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

Cotton_A_11125_BGI-A2_v1.0

Organism

Gossypium arboreum

Taxonomic ID

29729

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

GRAS

Protein Properties

Length: 541aa MW: 59367.1 Da PI: 5.6776

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_11125_BGI-A2_v1.0	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	426.9	1.6e-130	165	530	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlselaspdg..dpmqRlaayfteALaarlarsvselykalppsetseknsseelaal 81 lv+ L++cAe+v+ gd++la+++L+ ++ l + + ++a +f AL++r+++ ++ + e+ + Cotton_A_11125_BGI-A2_v1.0 165 LVHMLMTCAECVQRGDFSLATSCLEDMQGLLTRVNtvCGIGKVAGHFIDALSRRIFQ---GIGGGSVNG----GSAYENELLY 240 689***********************99555441269*************9...444322222....2356677788 PP GRAS 82 klfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetger 164 + f+e++P+lkf+h+taNqaIlea++g+++vH++Df++++GlQWpaL+qaLa Rp+gpp lR+Tg+g+p+++ +++l+e+g r Cotton_A_11125_BGI-A2_v1.0 241 HHFYEACPYLKFAHFTANQAILEAFDGHDCVHVVDFNLMHGLQWPALIQALALRPGGPPLLRLTGIGPPSPDGRDSLREIGLR 323 99***************************************************************************** PP GRAS 165 LakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveqead 247 La++A++++v+f f+ ++a+rled+++++L+v+p+E++aVn+++qlhrll ++ + +s++++vL+ ++sl+Pk+++vveqea+ Cotton_A_11125_BGI-A2_v1.0 324 LAELARSVNVRFAFRGVAASRLEDVKPWMLQVNPKESVAVNSIMQLHRLLGSDPNRNSPIETVLSWIRSLNPKIMTVVEQEAN 406 ******************************************************************************* PP GRAS 248 hnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvpls 330 hn++ Fl+rf+eal+yys++fdslea + + ++ + + +++rei nvv+ceg++r+erhe l+kWr rl+ aGF+p++l+ Cotton_A_11125_BGI-A2_v1.0 407 HNQPGFLDRFTEALHYYSTMFDSLEAC---TVQPNKALAEIYIQREIANVVSCEGSARVERHEPLSKWRTRLSGAGFRPLHLG 486 ********************998...578888899999************************************* PP GRAS 331 ekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 ++a+kqa++ll ++ +gy+vee++g+l+lgW++rpL+++SaW+ Cotton_A_11125_BGI-A2_v1.0 487 SNAYKQASMLLTLFSAEGYSVEENDGCLTLGWHSRPLIAASAWQ 530 *****************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF12041	4.2E-31	39	105	IPR021914	Transcriptional factor DELLA, N-terminal
SMART	SM01129	1.8E-20	39	111	No hit	No description
PROSITE profile	PS50985	63.61	139	510	IPR005202	Transcription factor GRAS
Pfam	PF03514	5.7E-128	165	530	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 541 aa Download sequence Send to blast
MVLYDSATLG GSCSGSSSSS SSSKPPPLQQ RQQTQQDIDG FLAGAGYRVR SSELRKVAQR 60 LERLETAMVN SPADLSQLAS DTIHYNPSDL ASWVDSLLSE LTQPPTCPSE FIMDPVSNQT 120 VVSDAWTTAE PHMPQVHQNI SYEQQSLNNQ LTVVPAMEED SGIRLVHMLM TCAECVQRGD 180 FSLATSCLED MQGLLTRVNT VCGIGKVAGH FIDALSRRIF QGIGGGSVNG GSAYENELLY 240 HHFYEACPYL KFAHFTANQA ILEAFDGHDC VHVVDFNLMH GLQWPALIQA LALRPGGPPL 300 LRLTGIGPPS PDGRDSLREI GLRLAELARS VNVRFAFRGV AASRLEDVKP WMLQVNPKES 360 VAVNSIMQLH RLLGSDPNRN SPIETVLSWI RSLNPKIMTV VEQEANHNQP GFLDRFTEAL 420 HYYSTMFDSL EACTVQPNKA LAEIYIQREI ANVVSCEGSA RVERHEPLSK WRTRLSGAGF 480 RPLHLGSNAY KQASMLLTLF SAEGYSVEEN DGCLTLGWHS RPLIAASAWQ AVSDGTADFP 540 A

Sequence ? help Back to Top

Protein Sequence Length: 541 aa Download sequence Send to blast

MVLYDSATLG GSCSGSSSSS SSSKPPPLQQ RQQTQQDIDG FLAGAGYRVR SSELRKVAQR  60
LERLETAMVN SPADLSQLAS DTIHYNPSDL ASWVDSLLSE LTQPPTCPSE FIMDPVSNQT  120
VVSDAWTTAE PHMPQVHQNI SYEQQSLNNQ LTVVPAMEED SGIRLVHMLM TCAECVQRGD  180
FSLATSCLED MQGLLTRVNT VCGIGKVAGH FIDALSRRIF QGIGGGSVNG GSAYENELLY  240
HHFYEACPYL KFAHFTANQA ILEAFDGHDC VHVVDFNLMH GLQWPALIQA LALRPGGPPL  300
LRLTGIGPPS PDGRDSLREI GLRLAELARS VNVRFAFRGV AASRLEDVKP WMLQVNPKES  360
VAVNSIMQLH RLLGSDPNRN SPIETVLSWI RSLNPKIMTV VEQEANHNQP GFLDRFTEAL  420
HYYSTMFDSL EACTVQPNKA LAEIYIQREI ANVVSCEGSA RVERHEPLSK WRTRLSGAGF  480
RPLHLGSNAY KQASMLLTLF SAEGYSVEEN DGCLTLGWHS RPLIAASAWQ AVSDGTADFP  540
A

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	4e-60	158	529	12	378	Protein SCARECROW
5b3h_A	4e-60	158	529	11	377	Protein SCARECROW
5b3h_D	4e-60	158	529	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	GQ290637	0.0	GQ290637.1 Gossypium hirsutum cultivar Xinluzao-13 GAI/RGA-like 3-b gene, complete cds.
GenBank	HM034763	0.0	HM034763.1 Gossypium hirsutum cultivar Xinluzao-13 GAI3b mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001313852.1	0.0	DELLA protein SLR1-like
Refseq	XP_017608160.1	0.0	PREDICTED: DELLA protein SLR1-like
Swissprot	Q9LQT8	1e-167	GAI_ARATH; DELLA protein GAI
TrEMBL	C9DA15	0.0	C9DA15_GOSHI; GAI/RGA-like 3-b
STRING	Gorai.009G021700.1	0.0	(Gossypium raimondii)

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-150	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]