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

Sobic.003G237201.1.p

Common Name

Sb03g029470, SORBIDRAFT_03g029470

Organism

Sorghum bicolor

Taxonomic ID

4558

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum

Family

GRAS

Protein Properties

Length: 296aa MW: 31529.2 Da PI: 4.9439

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.003G237201.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	291.6	2.1e-89	1	259	120	374
GRAS 120 sqGlQWpaLlqaLasRpegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvl 208 +qGlQWpaL+qaLa Rp+gppslR+Tg+g+p++ ++ l+ +g rLa++A++++v+f+f+ ++a+rl+++++++L+v +gEa+aVn+vl Sobic.003G237201.1.p 1 MQGLQWPALIQALALRPGGPPSLRLTGIGPPSPPGRDDLRDVGVRLADLARSVRVHFSFRGVAANRLDEVRPWMLQVAQGEAVAVNSVL 89 69************************************************************************************* PP GRAS 209 qlhrlldesvsles.......erdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErell 290 qlhrll++++s + ++d+vL++v s++Pkv++vveqeadhn++ Fl+rf+eal yysa+fdsl+a + +++l Sobic.003G237201.1.p 90 QLHRLLADDASFSAddarpraPIDAVLDCVASVRPKVLTVVEQEADHNKPGFLDRFTEALFYYSAVFDSLDAA---SGGAGDAAAEAYL 175 **88777665556666689********************************************998...235555666777 PP GRAS 291 greivnvvacegaerrerhetlekWrerleeaGFkpvplsekaakqaklllrkvksdgyrveeesgslvlgWkdrpLvsvSaWr 374 +rei+++v+ ega+rrerhe l +Wr+rl++aG+ +vpl+ +a qa++l+ ++++g+ vee +g+l+lgW++rpL+s+SaWr Sobic.003G237201.1.p 176 EREICDIVCGEGADRRERHEPLWRWRDRLGRAGLAAVPLGANALRQARMLVGLFSGEGHCVEEAEGCLTLGWHGRPLFSASAWR 259 ***********************************************************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03514	7.0E-87	1	259	IPR005202	Transcription factor GRAS
PROSITE profile	PS50985	42.067	1	239	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009723	Biological Process	response to ethylene
GO:0009737	Biological Process	response to abscisic acid
GO:0009863	Biological Process	salicylic acid mediated signaling pathway
GO:0009867	Biological Process	jasmonic acid mediated signaling pathway
GO:0009938	Biological Process	negative regulation of gibberellic acid mediated signaling pathway
GO:0010187	Biological Process	negative regulation of seed germination
GO:0042538	Biological Process	hyperosmotic salinity response
GO:2000033	Biological Process	regulation of seed dormancy process
GO:2000377	Biological Process	regulation of reactive oxygen species metabolic process
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0043565	Molecular Function	sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 296 aa Download sequence Send to blast
MQGLQWPALI QALALRPGGP PSLRLTGIGP PSPPGRDDLR DVGVRLADLA RSVRVHFSFR 60 GVAANRLDEV RPWMLQVAQG EAVAVNSVLQ LHRLLADDAS FSADDARPRA PIDAVLDCVA 120 SVRPKVLTVV EQEADHNKPG FLDRFTEALF YYSAVFDSLD AASGGAGDAA AEAYLEREIC 180 DIVCGEGADR RERHEPLWRW RDRLGRAGLA AVPLGANALR QARMLVGLFS GEGHCVEEAE 240 GCLTLGWHGR PLFSASAWRA AEENNQSDSC NADGSRSSGS GSGSGSEESN ISCSS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	4e-38	1	258	138	378	Protein SCARECROW
5b3h_A	4e-38	1	258	137	377	Protein SCARECROW
5b3h_D	4e-38	1	258	137	377	Protein SCARECROW
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Ubiquitously expressed. Expressed in rosette leaves, roots, stems and inflorescences of greenhouse grown. {ECO:0000269\|PubMed:11877383, ECO:0000269\|PubMed:9237632, ECO:0000269\|PubMed:9490740}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.003G237201.1.p

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EU969816	0.0	EU969816.1 Zea mays clone 336035 mRNA sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002458232.2	0.0	DELLA protein DWARF8
Swissprot	Q9LQT8	1e-92	GAI_ARATH; DELLA protein GAI
TrEMBL	A0A1W0VYQ0	0.0	A0A1W0VYQ0_SORBI; Uncharacterized protein
STRING	Sb03g029470.1	0.0	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP998	38	138
Representative plant	OGRP1251	15	50

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G14920.1	5e-83	GRAS family protein

Link Out ? help Back to Top
Phytozome	Sobic.003G237201.1.p
Entrez Gene	8058233

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]