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

AT5G43270.1

Common Name

MNL12.9, SPL2

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: 419aa MW: 46860.4 Da PI: 8.7732

Description

squamosa promoter binding protein-like 2

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G43270.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	129.1	1.7e-40	169	244	2	77
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 CqvegC+ dls+ak+yhr+h++Ce hsk p+v+vsg+e+rfCqqCsrfh lsefDe+krsCrrrL++hn+rrrk++ AT5G43270.1 169 CQVEGCNLDLSSAKDYHRKHRICENHSKFPKVVVSGVERRFCQQCSRFHCLSEFDEKKRSCRRRLSDHNARRRKPN 244 **************************************************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	3.1E-33	164	230	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.795	166	243	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	3.4E-38	167	247	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	3.2E-31	169	242	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:0048510	Biological Process	regulation of timing of transition from vegetative to reproductive phase
GO:0048653	Biological Process	anther development
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region 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:0000014	anatomy	rosette leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
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:0009049	anatomy	inflorescence
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
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: 419 aa Download sequence Send to blast
MECNAKPPFQ WELENLISFG TSTAEVPRKL KPMEWEIDGF DCTSLYSSSF AYAGSSGSDI 60 AHAFSKSSKS TSISSSSAEV RTHNFTSETG ESLPGEFAKG IDTSPSLELS FGSGDPVLGL 120 KLGKRTYFED FWEVENAKGL GLPVTLASSS VSPVKKSKSI PQRLQTPHCQ VEGCNLDLSS 180 AKDYHRKHRI CENHSKFPKV VVSGVERRFC QQCSRFHCLS EFDEKKRSCR RRLSDHNARR 240 RKPNPGRTYD GKPQVDFVWN RFALIHPRSE EKFIWPSSKH VPSRVLMPQP AKTEISDTEH 300 NRFGLLDPKT KTARAELFSK EKVTISSHMG ASQDLDGALS LLSNSTTWVS SSDQPRRFTL 360 DHHPSSNLQP VAHRSAAQLN SVSGYWQPDP PAVEGPTALH RNGVGQFNEN YFSLNQFYN

Sequence ? help Back to Top

Protein Sequence Length: 419 aa Download sequence Send to blast

MECNAKPPFQ WELENLISFG TSTAEVPRKL KPMEWEIDGF DCTSLYSSSF AYAGSSGSDI  60
AHAFSKSSKS TSISSSSAEV RTHNFTSETG ESLPGEFAKG IDTSPSLELS FGSGDPVLGL  120
KLGKRTYFED FWEVENAKGL GLPVTLASSS VSPVKKSKSI PQRLQTPHCQ VEGCNLDLSS  180
AKDYHRKHRI CENHSKFPKV VVSGVERRFC QQCSRFHCLS EFDEKKRSCR RRLSDHNARR  240
RKPNPGRTYD GKPQVDFVWN RFALIHPRSE EKFIWPSSKH VPSRVLMPQP AKTEISDTEH  300
NRFGLLDPKT KTARAELFSK EKVTISSHMG ASQDLDGALS LLSNSTTWVS SSDQPRRFTL  360
DHHPSSNLQP VAHRSAAQLN SVSGYWQPDP PAVEGPTALH RNGVGQFNEN YFSLNQFYN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	4e-26	169	242	11	84	squamosa promoter binding protein-like 4
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	224	241	KKRSCRRRLSDHNARRRK

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	186528814	0.0
Genevisible	249144_at	0.0
Expression Atlas	AT5G43270	-
AtGenExpress	AT5G43270	-
ATTED-II	AT5G43270	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed constitutively during plant development, weak increase during flowering. {ECO:0000269\|PubMed:10524240, ECO:0000269\|PubMed:14573523}.

Functional Description ? help Back to Top
Source	Description
TAIR	member of the SPL (squamosa-promoter binding protein-like) gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. In conjunction with SPL10 and SPL11, SPL2 redundantly controls proper development of lateral organs in association with shoot maturation in the reproductive phase.
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'.

Function -- GeneRIF ? help Back to Top
SPL10, SPL11 and SPL2 regulate morphological traits of cauline leaves and flowers, and control shoot maturation not only in the vegetative phase but also in the reproductive phase. [PMID: 19880401] SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2 controls floral organ development and plant fertility by activating ASYMMETRIC LEAVES 2 in Arabidopsis thaliana [PMID: 27605094] SPL1 and SPL12 confer thermotolerance in Arabidopsis at the reproductive stage [PMID: 28400323]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G43270.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156 and miR157 (Probable). Up-regulated by Turnip mosaic virus P1/HC-Pro protein, that acts as an antagonist of miR156. {ECO:0000269\|PubMed:12202040, ECO:0000269\|PubMed:12586064, ECO:0000305}.

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	AT4G13260(R), AT5G25620(R)

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

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G43270

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011626	0.0	AJ011626.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 2.
GenBank	AK230160	0.0	AK230160.1 Arabidopsis thaliana mRNA for squamosa promoter binding protein-like 2, complete cds, clone: RAFL22-87-G21.
GenBank	BT025984	0.0	BT025984.1 Arabidopsis thaliana At5g43270 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_199141.1	0.0	squamosa promoter binding protein-like 2
Refseq	NP_851122.1	0.0	squamosa promoter binding protein-like 2
Refseq	NP_974875.1	0.0	squamosa promoter binding protein-like 2
Swissprot	Q9S840	0.0	SPL2_ARATH; Squamosa promoter-binding-like protein 2
TrEMBL	A0A178ULK0	0.0	A0A178ULK0_ARATH; SPL2
STRING	AT5G43270.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6562	26	44
Representative plant	OGRP97	17	230

Link Out ? help Back to Top
Phytozome	AT5G43270.1
Entrez Gene	834345
iHOP	AT5G43270
wikigenes	AT5G43270

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] Rhoades MW, et al. Prediction of plant microRNA targets. Cell, 2002. 110(4): p. 513-20 [PMID:12202040] Kasschau KD, et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell, 2003. 4(2): p. 205-17 [PMID:12586064] Schmid M, et al. Dissection of floral induction pathways using global expression analysis. Development, 2003. 130(24): p. 6001-12 [PMID:14573523] Vazquez F,Gasciolli V,Cr The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing. Curr. Biol., 2004. 14(4): p. 346-51 [PMID:14972688] Yamasaki K, et al. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J. Mol. Biol., 2004. 337(1): p. 49-63 [PMID:15001351] Chen J,Li WX,Xie D,Peng JR,Ding SW Viral virulence protein suppresses RNA silencing-mediated defense but upregulates the role of microrna in host gene expression. Plant Cell, 2004. 16(5): p. 1302-13 [PMID:15100397] Yoo BC, et al. A systemic small RNA signaling system in plants. Plant Cell, 2004. 16(8): p. 1979-2000 [PMID:15258266] 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] Schwarz S,Grande AV,Bujdoso N,Saedler H,Huijser P The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis. Plant Mol. Biol., 2008. 67(1-2): p. 183-95 [PMID:18278578] 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] Li LC, et al. SPOROCYTELESS modulates YUCCA expression to regulate the development of lateral organs in Arabidopsis. New Phytol., 2008. 179(3): p. 751-64 [PMID:18557819] Shikata M,Koyama T,Mitsuda N,Ohme-Takagi M Arabidopsis SBP-box genes SPL10, SPL11 and SPL2 control morphological change in association with shoot maturation in the reproductive phase. Plant Cell Physiol., 2009. 50(12): p. 2133-45 [PMID:19880401] Xing S,Salinas M,H miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis. Plant Cell, 2010. 22(12): p. 3935-50 [PMID:21177480] Gaudinier A, et al. Enhanced Y1H assays for Arabidopsis. Nat. Methods, 2011. 8(12): p. 1053-5 [PMID:22037706] 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] Wang Z,Wang Y,Kohalmi SE,Amyot L,Hannoufa A SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2 controls floral organ development and plant fertility by activating ASYMMETRIC LEAVES 2 in Arabidopsis thaliana. Plant Mol. Biol., 2016. 92(6): p. 661-674 [PMID:27605094] Chao LM, et al. Arabidopsis Transcription Factors SPL1 and SPL12 Confer Plant Thermotolerance at Reproductive Stage. Mol Plant, 2017. 10(5): p. 735-748 [PMID:28400323]