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

Brast01G050100.1.p

Organism

Brachypodium stacei

Taxonomic ID

1071399

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: 715aa MW: 75613.3 Da PI: 8.3042

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Brast01G050100.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	52.2	1.1e-16	558	651	2	94
EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 +kvl++sdv+++gr+vlpk+ e+h ++k++ ++ + +ed ++ +W++++++ ++ks++y+l+ ++ +Fv++n+L+egDf+v++ ++ Brast01G050100.1.p 558 QKVLKQSDVGSLGRIVLPKEA-ETHlpELKTRDGISIPMEDiGTSLVWNMRYRFwpNNKSRMYLLE-NTGDFVRSNELQEGDFIVIY--SD 644 79***************995.7888999*********7777***99777777777777.*****************9..55 PP SEE..EE CS B3 88 sefelvv 94 ++++++ Brast01G050100.1.p 645 VKGRYLI 651 5555555 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.9E-23	548	648	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10015	1.68E-31	555	654	No hit	No description
SuperFamily	SSF101936	7.72E-19	556	650	IPR015300	DNA-binding pseudobarrel domain
PROSITE profile	PS50863	9.404	557	657	IPR003340	B3 DNA binding domain
SMART	SM01019	1.5E-12	557	657	IPR003340	B3 DNA binding domain
Pfam	PF02362	8.3E-14	558	649	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: 715 aa Download sequence Send to blast
MDASAGSPPP PHSQQNHGGG GRPGKAPVGE IRAGEASPDD FLFAGDTFPS LPDFPCLSSP 60 SSSTFSSSSS SNSSSAFTAA AAATRGGEHA AAADDGIDAL ADLDQLLDFA SLSVPSWEDE 120 PLFPDDVGMM LEDAMSDDHK PPARHAADVS CRAAGKVAAA SGGVPGGEAS GGGAAEDLPR 180 FFMEWLTNNR DCISAEDLRS IRLKRSTIEA AAARLGGGRQ GTMQLLKLIL TWVQNHHLHK 240 KRLRVDATME MDAEPGGPHG GHHQQQQLPS PGANPGSYEF PAAAPEGISS WTMPYQQTAF 300 TPPSAYGGET QAAIYPNAAS TTTTTTGPYP FQQSCSTSSV VVSSQPFSPP PATDMQTAPA 360 GGSGSGNHSV PLVWPQQYAF PGGAPAGNSH PLPQPFAPGF AMPMCPQRAA GGTEPSATKE 420 ARKRRMARQR RLSSSLQHQR SQQLNLGQIQ IVPQPPEQPS PRSAHSAPVT LTPPPSGAWG 480 LWSSPPGCHQ VPVQAQAQQA QAQNPPPKSS KPKQQKPSAP NAGATKLDGS PQPPAASDQK 540 RQGANKPAAD KNLRFLLQKV LKQSDVGSLG RIVLPKEAET HLPELKTRDG ISIPMEDIGT 600 SLVWNMRYRF WPNNKSRMYL LENTGDFVRS NELQEGDFIV IYSDVKGRYL IRGVKVRPVQ 660 QDQAGKHKHG IPGNRGGASD VKTGPEDRGC KEKSPHGAQR SRQEATSSMM SVRI*

Sequence ? help Back to Top

Protein Sequence Length: 715 aa Download sequence Send to blast

MDASAGSPPP PHSQQNHGGG GRPGKAPVGE IRAGEASPDD FLFAGDTFPS LPDFPCLSSP  60
SSSTFSSSSS SNSSSAFTAA AAATRGGEHA AAADDGIDAL ADLDQLLDFA SLSVPSWEDE  120
PLFPDDVGMM LEDAMSDDHK PPARHAADVS CRAAGKVAAA SGGVPGGEAS GGGAAEDLPR  180
FFMEWLTNNR DCISAEDLRS IRLKRSTIEA AAARLGGGRQ GTMQLLKLIL TWVQNHHLHK  240
KRLRVDATME MDAEPGGPHG GHHQQQQLPS PGANPGSYEF PAAAPEGISS WTMPYQQTAF  300
TPPSAYGGET QAAIYPNAAS TTTTTTGPYP FQQSCSTSSV VVSSQPFSPP PATDMQTAPA  360
GGSGSGNHSV PLVWPQQYAF PGGAPAGNSH PLPQPFAPGF AMPMCPQRAA GGTEPSATKE  420
ARKRRMARQR RLSSSLQHQR SQQLNLGQIQ IVPQPPEQPS PRSAHSAPVT LTPPPSGAWG  480
LWSSPPGCHQ VPVQAQAQQA QAQNPPPKSS KPKQQKPSAP NAGATKLDGS PQPPAASDQK  540
RQGANKPAAD KNLRFLLQKV LKQSDVGSLG RIVLPKEAET HLPELKTRDG ISIPMEDIGT  600
SLVWNMRYRF WPNNKSRMYL LENTGDFVRS NELQEGDFIV IYSDVKGRYL IRGVKVRPVQ  660
QDQAGKHKHG IPGNRGGASD VKTGPEDRGC KEKSPHGAQR SRQEATSSMM SVRI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9b_A	5e-33	553	655	1	105	B3 domain-containing transcription factor FUS3
6j9b_D	5e-33	553	655	1	105	B3 domain-containing transcription factor FUS3
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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	Brast01G050100.1.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	AJ001140	1e-117	AJ001140.1 Avena fatua mRNA for VIVIPAROUS 1 homologue transcription factor.

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	A0A0Q3GJ35	0.0	A0A0Q3GJ35_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

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	3e-56	B3 family protein

Link Out ? help Back to Top
Phytozome	Brast01G050100.1.p

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]