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

NNU_003621-RA

Organism

Nelumbo nucifera

Taxonomic ID

4432

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo

Family

GRAS

Protein Properties

Length: 541aa MW: 59193.3 Da PI: 5.0985

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_003621-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	427.4	1.1e-130	161	523	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlsel..aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklfsevsPilkfs 94 lv+lLl+cAe ++ gdl+la +lL++++ l + ++g + ++a yf AL++rl++ p++ ++ e+ ++ f+e++P+lkf+ NNU_003621-RA 161 LVHLLLTCAESIQRGDLALAGTLLEKMRALlsRVNTGCGIGKVAGYFIDALSRRLFS----------PQAVCAGSVLENEILYHHFYEACPYLKFA 246 68**************************555566789*************9..........222222336777788999******* PP GRAS 95 hltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledle 190 h+taNqaIlea++g+++vH++Df++++GlQWpaL+qaLa Rp+gpp lR+Tg+g+p+++ +++l+e+g +La++A++++v+f f+ ++a+rl+d++ NNU_003621-RA 247 HFTANQAILEAFDGHDCVHVVDFNLMHGLQWPALIQALALRPGGPPLLRLTGIGPPSPDGRDSLREIGLKLAELARSVNVRFAFRGVAASRLDDVK 342 ******************************************************************************************** PP GRAS 191 leeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvE 286 +++L+v p+Ea+a+n+++qlh+ll + + s++d+vL v+sl+Pk+++vveqea+hn+++Fl+rf+eal+yys++fdsle+ + + ++ v NNU_003621-RA 343 PWMLQVGPREAVAINSIMQLHKLLGPDPNRGSPIDSVLGWVRSLNPKIITVVEQEANHNQPEFLDRFTEALYYYSTMFDSLESC---TLQPEKAVA 435 *****************************************************************************888...568888899 PP GRAS 287 rellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 +++++rei+nvv+ceg++r+erhe l+kWr+rl+ aGF+p++l+++a kqa++ll ++ +gy vee++g+l+lgW++rpL+++SaW+ NNU_003621-RA 436 EMYIQREICNVVSCEGSARVERHEPLAKWRARLGGAGFRPLHLGSNAFKQASMLLTLFSAEGYCVEENQGCLTLGWHSRPLIAASAWQ 523 999**********************************************************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01129	4.7E-24	29	101	No hit	No description
Pfam	PF12041	5.5E-32	29	94	IPR021914	Transcriptional factor DELLA, N-terminal
PROSITE profile	PS50985	64.255	135	503	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.9E-128	161	523	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 541 aa Download sequence Send to blast
MGPYDYGISA GSSSSSSSSC AGGKPTELDG LLAGAGYKVR SSDLHQVAQR LEKLETFMVN 60 APTEISQLAS EAVHYNPSDL ASWVDSMLSE INQPFPVSSS DLSDFSDFHY MDDLVTPPLQ 120 HEVLTDAWAD QSAQQQQPQP PLQQQQLTVV AAIEEDSGIK LVHLLLTCAE SIQRGDLALA 180 GTLLEKMRAL LSRVNTGCGI GKVAGYFIDA LSRRLFSPQA VCAGSVLENE ILYHHFYEAC 240 PYLKFAHFTA NQAILEAFDG HDCVHVVDFN LMHGLQWPAL IQALALRPGG PPLLRLTGIG 300 PPSPDGRDSL REIGLKLAEL ARSVNVRFAF RGVAASRLDD VKPWMLQVGP REAVAINSIM 360 QLHKLLGPDP NRGSPIDSVL GWVRSLNPKI ITVVEQEANH NQPEFLDRFT EALYYYSTMF 420 DSLESCTLQP EKAVAEMYIQ REICNVVSCE GSARVERHEP LAKWRARLGG AGFRPLHLGS 480 NAFKQASMLL TLFSAEGYCV EENQGCLTLG WHSRPLIAAS AWQAVPLPDT NSLPTINDCV 540 L

Sequence ? help Back to Top

Protein Sequence Length: 541 aa Download sequence Send to blast

MGPYDYGISA GSSSSSSSSC AGGKPTELDG LLAGAGYKVR SSDLHQVAQR LEKLETFMVN  60
APTEISQLAS EAVHYNPSDL ASWVDSMLSE INQPFPVSSS DLSDFSDFHY MDDLVTPPLQ  120
HEVLTDAWAD QSAQQQQPQP PLQQQQLTVV AAIEEDSGIK LVHLLLTCAE SIQRGDLALA  180
GTLLEKMRAL LSRVNTGCGI GKVAGYFIDA LSRRLFSPQA VCAGSVLENE ILYHHFYEAC  240
PYLKFAHFTA NQAILEAFDG HDCVHVVDFN LMHGLQWPAL IQALALRPGG PPLLRLTGIG  300
PPSPDGRDSL REIGLKLAEL ARSVNVRFAF RGVAASRLDD VKPWMLQVGP REAVAINSIM  360
QLHKLLGPDP NRGSPIDSVL GWVRSLNPKI ITVVEQEANH NQPEFLDRFT EALYYYSTMF  420
DSLESCTLQP EKAVAEMYIQ REICNVVSCE GSARVERHEP LAKWRARLGG AGFRPLHLGS  480
NAFKQASMLL TLFSAEGYCV EENQGCLTLG WHSRPLIAAS AWQAVPLPDT NSLPTINDCV  540
L

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	7e-60	154	522	12	378	Protein SCARECROW
5b3h_A	6e-60	154	522	11	377	Protein SCARECROW
5b3h_D	6e-60	154	522	11	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_010249953.1	0.0	PREDICTED: DELLA protein SLR1-like
Swissprot	Q9LQT8	1e-165	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A1U7ZN02	0.0	A0A1U7ZN02_NELNU; DELLA protein SLR1-like
STRING	XP_010249953.1	0.0	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	1e-146	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]