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

AT2G33810.1

Common Name

SPL3, T1B8.11

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 131aa MW: 15304 Da PI: 8.15

Description

squamosa promoter binding protein-like 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G33810.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	137.4	4.3e-43	53	130	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +Cqve+C+ad+s+ak+yh+rhkvC++h+kap+v +sgl+qrfCqqCsrfh+lsefDe+krsCrrrLa+hnerrrk+++ AT2G33810.1 53 VCQVESCTADMSKAKQYHKRHKVCQFHAKAPHVRISGLHQRFCQQCSRFHALSEFDEAKRSCRRRLAGHNERRRKSTT 130 6**************************************************************************976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF037575	1.5E-59	1	131	IPR017238	Squamosa promoter-binding protein
Gene3D	G3DSA:4.10.1100.10	4.2E-33	46	115	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.257	51	128	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.47E-38	53	130	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.1E-32	54	127	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
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:0030154	Biological Process	cell differentiation
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000229	anatomy	flower meristem
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 131 aa Download sequence Send to blast
MSMRRSKAEG KRSLRELSEE EEEEEETEDE DTFEEEEALE KKQKGKATSS SGVCQVESCT 60 ADMSKAKQYH KRHKVCQFHA KAPHVRISGL HQRFCQQCSR FHALSEFDEA KRSCRRRLAG 120 HNERRRKSTT D

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	4e-38	47	127	2	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.25364	0.0	flower\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30685845	0.0
Genevisible	267460_at	0.0
Expression Atlas	AT2G33810	-
AtGenExpress	AT2G33810	-

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
TAIR	Encodes a member of the SPL (squamosa-promoter binding protein-like)gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. Contains the SBP-box, which encodes the SBP-domain, required and sufficient for interaction with DNA. It binds DNA, may directly regulate AP1, and is involved in regulation of flowering and vegetative phase change. Its temporal expression is regulated by the microRNA miR156. The target site for the microRNA is in the 3'UTR.
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}.

Function -- GeneRIF ? help Back to Top
Results show that vegetative phase change in Arabidopsis is regulated by an increase in the expression of SPL3. [PMID: 16914499] Data show that LEAFY, FRUITFULL, and APETALA1 are directly activated by the microRNA-targeted transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3) to control the timing of flower formation. [PMID: 19686687] Data indicate that although miR172 and miR156 play distinct roles in the timing of developmental phase transitions, there is a signaling crosstalk mediated by the SPL3/4/5 genes. [PMID: 21373962] SOC1-SPL module serves as a molecular link that integrates photoperiod and gibberellic acid signals to promote flowering in Arabidopsis. [PMID: 21988498] Overexpression of miR156-resistant SPL3 causes accelerated flowering at a low ambient temperature. [PMID: 22427344] SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering. [PMID: 27815142] the miR156-SPL3 module mediates regulation of FT expression by NaKR1 in response to potassium conditions. [PMID: 29253219]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00290	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G33810.1

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	Retrieve

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G69120(A), AT5G60910(A), AT5G61850(A)

Regulation -- MicroRNA ? help Back to Top
Source	Description
miRTarBase	Regulated by ath-miR157a, ath-miR156a, ath-miR156f

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Plants flower early and have a significantly reduced number of juvenile, adult and cauline leaves, with a shorter petiole and a more acute leaf base in the first two leaves. {ECO:0000269\|PubMed:16914499}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G33810

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011633	0.0	AJ011633.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 3.
GenBank	AJ242959	0.0	AJ242959.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 3 (SPL3 gene).
GenBank	AK118179	0.0	AK118179.1 Arabidopsis thaliana At2g33810 mRNA for putative squamosa-promoter binding protein, complete cds, clone: RAFL19-50-A02.
GenBank	BT005443	0.0	BT005443.1 Arabidopsis thaliana clone U50647 putative squamosa-promoter binding protein (At2g33810) mRNA, complete cds.
GenBank	Y09427	0.0	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	NP_565771.1	2e-89	squamosa promoter binding protein-like 3
Swissprot	P93015	1e-90	SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBL	A0A178W1W0	3e-88	A0A178W1W0_ARATH; Squamosa promoter-binding-like protein
STRING	AT2G33810.1	6e-89	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM868	28	118
Representative plant	OGRP97	17	230

Link Out ? help Back to Top
Phytozome	AT2G33810.1
Entrez Gene	817948
iHOP	AT2G33810
wikigenes	AT2G33810

Publications ? help Back to Top
Cardon G, et al. Molecular characterisation of the Arabidopsis SBP-box genes. Gene, 1999. 237(1): p. 91-104 [PMID:10524240] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Seki M, et al. Functional annotation of a full-length Arabidopsis cDNA collection. Science, 2002. 296(5565): p. 141-5 [PMID:11910074] Rhoades MW, et al. Prediction of plant microRNA targets. Cell, 2002. 110(4): p. 513-20 [PMID:12202040] Folta KM,Pontin MA,Karlin-Neumann G,Bottini R,Spalding EP Genomic and physiological studies of early cryptochrome 1 action demonstrate roles for auxin and gibberellin in the control of hypocotyl growth by blue light. Plant J., 2003. 36(2): p. 203-14 [PMID:14535885] Schmid M, et al. Dissection of floral induction pathways using global expression analysis. Development, 2003. 130(24): p. 6001-12 [PMID:14573523] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] L A new SBP-box gene BpSPL1 in silver birch (Betula pendula). Physiol Plant, 2004. 120(3): p. 491-500 [PMID:15032847] Kidner CA,Martienssen RA The role of ARGONAUTE1 (AGO1) in meristem formation and identity. Dev. Biol., 2005. 280(2): p. 504-17 [PMID:15882589] Birkenbihl RP,Jach G,Saedler H,Huijser P Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J. Mol. Biol., 2005. 352(3): p. 585-96 [PMID:16095614] Wu G,Poethig RS Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development, 2006. 133(18): p. 3539-47 [PMID:16914499] Gandikota M, et al. The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J., 2007. 49(4): p. 683-93 [PMID:17217458] Yamaguchi A, et al. The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1. Dev. Cell, 2009. 17(2): p. 268-78 [PMID:19686687] Sanchez SE,Cagnola JI,Crepy M,Yanovsky MJ,Casal JJ Balancing forces in the photoperiodic control of flowering. Photochem. Photobiol. Sci., 2011. 10(4): p. 451-60 [PMID:21125113] Jung JH,Seo PJ,Kang SK,Park CM miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions. Plant Mol. Biol., 2011. 76(1-2): p. 35-45 [PMID:21373962] Lal S,Pacis LB,Smith HM Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA156 module by the homeodomain proteins PENNYWISE and POUND-FOOLISH in Arabidopsis. Mol Plant, 2011. 4(6): p. 1123-32 [PMID:21653282] Jung JH,Ju Y,Seo PJ,Lee JH,Park CM The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis. Plant J., 2012. 69(4): p. 577-88 [PMID:21988498] Yang L,Wu G,Poethig RS Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2012. 109(1): p. 315-20 [PMID:22184231] Kim JJ, et al. The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Plant Physiol., 2012. 159(1): p. 461-78 [PMID:22427344] Hwan Lee J,Joon Kim J,Ahn JH Role of SEPALLATA3 (SEP3) as a downstream gene of miR156-SPL3-FT circuitry in ambient temperature-responsive flowering. Plant Signal Behav, 2012. 7(9): p. 1151-4 [PMID:22899051] 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] Le MH,Cao Y,Zhang XC,Stacey G LIK1, a CERK1-interacting kinase, regulates plant immune responses in Arabidopsis. PLoS ONE, 2014. 9(7): p. e102245 [PMID:25036661] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] 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] Cardon GH,Höhmann S,Nettesheim K,Saedler H,Huijser P Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J., 1997. 12(2): p. 367-77 [PMID:9301089]