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

RrC1216_p4

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

bHLH

Protein Properties

Length: 323aa MW: 34908.6 Da PI: 7.1094

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC1216_p4	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	51.1	2.4e-16	169	215	4	55
HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 hn E+rRR+riN+++ L++l+P++ K +Ka++L +A+eY+k+Lq RrC1216_p4 169 VHNLSEKRRRSRINEKMKALQSLIPNS-----NKTDKASMLDEAIEYLKQLQ 215 6***********************7.....5****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47459	4.71E-20	163	225	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	18.063	165	214	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.7E-19	166	225	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.35E-18	168	219	No hit	No description
Pfam	PF00010	8.5E-14	169	215	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	4.0E-18	171	220	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 323 aa Download sequence Send to blast
MADKKLISSA SSSSTSIYDP RGNNNHQPPS SSDEISQFLR HIFDRSSPLP SHYSPAYTAA 60 TGGDPHADNN TTRCFVSPPS SKRAAAAEFS DVPLGSASAV PCYGFSGGNN NVAQGSSSGT 120 RVSSSSLGAS GNETDEYDCE SEEGVEAVVD DEHPSKSRSS SKRCRAAEVH NLSEKRRRSR 180 INEKMKALQS LIPNSNKTDK ASMLDEAIEY LKQLQLQVQM LTMRNGINLH PLSLPGTSLH 240 PLQLSQIRPP ETTTDPLLNQ FASTSNAPDM INMPSAYTLE PSIRSHFGRF LPFTPPVEMN 300 REGGLTHQRL NIGGHPNANL TGK

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269\|PubMed:10225997, ECO:0000269\|Ref.8}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269\|PubMed:11245574}.

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	KF921090	1e-146	KF921090.1 Brassica oleracea var. capitata bHLH transcription factor SPT mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018468780.1	0.0	PREDICTED: transcription factor SPATULA
Swissprot	Q9FUA4	1e-129	SPT_ARATH; Transcription factor SPATULA
TrEMBL	A0A3P6G0E3	1e-169	A0A3P6G0E3_BRAOL; Uncharacterized protein (Fragment)
STRING	Bo1g004970.1	1e-170	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4199	27	54

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G36930.1	1e-128	bHLH family protein

Publications ? help Back to Top
Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation, 2010. 80(1): p. 1-8 [PMID:20219281] Pabón-Mora N,Wong GK,Ambrose BA Evolution of fruit development genes in flowering plants. Front Plant Sci, 2014. 5: p. 300 [PMID:25018763] Moubayidin L,Ostergaard L Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development. Curr. Biol., 2014. 24(22): p. 2743-8 [PMID:25455035] Pfannebecker KC,Lange M,Rupp O,Becker A Seed Plant-Specific Gene Lineages Involved in Carpel Development. Mol. Biol. Evol., 2017. 34(4): p. 925-942 [PMID:28087776] Zumajo-Cardona C,Ambrose BA,Pabón-Mora N Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae). Evodevo, 2017. 8: p. 5 [PMID:28331573] Reyes-Olalde JI, et al. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet., 2017. 13(4): p. e1006726 [PMID:28388635] Wu M, et al. SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis. Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385 [PMID:29966653]