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

evm.model.supercontig_75.88

Organism

Carica papaya

Taxonomic ID

3649

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Caricaceae; Carica

Family

GRAS

Protein Properties

Length: 547aa MW: 59779.8 Da PI: 5.295

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm.model.supercontig_75.88	genome	ASGPB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	421.1	9.2e-129	155	521	1	374
GRAS 1 lvelLlecAeavssgdlelaqalLarlsel..aspdgdpmqRlaayfteALaarlarsvselykalppsetseknsseelaa 80 lv+ L++cAe v+ g+l la +l++ ++ l ++g + ++a yf AL++r+++ ++l+ +++ s+ + + evm.model.supercontig_75.88 155 LVHMLMTCAESVQRGELPLAGSLIEDMRGLlaHVNQGCGIGKVAGYFIDALNRRILSPPQSLAVSVNGSAFE------NEIL 230 689***********************9987778899***************666666555555554......4556 PP GRAS 81 lklfsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetg 162 ++ f+e++P+lkf+h+taNqaIlea++g+++vH++Df++++GlQWpaL+qaLa Rp+gpp lR+Tg+g+p+++ +++l+e+g evm.model.supercontig_75.88 231 YHHFYEACPYLKFAHFTANQAILEAFDGHDCVHVVDFNLMHGLQWPALIQALALRPGGPPLLRLTGIGPPSPDGRDSLREIG 312 789*************************************************************************** PP GRAS 163 erLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlhrlldesvsleserdevLklvkslsPkvvvvveq 244 rLa++A++++v+f f+ ++a+rled+++++L+v+p+EalaVn+++qlhrll +++ +s+++ vL +++l+Pk+++vveq evm.model.supercontig_75.88 313 LRLAELARSVNVRFAFRGVAASRLEDVKPWMLQVSPKEALAVNSIMQLHRLLGADQNRNSPIEMVLGWIRNLNPKIMTVVEQ 394 ****************************************************************************** PP GRAS 245 eadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkp 326 ea+hn+++F++rf+eal+yys++fdslea + + e+++ E + ++rei+nv++ceg++r erhe lekWr+rl++aGFkp evm.model.supercontig_75.88 395 EASHNQPDFFDRFTEALYYYSTMFDSLEAC--AMQPEKAFAEIH-IQREICNVLCCEGSARLERHEPLEKWRSRLGRAGFKP 473 ***********************999..466777777777.********************************* PP GRAS 327 vplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 + l+++a kqa++ll ++ dgy vee++g+l+lgW++rpL+++SaW+ evm.model.supercontig_75.88 474 LYLGSNAFKQASMLLTLFSADGYCVEENEGCLTLGWHSRPLIAASAWQ 521 *********************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01129	1.2E-21	37	109	No hit	No description
Pfam	PF12041	2.3E-30	37	103	IPR021914	Transcriptional factor DELLA, N-terminal
PROSITE profile	PS50985	63.099	129	501	IPR005202	Transcription factor GRAS
Pfam	PF03514	3.2E-126	155	521	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 547 aa Download sequence Send to blast
MVLYDPATSA ATSSSGSTSA GSSFSYATKN PPPPDMDGLL AGAGYKVRSS DLRQVAQRLE 60 RLETAMVNSP SELSVLASDA VHYNPTDLAS WVDSLLSELA QPPPPPLPDF PPSDLFIGNA 120 VNHAAIDTDN SSWADQQGQQ LTVVTAMEED SGIRLVHMLM TCAESVQRGE LPLAGSLIED 180 MRGLLAHVNQ GCGIGKVAGY FIDALNRRIL SPPQSLAVSV NGSAFENEIL YHHFYEACPY 240 LKFAHFTANQ AILEAFDGHD CVHVVDFNLM HGLQWPALIQ ALALRPGGPP LLRLTGIGPP 300 SPDGRDSLRE IGLRLAELAR SVNVRFAFRG VAASRLEDVK PWMLQVSPKE ALAVNSIMQL 360 HRLLGADQNR NSPIEMVLGW IRNLNPKIMT VVEQEASHNQ PDFFDRFTEA LYYYSTMFDS 420 LEACAMQPEK AFAEIHIQRE ICNVLCCEGS ARLERHEPLE KWRSRLGRAG FKPLYLGSNA 480 FKQASMLLTL FSADGYCVEE NEGCLTLGWH SRPLIAASAW QATPNPSAPF AMISNHQTNG 540 NNNNLL*

Sequence ? help Back to Top

Protein Sequence Length: 547 aa Download sequence Send to blast

MVLYDPATSA ATSSSGSTSA GSSFSYATKN PPPPDMDGLL AGAGYKVRSS DLRQVAQRLE  60
RLETAMVNSP SELSVLASDA VHYNPTDLAS WVDSLLSELA QPPPPPLPDF PPSDLFIGNA  120
VNHAAIDTDN SSWADQQGQQ LTVVTAMEED SGIRLVHMLM TCAESVQRGE LPLAGSLIED  180
MRGLLAHVNQ GCGIGKVAGY FIDALNRRIL SPPQSLAVSV NGSAFENEIL YHHFYEACPY  240
LKFAHFTANQ AILEAFDGHD CVHVVDFNLM HGLQWPALIQ ALALRPGGPP LLRLTGIGPP  300
SPDGRDSLRE IGLRLAELAR SVNVRFAFRG VAASRLEDVK PWMLQVSPKE ALAVNSIMQL  360
HRLLGADQNR NSPIEMVLGW IRNLNPKIMT VVEQEASHNQ PDFFDRFTEA LYYYSTMFDS  420
LEACAMQPEK AFAEIHIQRE ICNVLCCEGS ARLERHEPLE KWRSRLGRAG FKPLYLGSNA  480
FKQASMLLTL FSADGYCVEE NEGCLTLGWH SRPLIAASAW QATPNPSAPF AMISNHQTNG  540
NNNNLL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	3e-61	148	520	12	378	Protein SCARECROW
5b3h_A	2e-61	148	520	11	377	Protein SCARECROW
5b3h_D	2e-61	148	520	11	377	Protein SCARECROW
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. Probably acts by participating in large multiprotein complexes that represses transcription of GA-inducible genes. Upon GA application, it is degraded by the proteasome, allowing the GA signaling pathway (By similarity). {ECO:0000250}.
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	evm.model.supercontig_75.88

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_021895234.1	0.0	DELLA protein SLR1-like
Swissprot	Q5BN22	1e-164	RGA2_BRACM; DELLA protein RGA2
Swissprot	Q9LQT8	1e-165	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A498KHD3	0.0	A0A498KHD3_MALDO; Uncharacterized protein
TrEMBL	Q0HA68	0.0	Q0HA68_MALDO; DELLA protein
STRING	evm.model.supercontig_75.88	0.0	(Carica papaya)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM16045	10	15
Representative plant	OGRP1251	15	50

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	evm.model.supercontig_75.88

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]