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

XP_009143829.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 150aa MW: 17408.3 Da PI: 8.0727

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009143829.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	135.2	2e-42	60	137	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +Cqve+C+ad+s+ak+yhrrhkvCe+h+kapvv + gl+qrfCqqCsrfh+l efDe+krsCrrrLa+hnerrrk+++ XP_009143829.1 60 ACQVERCTADMSRAKQYHRRHKVCEFHAKAPVVRIYGLHQRFCQQCSRFHDLGEFDESKRSCRRRLAGHNERRRKSAT 137 5**************************************************************************976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF037575	3.6E-57	7	148	IPR017238	Squamosa promoter-binding protein
Gene3D	G3DSA:4.10.1100.10	3.4E-33	53	122	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.043	58	135	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	3.53E-38	60	138	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	3.9E-32	61	134	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009908	Biological Process	flower development
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: 150 aa Download sequence Send to blast
MCNILQMSMK GSKAEAKRSL REMSEEEEEE EEEDTFEEEE ALVKKQKGKA TSSSSSSTGA 60 CQVERCTADM SRAKQYHRRH KVCEFHAKAP VVRIYGLHQR FCQQCSRFHD LGEFDESKRS 120 CRRRLAGHNE RRRKSATEGE RSQNHGSQDY

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	7e-40	52	134	2	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Increases during floral transition and stay high thereafter. {ECO:0000269\|PubMed:10524240, ECO:0000269\|PubMed:14573523, ECO:0000269\|PubMed:16914499, ECO:0000269\|PubMed:9301089}.
Uniprot	TISSUE SPECIFICITY: Expressed in vegetative and inflorescence apical meristems, floral meristems, leaf and flower organ primordia, inflorescence stem tissue and to lower extent in roots. {ECO:0000269\|PubMed:10524240, ECO:0000269\|PubMed:9301089}.

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009143829.1

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	1e-108	AJ011633.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 3.
GenBank	AJ242959	1e-108	AJ242959.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 3 (SPL3 gene).
GenBank	AK118179	1e-108	AK118179.1 Arabidopsis thaliana At2g33810 mRNA for putative squamosa-promoter binding protein, complete cds, clone: RAFL19-50-A02.
GenBank	Y09427	1e-108	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_009143829.1	1e-106	PREDICTED: squamosa promoter-binding-like protein 3
Swissprot	P93015	1e-57	SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBL	M4CMN2	3e-97	M4CMN2_BRARP; Squamosa promoter-binding-like protein
STRING	Bra005470.1-P	5e-98	(Brassica rapa)

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	7e-55	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]