PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Protein Features |

3D Structure |

Function |

Orthologous Group |

Publication

Basic Information? help Back to Top

TF ID

Itr_sc000495.1_g00005.1

Organism

Ipomoea trifida

Taxonomic ID

35884

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea

Family

GRAS

Protein Properties

Length: 519aa MW: 56465 Da PI: 5.3861

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Itr_sc000495.1_g00005.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	414.3	1.1e-126	152	515	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlsel..aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaalklf 84 lv++L++cA v+ g+++la +l+ +l+ l + ++g + ++a yf AL++rl+ ++ ++ + + e ++ f Itr_sc000495.1_g00005.1 152 LVHALMTCAVSVQRGEFSLAGSLIDELQLLltRVNSGCGIGKVAGYFIDALSKRLYT--PQGVSLM---GS----AYEDEILYSHF 228 689***********************9987889999***************9..3333222...22....3344456789 PP GRAS 85 sevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAe 170 +e+ P+lkf+h+taNqaIlea++g+++vH+iDf++++GlQWpaL+qaLa Rp+gpp lR+Tg+g+p+++ +++l+e+g +La++A+ Itr_sc000495.1_g00005.1 229 YEAAPYLKFAHFTANQAILEAFHGHDCVHVIDFNLMHGLQWPALIQALALRPGGPPLLRLTGIGPPSPDGRDSLREIGLKLAELAR 314 ************************************************************************************ PP GRAS 171 elgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFler 256 +++v+f f+ ++a+rl+d++ ++L+v ++Ea+aVn+++qlh+ll + s++d+vL ++sl+Pkvv+vveqea+hn+++Fl+r Itr_sc000495.1_g00005.1 315 SVNVRFAFRGVAASRLDDVKSWMLQVGSNEAVAVNSIMQLHKLLGPDPIRGSPIDTVLGWIRSLNPKVVTVVEQEANHNQPEFLDR 400 ****************************************99999999****************************** PP GRAS 257 flealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllr 342 f+e+l+yys++fdslea ++ ++ + +++++rei+nvv+ceg +r+erhe l+kW++rl+ aGFkp++l+++a kqa++ll Itr_sc000495.1_g00005.1 401 FTESLYYYSTMFDSLEAC---PAQPEKALAEMYIQREICNVVCCEGVARVERHEPLGKWKARLTGAGFKPLNLGSNAFKQASMLLT 483 ************99...566677788888************************************************* PP GRAS 343 kvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ++ +gy+vee +g+l+lgW++rpL+++SaW+ Itr_sc000495.1_g00005.1 484 LFSAEGYNVEETEGCLTLGWHSRPLIAASAWQ 515 *****************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01129	5.5E-16	28	103	No hit	No description
Pfam	PF12041	4.7E-26	28	97	IPR021914	Transcriptional factor DELLA, N-terminal
PROSITE profile	PS50985	62.142	126	495	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.8E-124	152	515	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 519 aa Download sequence Send to blast
MSPHDSSITS SSGSSSSSCS AAHVDQIDSL LAGAGYMVRS SDLRHVAQRL EHLESFMVNS 60 PMGSEISQHL GNDVVHQNPS DLGSWVDSLL SELHPPPVPE FAAPCPSDSN YVAAGPTGWS 120 ECEAMQQQPQ IVSPSHLTVV TATEQEDSGI RLVHALMTCA VSVQRGEFSL AGSLIDELQL 180 LLTRVNSGCG IGKVAGYFID ALSKRLYTPQ GVSLMGSAYE DEILYSHFYE AAPYLKFAHF 240 TANQAILEAF HGHDCVHVID FNLMHGLQWP ALIQALALRP GGPPLLRLTG IGPPSPDGRD 300 SLREIGLKLA ELARSVNVRF AFRGVAASRL DDVKSWMLQV GSNEAVAVNS IMQLHKLLGP 360 DPIRGSPIDT VLGWIRSLNP KVVTVVEQEA NHNQPEFLDR FTESLYYYST MFDSLEACPA 420 QPEKALAEMY IQREICNVVC CEGVARVERH EPLGKWKARL TGAGFKPLNL GSNAFKQASM 480 LLTLFSAEGY NVEETEGCLT LGWHSRPLIA ASAWQASRD

Sequence ? help Back to Top

Protein Sequence Length: 519 aa Download sequence Send to blast

MSPHDSSITS SSGSSSSSCS AAHVDQIDSL LAGAGYMVRS SDLRHVAQRL EHLESFMVNS  60
PMGSEISQHL GNDVVHQNPS DLGSWVDSLL SELHPPPVPE FAAPCPSDSN YVAAGPTGWS  120
ECEAMQQQPQ IVSPSHLTVV TATEQEDSGI RLVHALMTCA VSVQRGEFSL AGSLIDELQL  180
LLTRVNSGCG IGKVAGYFID ALSKRLYTPQ GVSLMGSAYE DEILYSHFYE AAPYLKFAHF  240
TANQAILEAF HGHDCVHVID FNLMHGLQWP ALIQALALRP GGPPLLRLTG IGPPSPDGRD  300
SLREIGLKLA ELARSVNVRF AFRGVAASRL DDVKSWMLQV GSNEAVAVNS IMQLHKLLGP  360
DPIRGSPIDT VLGWIRSLNP KVVTVVEQEA NHNQPEFLDR FTESLYYYST MFDSLEACPA  420
QPEKALAEMY IQREICNVVC CEGVARVERH EPLGKWKARL TGAGFKPLNL GSNAFKQASM  480
LLTLFSAEGY NVEETEGCLT LGWHSRPLIA ASAWQASRD

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	3e-60	140	514	7	378	Protein SCARECROW
5b3h_A	3e-60	140	514	6	377	Protein SCARECROW
5b3h_D	3e-60	140	514	6	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_019192394.1	0.0	PREDICTED: DELLA protein DWARF8-like
Swissprot	Q9LQT8	1e-161	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A328CVB6	0.0	A0A328CVB6_9ASTE; Uncharacterized protein
TrEMBL	A0A484NC12	0.0	A0A484NC12_9ASTE; Uncharacterized protein
STRING	XP_010249953.1	0.0	(Nelumbo nucifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA15141	5	8

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	1e-138	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]