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

OGLUM03G31610.1

Organism

Oryza glumaepatula

Taxonomic ID

40148

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

GRAS

Protein Properties

Length: 626aa MW: 65472.3 Da PI: 4.9556

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
OGLUM03G31610.1	genome	OGE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	458.3	4.5e-140	241	622	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalkl...fsevsPil 91 lv++Ll+cAeav+++++++a+al++++ +la+++g +m+++aayf eALa+r++r ++p +++ ++++a+ l f+e +P+l OGLUM03G31610.1 241 LVHALLACAEAVQQENFAAAEALVKQIPTLAASQGGAMRKVAAYFGEALARRVYR--------FRPADST---LLDAAFADLLhahFYESCPYL 323 689**************************************************........5565555...3333333333334**** PP GRAS 92 kfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakr 185 kf+h+taNqaIlea++g++rvH++Df+i+qG+QWpaLlqaLa Rp+gpps+R+Tgvg+p+++++++l+++g++La+fA++++v+f+++ lva + OGLUM03G31610.1 324 KFAHFTANQAILEAFAGCRRVHVVDFGIKQGMQWPALLQALALRPGGPPSFRLTGVGPPQPDETDALQQVGWKLAQFAHTIRVDFQYRGLVAAT 417 ****************************************************************************************** PP GRAS 186 ledleleeL......rvkp...gEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfds 270 l+dle+ +L + E++aVn+v++lhrll+++++le+ vL +v ++P++v+vveqea+hns+sFl+rf+e+l+yys++fds OGLUM03G31610.1 418 LADLEPFMLqpegeaD--AneePEVIAVNSVFELHRLLAQPGALEK----VLGTVHAVRPRIVTVVEQEANHNSGSFLDRFTESLHYYSTMFDS 505 *****6555442..15579*******************....****************************************** PP GRAS 271 leak..........lpres.....eerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvk.sdg 348 le + + + +++++++++lgr+i+nvvacegaer+erhetl++Wr+rl++aGF+pv+l+++a+kqa++ll+ ++ +dg OGLUM03G31610.1 506 LEGGssgqaelsppA---AgggggGTDQVMSEVYLGRQICNVVACEGAERTERHETLGQWRNRLGRAGFEPVHLGSNAYKQASTLLALFAgGDG 596 88878888875441...2455679****************************************************************** PP GRAS 349 yrveeesgslvlgWkdrpLvsvSaWr 374 yrvee++g+l+lgW++rpL+++SaWr OGLUM03G31610.1 597 YRVEEKEGCLTLGWHTRPLIATSAWR 622 ***********************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12041	5.1E-35	39	113	IPR021914	Transcriptional factor DELLA, N-terminal
SMART	SM01129	1.7E-31	39	120	No hit	No description
PROSITE profile	PS50985	66.413	215	601	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.6E-137	241	622	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0006808	Biological Process	regulation of nitrogen utilization
GO:0009723	Biological Process	response to ethylene
GO:0009737	Biological Process	response to abscisic acid
GO:0009863	Biological Process	salicylic acid mediated signaling pathway
GO:0009867	Biological Process	jasmonic acid mediated signaling pathway
GO:0009938	Biological Process	negative regulation of gibberellic acid mediated signaling pathway
GO:0010187	Biological Process	negative regulation of seed germination
GO:0010218	Biological Process	response to far red light
GO:0010233	Biological Process	phloem transport
GO:0042538	Biological Process	hyperosmotic salinity response
GO:2000033	Biological Process	regulation of seed dormancy process
GO:2000377	Biological Process	regulation of reactive oxygen species metabolic process
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 626 aa Download sequence Send to blast
MKREYQEAGG SSGGGSSADM GSCKDKVMAG AAGEEEDVDE LLAALGYKVR SSDMADVAQK 60 LEQLEMAMGM GGVSAPGAAD DGFVSHLATD TVHYNPSDLS SWVESMLSEL NAPLPPIPPA 120 PPAARHASTS STVTGGGGSG FFELPAAADS SSSTYALRSI SLPVVATADP SAADSARDTK 180 RMRTGGGSTS SSSSSSSSLG GGASRGSVVE AAPPATQGAA AANAPAVPVV VVDTQEAGIR 240 LVHALLACAE AVQQENFAAA EALVKQIPTL AASQGGAMRK VAAYFGEALA RRVYRFRPAD 300 STLLDAAFAD LLHAHFYESC PYLKFAHFTA NQAILEAFAG CRRVHVVDFG IKQGMQWPAL 360 LQALALRPGG PPSFRLTGVG PPQPDETDAL QQVGWKLAQF AHTIRVDFQY RGLVAATLAD 420 LEPFMLQPEG EADANEEPEV IAVNSVFELH RLLAQPGALE KVLGTVHAVR PRIVTVVEQE 480 ANHNSGSFLD RFTESLHYYS TMFDSLEGGS SGQAELSPPA AGGGGGGTDQ VMSEVYLGRQ 540 ICNVVACEGA ERTERHETLG QWRNRLGRAG FEPVHLGSNA YKQASTLLAL FAGGDGYRVE 600 EKEGCLTLGW HTRPLIATSA WRVAAA

Sequence ? help Back to Top

Protein Sequence Length: 626 aa Download sequence Send to blast

MKREYQEAGG SSGGGSSADM GSCKDKVMAG AAGEEEDVDE LLAALGYKVR SSDMADVAQK  60
LEQLEMAMGM GGVSAPGAAD DGFVSHLATD TVHYNPSDLS SWVESMLSEL NAPLPPIPPA  120
PPAARHASTS STVTGGGGSG FFELPAAADS SSSTYALRSI SLPVVATADP SAADSARDTK  180
RMRTGGGSTS SSSSSSSSLG GGASRGSVVE AAPPATQGAA AANAPAVPVV VVDTQEAGIR  240
LVHALLACAE AVQQENFAAA EALVKQIPTL AASQGGAMRK VAAYFGEALA RRVYRFRPAD  300
STLLDAAFAD LLHAHFYESC PYLKFAHFTA NQAILEAFAG CRRVHVVDFG IKQGMQWPAL  360
LQALALRPGG PPSFRLTGVG PPQPDETDAL QQVGWKLAQF AHTIRVDFQY RGLVAATLAD  420
LEPFMLQPEG EADANEEPEV IAVNSVFELH RLLAQPGALE KVLGTVHAVR PRIVTVVEQE  480
ANHNSGSFLD RFTESLHYYS TMFDSLEGGS SGQAELSPPA AGGGGGGTDQ VMSEVYLGRQ  540
ICNVVACEGA ERTERHETLG QWRNRLGRAG FEPVHLGSNA YKQASTLLAL FAGGDGYRVE  600
EKEGCLTLGW HTRPLIATSA WRVAAA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	7e-59	248	621	26	378	Protein SCARECROW
5b3h_A	7e-59	248	621	25	377	Protein SCARECROW
5b3h_D	7e-59	248	621	25	377	Protein SCARECROW
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Upon GA application, it is degraded by the proteasome, allowing the GA signaling pathway. In contrast, its overexpression prevents the GA signaling pathway and induces a dwarf phenotype. {ECO:0000250\|UniProtKB:Q7G7J6}.
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Upon GA application, it is degraded by the proteasome, allowing the GA signaling pathway. In contrast, its overexpression prevents the GA signaling pathway and induces a dwarf phenotype. {ECO:0000269\|PubMed:10713441, ECO:0000269\|PubMed:11826299, ECO:0000269\|PubMed:20400938}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Up-regulated following GA3 but not ABA application. {ECO:0000269\|PubMed:10713441}.

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	AB030956	0.0	AB030956.1 Oryza sativa Japonica Group mRNA for OsGAI, complete cds.
GenBank	AB262980	0.0	AB262980.1 Oryza sativa Japonica Group SLR1 gene for DELLA protein, complete cds.
GenBank	AC087797	0.0	AC087797.5 Oryza sativa chromosome 3 BAC OSJNBb0022E02 genomic sequence, complete sequence.
GenBank	AP014959	0.0	AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015631543.1	0.0	DELLA protein SLR1
Swissprot	Q2TN88	0.0	SLR1_ORYSI; DELLA protein SLR1
Swissprot	Q7G7J6	0.0	SLR1_ORYSJ; DELLA protein SLR1
TrEMBL	A0A0D9ZC93	0.0	A0A0D9ZC93_9ORYZ; Uncharacterized protein
STRING	OGLUM03G31610.1	0.0	(Oryza glumipatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP998	38	138

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	0.0	GRAS family protein

Publications ? help Back to Top
Ueguchi-Tanaka M, et al. Rice dwarf mutant d1, which is defective in the alpha subunit of the heterotrimeric G protein, affects gibberellin signal transduction. Proc. Natl. Acad. Sci. U.S.A., 2000. 97(21): p. 11638-43 [PMID:11027362] Ikeda A, et al. The slender rice mutant, with constitutively activated gibberellin signal transduction, has enhanced capacity for abscisic acid level. Plant Cell Physiol., 2002. 43(9): p. 974-9 [PMID:12354914] Itoh H,Matsuoka M,Steber CM A role for the ubiquitin-26S-proteasome pathway in gibberellin signaling. Trends Plant Sci., 2003. 8(10): p. 492-7 [PMID:14557046] Oguchi K,Tanaka N,Komatsu S,Akao S Methylmalonate-semialdehyde dehydrogenase is induced in auxin-stimulated and zinc-stimulated root formation in rice. Plant Cell Rep., 2004. 22(11): p. 848-58 [PMID:15045523] Day RB, et al. Two rice GRAS family genes responsive to N -acetylchitooligosaccharide elicitor are induced by phytoactive gibberellins: evidence for cross-talk between elicitor and gibberellin signaling in rice cells. Plant Mol. Biol., 2004. 54(2): p. 261-72 [PMID:15159627] Oikawa T,Koshioka M,Kojima K,Yoshida H,Kawata M A role of OsGA20ox1 , encoding an isoform of gibberellin 20-oxidase, for regulation of plant stature in rice. Plant Mol. Biol., 2004. 55(5): p. 687-700 [PMID:15604710] Komorisono M, et al. Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling. Plant Physiol., 2005. 138(4): p. 1982-93 [PMID:16040652] Tanaka N, et al. Proteome approach to characterize the methylmalonate-semialdehyde dehydrogenase that is regulated by gibberellin. J. Proteome Res., 2005 Sep-Oct. 4(5): p. 1575-82 [PMID:16212409] Itoh H, et al. Overexpression of a GRAS protein lacking the DELLA domain confers altered gibberellin responses in rice. Plant J., 2005. 44(4): p. 669-79 [PMID:16262715] Luo A, et al. EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice. Plant Cell Physiol., 2006. 47(2): p. 181-91 [PMID:16306061] Tsuji H, et al. GAMYB controls different sets of genes and is differentially regulated by microRNA in aleurone cells and anthers. Plant J., 2006. 47(3): p. 427-44 [PMID:16792694] Shimada A, et al. The rice SPINDLY gene functions as a negative regulator of gibberellin signaling by controlling the suppressive function of the DELLA protein, SLR1, and modulating brassinosteroid synthesis. Plant J., 2006. 48(3): p. 390-402 [PMID:17052323] Ueguchi-Tanaka M,Nakajima M,Motoyuki A,Matsuoka M Gibberellin receptor and its role in gibberellin signaling in plants. Annu Rev Plant Biol, 2007. 58: p. 183-98 [PMID:17472566] Liu T,Gu JY,Xu CJ,Gao Y,An CC Overproduction of OsSLRL2 alters the development of transgenic Arabidopsis plants. Biochem. Biophys. Res. Commun., 2007. 358(4): p. 983-9 [PMID:17521606] Ueguchi-Tanaka M, et al. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. Plant Cell, 2007. 19(7): p. 2140-55 [PMID:17644730] Eckardt NA GA perception and signal transduction: molecular interactions of the GA receptor GID1 with GA and the DELLA protein SLR1 in rice. Plant Cell, 2007. 19(7): p. 2095-7 [PMID:17918309] Zhang Y, et al. Gibberellin homeostasis and plant height control by EUI and a role for gibberellin in root gravity responses in rice. Cell Res., 2008. 18(3): p. 412-21 [PMID:18268540] Aleman L, et al. Functional analysis of cotton orthologs of GA signal transduction factors GID1 and SLR1. Plant Mol. Biol., 2008. 68(1-2): p. 1-16 [PMID:18506581] Ueguchi-Tanaka M,Hirano K,Hasegawa Y,Kitano H,Matsuoka M Release of the repressive activity of rice DELLA protein SLR1 by gibberellin does not require SLR1 degradation in the gid2 mutant. Plant Cell, 2008. 20(9): p. 2437-46 [PMID:18827181] Fukao T,Bailey-Serres J Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc. Natl. Acad. Sci. U.S.A., 2008. 105(43): p. 16814-9 [PMID:18936491] Asano K, et al. Isolation and characterization of dominant dwarf mutants, Slr1-d, in rice. Mol. Genet. Genomics, 2009. 281(2): p. 223-31 [PMID:19066966] Kojima M, et al. Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa. Plant Cell Physiol., 2009. 50(7): p. 1201-14 [PMID:19369275] Hirano K, et al. Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice. Plant Cell, 2010. 22(8): p. 2680-96 [PMID:20716699] Hayashi-Tsugane M, et al. A rice mutant displaying a heterochronically elongated internode carries a 100 kb deletion. J Genet Genomics, 2011. 38(3): p. 123-8 [PMID:21477784] Fukumoto T, et al. Rare sugar D-allose suppresses gibberellin signaling through hexokinase-dependent pathway in Oryza sativa L. Planta, 2011. 234(6): p. 1083-95 [PMID:21717189] Bhattacharyya J, et al. Native polyubiquitin promoter of rice provides increased constitutive expression in stable transgenic rice plants. Plant Cell Rep., 2012. 31(2): p. 271-9 [PMID:21996937] Wu J, et al. Dominant and pleiotropic effects of a GAI gene in wheat results from a lack of interaction between DELLA and GID1. Plant Physiol., 2011. 157(4): p. 2120-30 [PMID:22010107] De Vleesschauwer D, et al. Brassinosteroids antagonize gibberellin- and salicylate-mediated root immunity in rice. Plant Physiol., 2012. 158(4): p. 1833-46 [PMID:22353574] Phanchaisri B,Samsang N,Yu L,Singkarat S,Anuntalabhochai S Expression of OsSPY and 14-3-3 genes involved in plant height variations of ion-beam-induced KDML 105 rice mutants. Mutat. Res., 2012. 734(1-2): p. 56-61 [PMID:22445891] Mimura M,Nagato Y,Itoh J Rice PLASTOCHRON genes regulate leaf maturation downstream of the gibberellin signal transduction pathway. Planta, 2012. 235(5): p. 1081-9 [PMID:22476293] Jiang X, et al. Gibberellin indirectly promotes chloroplast biogenesis as a means to maintain the chloroplast population of expanded cells. Plant J., 2012. 72(5): p. 768-80 [PMID:23020316] Schmitz AJ,Folsom JJ,Jikamaru Y,Ronald P,Walia H SUB1A-mediated submergence tolerance response in rice involves differential regulation of the brassinosteroid pathway. New Phytol., 2013. 198(4): p. 1060-70 [PMID:23496140] Hori K, et al. Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant J., 2013. 76(1): p. 36-46 [PMID:23789941] Sato T, et al. Expression and purification of a GRAS domain of SLR1, the rice DELLA protein. Protein Expr. Purif., 2014. 95: p. 248-58 [PMID:24463428] Sakata T, et al. Reduction of gibberellin by low temperature disrupts pollen development in rice. Plant Physiol., 2014. 164(4): p. 2011-9 [PMID:24569847] Wang W, et al. Dwarf Tiller1, a Wuschel-related homeobox transcription factor, is required for tiller growth in rice. PLoS Genet., 2014. 10(3): p. e1004154 [PMID:24625559] Mimura M,Itoh J Genetic interaction between rice PLASTOCHRON genes and the gibberellin pathway in leaf development. Rice (N Y), 2014. 7(1): p. 25 [PMID:25243048] Yano K, et al. Comprehensive gene expression analysis of rice aleurone cells: probing the existence of an alternative gibberellin receptor. Plant Physiol., 2015. 167(2): p. 531-44 [PMID:25511432] Fan T, et al. Rice osa-miR171c Mediates Phase Change from Vegetative to Reproductive Development and Shoot Apical Meristem Maintenance by Repressing Four OsHAM Transcription Factors. PLoS ONE, 2015. 10(5): p. e0125833 [PMID:26023934] Zhu N, et al. The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice. Plant Sci., 2015. 236: p. 146-56 [PMID:26025528] Ye Y, et al. CEF1/OsMYB103L is involved in GA-mediated regulation of secondary wall biosynthesis in rice. Plant Mol. Biol., 2015. 89(4-5): p. 385-401 [PMID:26350403] Zhao QC, et al. Generation of insect-resistant and glyphosate-tolerant rice by introduction of a T-DNA containing two Bt insecticidal genes and an EPSPS gene. J Zhejiang Univ Sci B, 2015. 16(10): p. 824-31 [PMID:26465130] De Vleesschauwer D, et al. The DELLA Protein SLR1 Integrates and Amplifies Salicylic Acid- and Jasmonic Acid-Dependent Innate Immunity in Rice. Plant Physiol., 2016. 170(3): p. 1831-47 [PMID:26829979] Yang C,Ma Y,Li J The rice YABBY4 gene regulates plant growth and development through modulating the gibberellin pathway. J. Exp. Bot., 2016. 67(18): p. 5545-5556 [PMID:27578842]