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

RrC8312_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

GRAS

Protein Properties

Length: 325aa MW: 36339.5 Da PI: 6.0455

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC8312_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	397.2	1.7e-121	1	320	38	374
GRAS 38 mqRlaayfteALaarlarsvselykalppsetseknsseelaalkl.fsevsPilkfshltaNqaIleavegeervHiiDfdisqGlQWpaLlqaLasR 135 m+++a+yf+e+La+r++r +y p + s+ l++ f+e +P+lkf+h+taNqaIle+++++e+vH+iD++++qGlQWpaL+qaLa R RrC8312_p1 1 MRKVATYFAEGLARRIYR----IY---PHDDVG---LSSFSDTLQIhFYESCPYLKFAHFTANQAILESFATAEKVHVIDLGLNQGLQWPALIQALALR 89 79**************....55...222222...33333334444************************************************ PP GRAS 136 pegppslRiTgvgspesgskeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkp.gEalaVnlvlqlhrlldesvsleserdevLklvks 233 p+gpp +R+Tg+gs s ++++e+g++L ++A+++gv+fef+ +v ++l+dl++e+L++++ E++aVn+v++lhrll++++s+++ +L ++ks RrC8312_p1 90 PGGPPDIRLTGIGS--SLTGQSIQEVGWKLGQLANAVGVNFEFKSIVLNSLSDLKPEMLEIRTgLESIAVNSVFELHRLLAHPGSIDN----ILFTIKS 182 **********..5699***************************************88**************99999....*** PP GRAS 234 lsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgreivnvvacegaerrerhetlekWrerleeaGFkpvplsek 332 ++P++++vveqeadhn++ Fl+rf+e+l+yys+lfdsle ++++++++ +lgr+i n+vaceg++r+erhetl +Wr+r+++ GFkpv+++++ RrC8312_p1 183 IKPDIITVVEQEADHNGALFLDRFTESLHYYSSLFDSLEGP----PSQERVMSELYLGRQILNLVACEGEDRVERHETLVQWRNRFSMGGFKPVNIGSY 277 **********************************999....45566777788*************************************** PP GRAS 333 aakqaklllrkvk.sdgyrveeesgslvlgWkdrpLvsvSaWr 374 a+kqa++ll+ ++ dgy+vee++g+l+lgW++rpL+++SaWr RrC8312_p1 278 AYKQASMLLALYAgADGYKVEENEGCLLLGWQTRPLIATSAWR 320 ****************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03514	5.8E-119	1	320	IPR005202	Transcription factor GRAS
PROSITE profile	PS50985	60.607	1	299	IPR005202	Transcription factor GRAS

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
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:0042538	Biological Process	hyperosmotic salinity response
GO:2000377	Biological Process	regulation of reactive oxygen species metabolic process
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 325 aa Download sequence Send to blast
MRKVATYFAE GLARRIYRIY PHDDVGLSSF SDTLQIHFYE SCPYLKFAHF TANQAILESF 60 ATAEKVHVID LGLNQGLQWP ALIQALALRP GGPPDIRLTG IGSSLTGQSI QEVGWKLGQL 120 ANAVGVNFEF KSIVLNSLSD LKPEMLEIRT GLESIAVNSV FELHRLLAHP GSIDNILFTI 180 KSIKPDIITV VEQEADHNGA LFLDRFTESL HYYSSLFDSL EGPPSQERVM SELYLGRQIL 240 NLVACEGEDR VERHETLVQW RNRFSMGGFK PVNIGSYAYK QASMLLALYA GADGYKVEEN 300 EGCLLLGWQT RPLIATSAWR FNRVG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	3e-62	2	319	57	378	Protein SCARECROW
5b3h_A	4e-62	2	319	56	377	Protein SCARECROW
5b3h_D	4e-62	2	319	56	377	Protein SCARECROW
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Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcriptional regulator that acts as a repressor of the gibberellin (GA) signaling pathway. No effect of the BOI proteins on its stability. Probably acts by participating in large multiprotein complexes that repress transcription of GA-inducible genes. Has overlapping but distinct roles in GA signaling compared to RGA and GAI. Regulates the floral development. May also participate in seed germination and in ovule and anther development. Its activity is probably regulated by other phytohormones such as auxin and ethylene. {ECO:0000269\|PubMed:11826301, ECO:0000269\|PubMed:11877383, ECO:0000269\|PubMed:12610625, ECO:0000269\|PubMed:14615596, ECO:0000269\|PubMed:14973286, ECO:0000269\|PubMed:15128937, ECO:0000269\|PubMed:16034591}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Not up-regulated upon GA treatment.

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_018447161.1	0.0	PREDICTED: LOW QUALITY PROTEIN: DELLA protein RGL1
Swissprot	Q9C8Y3	0.0	RGL1_ARATH; DELLA protein RGL1
TrEMBL	A0A078JY94	0.0	A0A078JY94_BRANA; BnaCnng68300D protein
STRING	Bra039762.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM837	28	121

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G66350.1	0.0	RGA-like 1

Publications ? help Back to Top
Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Yan A, et al. AtEXP2 is involved in seed germination and abiotic stress response in Arabidopsis. PLoS ONE, 2014. 9(1): p. e85208 [PMID:24404203] 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] 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] 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] Li Y,Wang H,Li X,Liang G,Yu D Two DELLA-interacting proteins bHLH48 and bHLH60 regulate flowering under long-day conditions in Arabidopsis thaliana. J. Exp. Bot., 2017. 68(11): p. 2757-2767 [PMID:28591805] Chen L,Xiang S,Chen Y,Li D,Yu D Arabidopsis WRKY45 Interacts with the DELLA Protein RGL1 to Positively Regulate Age-Triggered Leaf Senescence. Mol Plant, 2017. 10(9): p. 1174-1189 [PMID:28735023] 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]