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

Neem_9969_f_1

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

GRAS

Protein Properties

Length: 526aa MW: 57959.8 Da PI: 5.205

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_9969_f_1	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	418.4	6.2e-128	154	516	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlsel..aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 lv+ L++cAe v+ gdl+la +l++ l+ l + ++ + + ++a yf AL+ r+++ + +++ +s e+ ++ f+e++P+lkf+ Neem_9969_f_1 154 LVHILMTCAESVQRGDLALAGSLIEDLKALltRVNTTRGIGKVAGYFIDALNLRILGVGGSVC----AS------AYENEILYHHFYEACPYLKFA 239 689************************9655666689**************444433....22......3445567889******* PP GRAS 95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledle 190 h+taNqaIlea++g++ vH++Df++++GlQWpaL+qaLa Rp+gpp lR+Tg+g+p+++ +++l+e+g rLa++A++++++f f+ ++a+rled++ Neem_9969_f_1 240 HFTANQAILEAFDGHDSVHVVDFNLMHGLQWPALIQALALRPGGPPLLRLTGIGPPSPDGRDSLREIGLRLAELARSVNIRFAFRGVAASRLEDVK 335 ******************************************************************************************** PP GRAS 191 leeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvE 286 +++L+v+p+EalaVn+++qlh+ll ++ +s+ + vL +++l+Pk+++vveqea+hn+++Fl+rf+ al+yys++fdslea + ++ + Neem_9969_f_1 336 PWMLQVRPKEALAVNSIMQLHKLLGSDPIRNSPMEMVLGWIRNLNPKIMTVVEQEANHNQPEFLDRFTTALYYYSTMFDSLEAC---PLQPEKALA 428 ************************9************************************************998...345666677 PP GRAS 287 rellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 + +++rei+nvv+ceg++r+erhe l++Wr rl+eaGF+p++l+++a qa++ll ++ +gy vee++g+l+lgW++rpL+++SaW+ Neem_9969_f_1 429 EIYIQREICNVVCCEGSARVERHEPLAEWRGRLSEAGFRPLHLGSNAFRQASMLLTLFSAEGYCVEENEGCLTLGWHNRPLIAASAWQ 516 788**********************************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12041	2.0E-33	29	95	IPR021914	Transcriptional factor DELLA, N-terminal
SMART	SM01129	6.3E-24	29	101	No hit	No description
PROSITE profile	PS50985	63.699	128	496	IPR005202	Transcription factor GRAS
Pfam	PF03514	2.1E-125	154	516	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 526 aa Download sequence Send to blast
MEQYDSTASA GSSSGSSSCS ATKPSPDIDG LLAGAGYKVR SSELRQVAQR LERLENVMVN 60 STAEISQLAS DTVHYNPSDL ASWVDSLLSE FNHPASLPSD LPDFPDLIAG PSVNHAVVNN 120 FVSDNHFTPQ QDISQQQQQL MLVSSMEEDS GIRLVHILMT CAESVQRGDL ALAGSLIEDL 180 KALLTRVNTT RGIGKVAGYF IDALNLRILG VGGSVCASAY ENEILYHHFY EACPYLKFAH 240 FTANQAILEA FDGHDSVHVV DFNLMHGLQW PALIQALALR PGGPPLLRLT GIGPPSPDGR 300 DSLREIGLRL AELARSVNIR FAFRGVAASR LEDVKPWMLQ VRPKEALAVN SIMQLHKLLG 360 SDPIRNSPME MVLGWIRNLN PKIMTVVEQE ANHNQPEFLD RFTTALYYYS TMFDSLEACP 420 LQPEKALAEI YIQREICNVV CCEGSARVER HEPLAEWRGR LSEAGFRPLH LGSNAFRQAS 480 MLLTLFSAEG YCVEENEGCL TLGWHNRPLI AASAWQAMIS ISSREN

Sequence ? help Back to Top

Protein Sequence Length: 526 aa Download sequence Send to blast

MEQYDSTASA GSSSGSSSCS ATKPSPDIDG LLAGAGYKVR SSELRQVAQR LERLENVMVN  60
STAEISQLAS DTVHYNPSDL ASWVDSLLSE FNHPASLPSD LPDFPDLIAG PSVNHAVVNN  120
FVSDNHFTPQ QDISQQQQQL MLVSSMEEDS GIRLVHILMT CAESVQRGDL ALAGSLIEDL  180
KALLTRVNTT RGIGKVAGYF IDALNLRILG VGGSVCASAY ENEILYHHFY EACPYLKFAH  240
FTANQAILEA FDGHDSVHVV DFNLMHGLQW PALIQALALR PGGPPLLRLT GIGPPSPDGR  300
DSLREIGLRL AELARSVNIR FAFRGVAASR LEDVKPWMLQ VRPKEALAVN SIMQLHKLLG  360
SDPIRNSPME MVLGWIRNLN PKIMTVVEQE ANHNQPEFLD RFTTALYYYS TMFDSLEACP  420
LQPEKALAEI YIQREICNVV CCEGSARVER HEPLAEWRGR LSEAGFRPLH LGSNAFRQAS  480
MLLTLFSAEG YCVEENEGCL TLGWHNRPLI AASAWQAMIS ISSREN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3h_A	6e-63	129	515	2	377	Protein SCARECROW
5b3h_D	6e-63	129	515	2	377	Protein SCARECROW
Search in ModeBase

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006475770.1	0.0	DELLA protein GAI
Swissprot	Q9LQT8	1e-167	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A067GKY1	0.0	A0A067GKY1_CITSI; Uncharacterized protein
STRING	XP_006475770.1	0.0	(Citrus sinensis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16045	10	15

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	1e-148	GRAS family protein

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]