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

RrC59579_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

SBP

Protein Properties

Length: 107aa MW: 12156.3 Da PI: 5.3126

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC59579_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	68.9	9.7e-22	62	107	2	47
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTS CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCs 47 Cqve+C+ad+s+ak+yh+rhkvCe+h+kap+v + g qrfCqqCs RrC59579_p1 62 CQVERCTADMSRAKQYHKRHKVCEFHAKAPAVRIFGGYQRFCQQCS 107 *********************************************8 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	7.9E-21	55	107	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	18.7	59	107	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	7.06E-20	61	107	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.5E-16	62	107	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 107 aa Download sequence Send to blast
MSVRRSNADG KRSLREMSEE EEEDEDTFEE EDNGGEQEQE EALEKKQKGK AASSSTSSGV 60 SCQVERCTAD MSRAKQYHKR HKVCEFHAKA PAVRIFGGYQ RFCQQCS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	2e-18	54	107	2	56	squamosa promoter binding protein-like 4
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Binds specifically to the 5'-GTAC-3' core sequence. Promotes both vegetative phase change and flowering. Regulates phase-specific patterns of leaf epidermal differentiation and flowering time, but does not seem to affect leaf shape. {ECO:0000269\|PubMed:16095614, ECO:0000269\|PubMed:16914499, ECO:0000269\|PubMed:9301089}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156. {ECO:0000269\|PubMed:12202040, ECO:0000269\|PubMed:16914499}.

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_018465582.1	6e-53	PREDICTED: squamosa promoter-binding-like protein 3
Swissprot	P93015	1e-35	SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBL	A0A0D3B4R8	2e-40	A0A0D3B4R8_BRAOL; Uncharacterized protein
TrEMBL	A0A3P6ATU2	2e-40	A0A3P6ATU2_BRAOL; Uncharacterized protein
STRING	Bo3g027460.1	3e-41	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM868	28	118

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33810.1	1e-23	squamosa promoter binding protein-like 3

Publications ? help Back to Top
Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A. PLoS ONE, 2013. 8(7): p. e67987 [PMID:23976921] Jorgensen SA,Preston JC Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis. Mol. Phylogenet. Evol., 2014. 73: p. 129-39 [PMID:24508602] Yu N,Niu QW,Ng KH,Chua NH The role of miR156/SPLs modules in Arabidopsis lateral root development. Plant J., 2015. 83(4): p. 673-85 [PMID:26096676] Lei KJ, et al. Modulation of the Phosphate-Deficient Responses by MicroRNA156 and its Targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 in Arabidopsis. Plant Cell Physiol., 2016. 57(1): p. 192-203 [PMID:26647245] Xu M, et al. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet., 2016. 12(8): p. e1006263 [PMID:27541584] Jung JH,Lee HJ,Ryu JY,Park CM SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering. Mol Plant, 2016. 9(12): p. 1647-1659 [PMID:27815142] Duan HC, et al. ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. Plant Cell, 2017. 29(12): p. 2995-3011 [PMID:29180595] Negishi K,Endo M,Abe M,Araki T SODIUM POTASSIUM ROOT DEFECTIVE1 regulates FLOWERING LOCUS T expression via the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module in response to potassium conditions. Plant Cell Physiol., 2018. 59(2): p. 404-413 [PMID:29253219]