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

MDP0000134341

Common Name

L3b

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

GRAS

Protein Properties

Length: 523aa MW: 57311.6 Da PI: 5.9911

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000134341	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	70.2	4.1e-22	156	257	1	108
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdgd..pmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 lv+lL++cAe v+ g+l+la +l+++++ l + + + ++a yf AL++r+++ ++ ++ + + ++ e+ +++f+e++P+lkf+ MDP0000134341 156 LVHLLVTCAESVQRGELALAGSLIENMQALMTRVNTscGIGKVAGYFIDALSRRIFS--PQ---SVGSAAG---STHENELLYHYFYEACPYLKFA 243 68**************************66665422799***********9..22...2222222...24555678899******* PP GRAS 95 hltaNqaIleaveg 108 h+taNqaIlea++g MDP0000134341 244 HFTANQAILEAFHG 257 **********97 PP
2	GRAS	283.1	7.8e-87	263	497	137	374
GRAS 137 egppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvk 232 + +p lR+Tg+g+p+++ +++l+e+g rLa++A++++v+f f+ ++a+rled+++++L+v+p+Ea+aVn+++qlhrll ++ + +s+++ +L+ ++ MDP0000134341 263 RRAPLLRLTGIGPPSPDGRDSLREIGLRLAELARSVNVRFAFRGVAASRLEDVKPWMLQVSPKEAVAVNSIMQLHRLLGSDPNRNSPIEMMLSWIR 358 6789****************************************************************************************** PP GRAS 233 slsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvp 328 +l+Pk+v+vveqeadhn++ Fl+rf+eal+yys++fdslea + ++++ +++++rei+nvv+cega+r+erhe l+kWr rl++aGF+p++ MDP0000134341 359 NLNPKIVTVVEQEADHNKPGFLDRFTEALYYYSTMFDSLEAC---PMQPEKTLAEMYIQREICNVVCCEGAARVERHEPLSKWRTRLGQAGFSPLH 451 ***********************************999...567778888899*********************************** PP GRAS 329 lsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 l+++a kqa++ll ++ +gyrvee++g+l+lgW++rpL+++SaW+ MDP0000134341 452 LGSNAFKQASMLLTLFSAEGYRVEENQGCLTLGWHSRPLIAASAWQ 497 *******************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01129	1.4E-19	32	104	No hit	No description
Pfam	PF12041	4.3E-31	32	98	IPR021914	Transcriptional factor DELLA, N-terminal
PROSITE profile	PS50985	40.132	130	477	IPR005202	Transcription factor GRAS
Pfam	PF03514	1.4E-19	156	257	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.7E-84	263	497	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

Sequence ? help Back to Top
Protein Sequence Length: 523 aa Download sequence Send to blast
MGPYGSTTCS GVSSSASSSS SSSVTKSPAE IDGYLADAGY KVRSSDLRHV AQRLERLETV 60 MVNSPSDLSQ LASDAVLYNP SDIATWVDSL LSEFNHQPLM SLPSDLDFPD SAVINNPAAL 120 SGETWTDNSS FASAVPQQNH QLTVVTAMEE DSGIRLVHLL VTCAESVQRG ELALAGSLIE 180 NMQALMTRVN TSCGIGKVAG YFIDALSRRI FSPQSVGSAA GSTHENELLY HYFYEACPYL 240 KFAHFTANQA ILEAFHGPCS PPRRAPLLRL TGIGPPSPDG RDSLREIGLR LAELARSVNV 300 RFAFRGVAAS RLEDVKPWML QVSPKEAVAV NSIMQLHRLL GSDPNRNSPI EMMLSWIRNL 360 NPKIVTVVEQ EADHNKPGFL DRFTEALYYY STMFDSLEAC PMQPEKTLAE MYIQREICNV 420 VCCEGAARVE RHEPLSKWRT RLGQAGFSPL HLGSNAFKQA SMLLTLFSAE GYRVEENQGC 480 LTLGWHSRPL IAASAWQVMX VAEATINHQT VGILNQNNNA NHV

Sequence ? help Back to Top

Protein Sequence Length: 523 aa Download sequence Send to blast

MGPYGSTTCS GVSSSASSSS SSSVTKSPAE IDGYLADAGY KVRSSDLRHV AQRLERLETV  60
MVNSPSDLSQ LASDAVLYNP SDIATWVDSL LSEFNHQPLM SLPSDLDFPD SAVINNPAAL  120
SGETWTDNSS FASAVPQQNH QLTVVTAMEE DSGIRLVHLL VTCAESVQRG ELALAGSLIE  180
NMQALMTRVN TSCGIGKVAG YFIDALSRRI FSPQSVGSAA GSTHENELLY HYFYEACPYL  240
KFAHFTANQA ILEAFHGPCS PPRRAPLLRL TGIGPPSPDG RDSLREIGLR LAELARSVNV  300
RFAFRGVAAS RLEDVKPWML QVSPKEAVAV NSIMQLHRLL GSDPNRNSPI EMMLSWIRNL  360
NPKIVTVVEQ EADHNKPGFL DRFTEALYYY STMFDSLEAC PMQPEKTLAE MYIQREICNV  420
VCCEGAARVE RHEPLSKWRT RLGQAGFSPL HLGSNAFKQA SMLLTLFSAE GYRVEENQGC  480
LTLGWHSRPL IAASAWQVMX VAEATINHQT VGILNQNNNA NHV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	2e-42	149	496	12	378	Protein SCARECROW
5b3h_A	2e-42	149	496	11	377	Protein SCARECROW
5b3h_D	2e-42	149	496	11	377	Protein SCARECROW
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.13732	0.0	bud\| fruit\| leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitously expressed. Expressed in rosette leaves, roots, stems and inflorescences of greenhouse grown. {ECO:0000269\|PubMed:11877383, ECO:0000269\|PubMed:9237632, ECO:0000269\|PubMed:9490740}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. Transcription coactivator of the zinc finger transcription factors GAF1/IDD2 and ENY/IDD1 in regulation of gibberellin homeostasis and signaling (PubMed:25035403). No effect of the BOI proteins on its stability. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Positively regulates XERICO expression. In contrast to RGA, it is less sensitive to GA. Its activity is probably regulated by other phytohormones such as auxin and ethylene. {ECO:0000269\|PubMed:11487693, ECO:0000269\|PubMed:11606551, ECO:0000269\|PubMed:11606552, ECO:0000269\|PubMed:14973286, ECO:0000269\|PubMed:15128937, ECO:0000269\|PubMed:16034591, ECO:0000269\|PubMed:17933900, ECO:0000269\|PubMed:25035403, ECO:0000269\|PubMed:9389651}.

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	DQ007888	0.0	DQ007888.1 Malus x domestica DELLA protein (L3b) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001315676.1	0.0	DELLA protein GAI-like
Swissprot	Q9LQT8	1e-144	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A498KHD3	0.0	A0A498KHD3_MALDO; Uncharacterized protein
STRING	XP_008343960.1	0.0	(Malus domestica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF803	34	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	1e-145	GRAS family protein

Link Out ? help Back to Top
Phytozome	MDP0000134341

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Gallego-Giraldo C, et al. Role of the gibberellin receptors GID1 during fruit-set in Arabidopsis. Plant J., 2014. 79(6): p. 1020-1032 [PMID:24961590] Fukazawa J, et al. DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis. Plant Cell, 2014. 26(7): p. 2920-38 [PMID:25035403] Marín-de la Rosa N, et al. Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genet., 2015. 11(7): p. e1005337 [PMID:26134422] Shi H,Wei Y,Wang Q,Reiter RJ,He C Melatonin mediates the stabilization of DELLA proteins to repress the floral transition in Arabidopsis. J. Pineal Res., 2016. 60(3): p. 373-9 [PMID:26887824] Lee SA, et al. Interplay between ABA and GA Modulates the Timing of Asymmetric Cell Divisions in the Arabidopsis Root Ground Tissue. Mol Plant, 2016. 9(6): p. 870-84 [PMID:26970019] Qu J,Kang SG,Hah C,Jang JC Molecular and cellular characterization of GA-Stimulated Transcripts GASA4 and GASA6 in Arabidopsis thaliana. Plant Sci., 2016. 246: p. 1-10 [PMID:26993231] Shahnejat-Bushehri S,Nobmann B,Devi Allu A,Balazadeh S JUB1 suppresses Pseudomonas syringae-induced defense responses through accumulation of DELLA proteins. Plant Signal Behav, 2016. 11(6): p. e1181245 [PMID:27159137] Shahnejat-Bushehri S,Tarkowska D,Sakuraba Y,Balazadeh S Arabidopsis NAC transcription factor JUB1 regulates GA/BR metabolism and signalling. Nat Plants, 2016. 2: p. 16013 [PMID:27249348] Wang H, et al. The DELLA-CONSTANS Transcription Factor Cascade Integrates Gibberellic Acid and Photoperiod Signaling to Regulate Flowering. Plant Physiol., 2016. 172(1): p. 479-88 [PMID:27406167] Li W,Wang H,Yu D Arabidopsis WRKY Transcription Factors WRKY12 and WRKY13 Oppositely Regulate Flowering under Short-Day Conditions. Mol Plant, 2016. 9(11): p. 1492-1503 [PMID:27592586] Liu B,De Storme N,Geelen D Gibberellin Induces Diploid Pollen Formation by Interfering with Meiotic Cytokinesis. Plant Physiol., 2017. 173(1): p. 338-353 [PMID:27621423] Matsuoka K, et al. Differential Cellular Control by Cotyledon-Derived Phytohormones Involved in Graft Reunion of Arabidopsis Hypocotyls. Plant Cell Physiol., 2016. 57(12): p. 2620-2631 [PMID:27986917] Zentella R, et al. The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA. Nat. Chem. Biol., 2017. 13(5): p. 479-485 [PMID:28244988] Zhang Y, et al. GA-DELLA pathway is involved in regulation of nitrogen deficiency-induced anthocyanin accumulation. Plant Cell Rep., 2017. 36(4): p. 557-569 [PMID:28275852] Zhang L,Chen L,Yu D Transcription Factor WRKY75 Interacts with DELLA Proteins to Affect Flowering. Plant Physiol., 2018. 176(1): p. 790-803 [PMID:29133369] Nelson SK,Ariizumi T,Steber CM Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant. Front Plant Sci, 2017. 8: p. 2158 [PMID:29312402] Liu B,De Storme N,Geelen D Cold-Induced Male Meiotic Restitution in Arabidopsis thaliana Is Not Mediated by GA-DELLA Signaling. Front Plant Sci, 2018. 9: p. 91 [PMID:29459879] Zhang Y, et al. DELLA proteins negatively regulate dark-induced senescence and chlorophyll degradation in Arabidopsis through interaction with the transcription factor WRKY6. Plant Cell Rep., 2018. 37(7): p. 981-992 [PMID:29574486] Felipo-Benavent A, et al. Regulation of xylem fiber differentiation by gibberellins through DELLA-KNAT1 interaction. Development, 2019. [PMID:30389856] Wright DA, et al. Recovery of YAC-end sequences through complementation of an Escherichia coli pyrF mutation. Nucleic Acids Res., 1997. 25(13): p. 2679-80 [PMID:9185581]