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

Rsa1.0_00948.1_g00009.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 122aa MW: 14105.8 Da PI: 9.4584

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00948.1_g00009.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	140.6	4.1e-44	43	120	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +Cqve+C+ad+s+ak+yh+rhkvCevh+kapvv +sgl qrfCqqCsrfhelsefDe+krsCrrrLa+hnerrrk+++ Rsa1.0_00948.1_g00009.1 43 ACQVERCTADMSRAKQYHKRHKVCEVHAKAPVVWISGLGQRFCQQCSRFHELSEFDEAKRSCRRRLAGHNERRRKSTS 120 5**************************************************************************976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF037575	5.4E-56	1	122	IPR017238	Squamosa promoter-binding protein
Gene3D	G3DSA:4.10.1100.10	3.2E-34	37	105	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.18	41	118	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.67E-39	43	119	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.6E-33	44	117	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009911	Biological Process	positive regulation of flower development
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0010229	Biological Process	inflorescence development
GO:0010321	Biological Process	regulation of vegetative phase change
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 122 aa Download sequence Send to blast
MRRSKEEGKS SLREMSEEEE EEEAWEKKQK GKATSSSSSS IGACQVERCT ADMSRAKQYH 60 KRHKVCEVHA KAPVVWISGL GQRFCQQCSR FHELSEFDEA KRSCRRRLAG HNERRRKSTS 120 EG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	2e-43	35	117	2	84	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00290	DAP	Transfer from AT2G33810	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00948.1_g00009.1

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011633	5e-86	AJ011633.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 3.
GenBank	AJ242959	5e-86	AJ242959.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 3 (SPL3 gene).
GenBank	AK118179	5e-86	AK118179.1 Arabidopsis thaliana At2g33810 mRNA for putative squamosa-promoter binding protein, complete cds, clone: RAFL19-50-A02.
GenBank	BT005443	5e-86	BT005443.1 Arabidopsis thaliana clone U50647 putative squamosa-promoter binding protein (At2g33810) mRNA, complete cds.
GenBank	Y09427	5e-86	Y09427.1 A.thaliana mRNA for squamosa-promoter binding protein like 3.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018437758.1	2e-82	PREDICTED: squamosa promoter-binding-like protein 3
Swissprot	P93015	4e-57	SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBL	S4WY88	3e-61	S4WY88_ARAAL; Squamosa promoter-binding-like protein
STRING	S4WY88	5e-62	(Arabis alpina)

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	2e-56	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]