEA 420 RKRRMARQRR LSSSLQHQRS QQLNLGQIQI VPQPPQEHSA PVTLTPPPSG AWGLWSSPPG 480 CQQVPVQAQA QNPPSKPSSS SKPKQQKPSA PDAGATPAAS EKRQGANNKP AADKNLRFLL 540 QKVLKQSDVG SLGRIVLPKK EAETHLPELK TRDGISIPME DIGTSRVWNM RYRFWPNNKS 600 RMYLLENTGD FVRSNELQEG DFIVIYSDVK GRYLIRGVKV RPVQDQAGKH KYGIPGNKGG 660 ASDVKTGPED RGCKEKSPHG AQRSRQEATG SNMMAVRI*

Sequence ? help Back to Top

Protein Sequence Length: 699 aa Download sequence Send to blast

MDASAGSPPP PHSQQKHGGG AWPGKAPAGE IPPGEDDFLF ADDTFPSLPD FPCLSSPSSS  60
TFSSSSSSNS SSAFTAAATR GGGEQHAAAE DGIDALADLD QLLDFASLSV PSWEDEPLFP  120
DDVGMMLEDA DAMSDDHKPP ARHAADAGCR AAGKAAAAAS GGGEGFVASG GGAAEDLPRF  180
FMEWLTNNRD CISAEDLRSI RLKRSTIEAA AARLGGGRQG TMQLLKLILT WVQNHHLQKK  240
RLRVDASMEM DASPAGPHGS HHHHHQLPSP GANPGYEFPA AAPEGTSWTM PYQQAAFTPP  300
SAYGGETQTA IYPNTTSTTT AATGPYPFQQ SCSTSSVVVS SQPFSPPAAA TDMQTAPMSG  360
SAGSGNNSVP LVWPQQYAFP GGAPTGNSYP MLQPFAPGFA MPMCPQRAAG GTEPSATKEA  420
RKRRMARQRR LSSSLQHQRS QQLNLGQIQI VPQPPQEHSA PVTLTPPPSG AWGLWSSPPG  480
CQQVPVQAQA QNPPSKPSSS SKPKQQKPSA PDAGATPAAS EKRQGANNKP AADKNLRFLL  540
QKVLKQSDVG SLGRIVLPKK EAETHLPELK TRDGISIPME DIGTSRVWNM RYRFWPNNKS  600
RMYLLENTGD FVRSNELQEG DFIVIYSDVK GRYLIRGVKV RPVQDQAGKH KYGIPGNKGG  660
ASDVKTGPED RGCKEKSPHG AQRSRQEATG SNMMAVRI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9b_A	2e-35	536	639	1	105	B3 domain-containing transcription factor FUS3
6j9b_D	2e-35	536	639	1	105	B3 domain-containing transcription factor FUS3
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor that may participate in abscisic acid-regulated gene expression during seed development. May be required for seed maturation and dormancy induction.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00083	PBM	Transfer from AT3G24650	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Bradi2g58390.1.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	DQ416753	1e-129	DQ416753.1 Avena fatua clone 1 viviparous 1 mRNA, partial cds.
GenBank	DQ416754	1e-129	DQ416754.1 Avena fatua clone 2 viviparous 1 mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010232722.1	0.0	B3 domain-containing protein VP1
Swissprot	P37398	0.0	VIV_ORYSJ; B3 domain-containing protein VP1
TrEMBL	I1HUG6	0.0	I1HUG6_BRADI; Uncharacterized protein
STRING	BRADI2G58390.1	0.0	(Brachypodium distachyon)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP7529	34	43
Representative plant	OGRP788	17	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	1e-59	B3 family protein

Link Out ? help Back to Top
Phytozome	Bradi2g58390.1.p
Entrez Gene	100840416

Publications ? help Back to Top
Espelund M,Bekele E,Holst-Jensen A,Jakobsen KS,Nordal I A molecular genetic analysis of Eragrostis tef (Zucc.) Trotter: non-coding regions of chloroplast DNA, 18S rDNA and the transcription factor VP1. Hereditas, 2000. 132(3): p. 193-202 [PMID:11075514] Gampala SS,Hagenbeek D,Rock CD Functional interactions of lanthanum and phospholipase D with the abscisic acid signaling effectors VP1 and ABI1-1 in rice protoplasts. J. Biol. Chem., 2001. 276(13): p. 9855-60 [PMID:11139577] Carrari F, et al. Cloning and expression of a sorghum gene with homology to maize vp1. Its potential involvement in pre-harvest sprouting resistance. Plant Mol. Biol., 2001. 45(6): p. 631-40 [PMID:11430426] Hagiwara K,Rao S,Scott SW,Carner GR Nucleotide sequences of segments 1, 3 and 4 of the genome of Bombyx mori cypovirus 1 encoding putative capsid proteins VP1, VP3 and VP4, respectively. J. Gen. Virol., 2002. 83(Pt 6): p. 1477-82 [PMID:12029163] Zhao SL,Liang CY,Hong JJ,Peng HY Genomic sequence analyses of segments 1 to 6 of Dendrolimus punctatus cytoplasmic polyhedrosis virus. Arch. Virol., 2003. 148(7): p. 1357-68 [PMID:12827465] 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] Suzuki N, et al. Molecular analysis of rice dwarf phytoreovirus segment S1: interviral homology of the putative RNA-dependent RNA polymerase between plant- and animal-infecting reoviruses. Virology, 1992. 190(1): p. 240-7 [PMID:1529532] Fan J, et al. Short, direct repeats (SDRs)-mediated post-transcriptional processing of a transcription factor gene OsVP1 in rice (Oryza sativa). J. Exp. Bot., 2007. 58(13): p. 3811-7 [PMID:18057047] Sugimoto K, et al. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(13): p. 5792-7 [PMID:20220098] Sharoni AM, et al. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol., 2011. 52(2): p. 344-60 [PMID:21169347] Kumar S,Jiang S,Jami SK,Hill RD Cloning and characterization of barley caryopsis FCA. Physiol Plant, 2011. 143(1): p. 93-106 [PMID:21645000] Cao G, et al. Characterization of the complete genome segments from BmCPV-SZ, a novel Bombyx mori cypovirus 1 isolate. Can. J. Microbiol., 2012. 58(7): p. 872-83 [PMID:22712678] Ye H,Beighley DH,Feng J,Gu XY Genetic and physiological characterization of two clusters of quantitative trait Loci associated with seed dormancy and plant height in rice. G3 (Bethesda), 2013. 3(2): p. 323-31 [PMID:23390608] Guo X, et al. The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism. Plant J., 2013. 75(3): p. 403-16 [PMID:23581288] Lata C, et al. Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.). PLoS ONE, 2014. 9(11): p. e113092 [PMID:25409524] Matsuno K,Fujimura T Do rice suspension-cultured cells treated with abscisic acid mimic developing seeds? Mol. Genet. Genomics, 2015. 290(4): p. 1551-62 [PMID:25732383] Li S, et al. Facilitation of rice stripe virus accumulation in the insect vector by Himetobi P virus VP1. Viruses, 2015. 7(3): p. 1492-504 [PMID:25807055] Mukhopadhyay P,Tyagi AK OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci Rep, 2015. 5: p. 9998 [PMID:25925167] Du W, et al. Physiological characteristics and related gene expression of after-ripening on seed dormancy release in rice. Plant Biol (Stuttg), 2015. 17(6): p. 1156-64 [PMID:26205956] Zhang X,Sun J,Cao X,Song X Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice. Plant Physiol., 2015. 169(3): p. 2118-28 [PMID:26351308] Duan YB, et al. Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis. Plant Mol. Biol., 2016. 90(1-2): p. 49-62 [PMID:26482477] Zhao Y, et al. ABA receptor PYL9 promotes drought resistance and leaf senescence. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(7): p. 1949-54 [PMID:26831097] Chen L, et al. Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. Sci Rep, 2016. 6: p. 21623 [PMID:26869021] Li Z, et al. Serine carboxypeptidase 46 Regulates Grain Filling and Seed Germination in Rice (Oryza sativa L.). PLoS ONE, 2016. 11(7): p. e0159737 [PMID:27448032] Zhu Z, et al. Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance. Front Plant Sci, 2016. 7: p. 1285 [PMID:27625663] Hattori T,Terada T,Hamasuna S Regulation of the Osem gene by abscisic acid and the transcriptional activator VP1: analysis of cis-acting promoter elements required for regulation by abscisic acid and VP1. Plant J., 1995. 7(6): p. 913-25 [PMID:7599651] Hollung K,Espelund M,Schou K,Jakobsen KS Developmental, stress and ABA modulation of mRNA levels for bZip transcription factors and Vp1 in barley embryos and embryo-derived suspension cultures. Plant Mol. Biol., 1997. 35(5): p. 561-71 [PMID:9349278] Schultz TF,Medina J,Hill A,Quatrano RS 14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1. Plant Cell, 1998. 10(5): p. 837-47 [PMID:9596641]