PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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: 181aa MW: 20991.5 Da PI: 10.3634

Description

squamosa promoter binding protein-like 5

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G15270.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	132.6	1.3e-41	63	138	2	77
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 Cqv++C+++l+eak+y+rrh+vCevh+ka++++v+g++qrfCqqCsrfhel efDe+krsCrrrLa+hnerrrk + AT3G15270.1 63 CQVDRCTVNLTEAKQYYRRHRVCEVHAKASAATVAGVRQRFCQQCSRFHELPEFDEAKRSCRRRLAGHNERRRKIS 138 *************************************************************************976 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51141	31.539	60	137	IPR004333	Transcription factor, SBP-box
Gene3D	G3DSA:4.10.1100.10	8.4E-32	60	124	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	3.14E-38	62	141	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	8.1E-32	63	136	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:0010321	Biological Process	regulation of vegetative phase change
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:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
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:0009062	anatomy	gynoecium
PO:0025022	anatomy	collective leaf structure
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:0007115	developmental stage	LP.04 four 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: 181 aa Download sequence Send to blast
MEGQRTQRRG YLKDKATVSN LVEEEMENGM DGEEEDGGDE DKRKKVMERV RGPSTDRVPS 60 RLCQVDRCTV NLTEAKQYYR RHRVCEVHAK ASAATVAGVR QRFCQQCSRF HELPEFDEAK 120 RSCRRRLAGH NERRRKISGD SFGEGSGRRG FSGQLIQTQE RNRVDRKLPM TNSSFKRPQI 180 R

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	5e-39	61	136	9	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	257051_at	0.0
Expression Atlas	AT3G15270	-
AtGenExpress	AT3G15270	-
ATTED-II	AT3G15270	-

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}.
Uniprot	TISSUE SPECIFICITY: Expressed in the inflorescence apical meristem and young flowers. {ECO:0000269\|PubMed:10524240}.

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 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. Promotes both vegetative phase change and flowering. {ECO:0000269\|PubMed:10524240, ECO:0000269\|PubMed:16914499}.

Function -- GeneRIF ? help Back to Top
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] SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering. [PMID: 27815142]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00359	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G15270.1

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

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

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

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G14920

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G15270

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011610	0.0	AJ011610.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 5.
GenBank	AJ242960	0.0	AJ242960.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 5, (SPL5 gene).
GenBank	AK118611	0.0	AK118611.1 Arabidopsis thaliana At3g15270 mRNA for squamosa promoter binding protein-like 5, putative, complete cds, clone: RAFL19-86-N19.
GenBank	BT003714	0.0	BT003714.1 Arabidopsis thaliana At3g15270 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_188145.1	1e-131	squamosa promoter binding protein-like 5
Swissprot	Q9S758	1e-132	SPL5_ARATH; Squamosa promoter-binding-like protein 5
TrEMBL	A0A178VL13	1e-129	A0A178VL13_ARATH; SPL5
STRING	AT3G15270.1	1e-130	(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	AT3G15270.1
Entrez Gene	820758
iHOP	AT3G15270
wikigenes	AT3G15270

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] 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] Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J., 2004. 38(2): p. 366-79 [PMID:15078338] Yoo BC, et al. A systemic small RNA signaling system in plants. Plant Cell, 2004. 16(8): p. 1979-2000 [PMID:15258266] 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] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] Wang JW,Schwab R,Czech B,Mica E,Weigel D Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana. Plant Cell, 2008. 20(5): p. 1231-43 [PMID:18492871] Cheng H, et al. Gibberellin acts through jasmonate to control the expression of MYB21, MYB24, and MYB57 to promote stamen filament growth in Arabidopsis. PLoS Genet., 2009. 5(3): p. e1000440 [PMID:19325888] 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] 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] Mar Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners. Plant Physiol., 2014. 166(2): p. 1022-32 [PMID:25118255] 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] Ioannidi E, et al. Trichome patterning control involves TTG1 interaction with SPL transcription factors. Plant Mol. Biol., 2016. 92(6): p. 675-687 [PMID:27631431] 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]