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

AT2G42200.1

Common Name

AtSPL9, SPL9, T24P15.11

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: 375aa MW: 40846.6 Da PI: 8.2276

Description

squamosa promoter binding protein-like 9

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G42200.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	136.6	7.5e-43	73	150	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +CqvegC +dl++ak y++rh+vC vhsk+p+v+v+g+eqrfCqqCsrfh+l efD ekrsCrrrLa+hnerrrk+q+ AT2G42200.1 73 RCQVEGCGMDLTNAKGYYSRHRVCGVHSKTPKVTVAGIEQRFCQQCSRFHQLPEFDLEKRSCRRRLAGHNERRRKPQP 150 6**************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	2.9E-34	66	135	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	31.838	71	148	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.96E-40	72	152	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	5.1E-32	74	147	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:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0048653	Biological Process	anther development
GO:2000025	Biological Process	regulation of leaf formation
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:0000017	anatomy	vascular leaf primordium
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009015	anatomy	portion of vascular tissue
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:0009105	anatomy	inflorescence branch meristem
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:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 375 aa Download sequence Send to blast
MEMGSNSGPG HGPGQAESGG SSTESSSFSG GLMFGQKIYF EDGGGGSGSS SSGGRSNRRV 60 RGGGSGQSGQ IPRCQVEGCG MDLTNAKGYY SRHRVCGVHS KTPKVTVAGI EQRFCQQCSR 120 FHQLPEFDLE KRSCRRRLAG HNERRRKPQP ASLSVLASRY GRIAPSLYEN GDAGMNGSFL 180 GNQEIGWPSS RTLDTRVMRR PVSSPSWQIN PMNVFSQGSV GGGGTSFSSP EIMDTKLESY 240 KGIGDSNCAL SLLSNPHQPH DNNNNNNNNN NNNNNTWRAS SGFGPMTVTM AQPPPAPSQH 300 QYLNPPWVFK DNDNDMSPVL NLGRYTEPDN CQISSGTAMG EFELSDHHHQ SRRQYMEDEN 360 TRAYDSSSHH TNWSL

Sequence ? help Back to Top

Protein Sequence Length: 375 aa Download sequence Send to blast

MEMGSNSGPG HGPGQAESGG SSTESSSFSG GLMFGQKIYF EDGGGGSGSS SSGGRSNRRV  60
RGGGSGQSGQ IPRCQVEGCG MDLTNAKGYY SRHRVCGVHS KTPKVTVAGI EQRFCQQCSR  120
FHQLPEFDLE KRSCRRRLAG HNERRRKPQP ASLSVLASRY GRIAPSLYEN GDAGMNGSFL  180
GNQEIGWPSS RTLDTRVMRR PVSSPSWQIN PMNVFSQGSV GGGGTSFSSP EIMDTKLESY  240
KGIGDSNCAL SLLSNPHQPH DNNNNNNNNN NNNNNTWRAS SGFGPMTVTM AQPPPAPSQH  300
QYLNPPWVFK DNDNDMSPVL NLGRYTEPDN CQISSGTAMG EFELSDHHHQ SRRQYMEDEN  360
TRAYDSSSHH TNWSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	4e-29	63	147	1	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.498	0.0	bud\| leaf\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	15028114	0.0
Genevisible	267639_at	0.0
Expression Atlas	AT2G42200	-
AtGenExpress	AT2G42200	-
ATTED-II	AT2G42200	-

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

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expression is regulated by MIR156b. SPL activity nonautonomously inhibits initiation of new leaves at the shoot apical meristem.
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
SPL9 has a role in shoot maturation. [PMID: 18278578] Data demonstrate that miR156 is a quantitative, rather than spatial, modulator of SPL9 expression in leaf primordia and that SPL9 activity nonautonomously inhibits initiation of new leaves at the shoot apical meristem. [PMID: 18492871] One of the miR156 targets, SPL9, negatively regulates anthocyanin accumulation. [PMID: 21487097] Our results uncover a molecular mechanism for plant adaptation to the environment through the miR156-SPLs-DFR pathway, which coordinates development and abiotic stress tolerance. [PMID: 25345491] Analysis of plants carrying microRNA miR156-resistant forms of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes showed that wall ingrowth deposition was increased in SPL9-group. [PMID: 28082719] Results suggest the mechanism by which miR156 and miR157 regulate gene expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors SPL9 and SPL13. [PMID: 29672610]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00307	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G42200.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305\|PubMed:12202040}.

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	AT2G30432(A), AT5G53200(A)

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

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G42200

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011638	0.0	AJ011638.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 9.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_181749.1	0.0	squamosa promoter binding protein-like 9
Swissprot	Q700W2	0.0	SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBL	D7LI29	0.0	D7LI29_ARALL; Uncharacterized protein
STRING	AT2G42200.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2144	27	75
Representative plant	OGRP97	17	230

Link Out ? help Back to Top
Phytozome	AT2G42200.1
Entrez Gene	818820
iHOP	AT2G42200
wikigenes	AT2G42200

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] 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] 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] Gong W, et al. Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol., 2004. 135(2): p. 773-82 [PMID:15208423] Yoo BC, et al. A systemic small RNA signaling system in plants. Plant Cell, 2004. 16(8): p. 1979-2000 [PMID:15258266] Scheible WR, et al. Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen. Plant Physiol., 2004. 136(1): p. 2483-99 [PMID:15375205] 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] Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] 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] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Wu G, et al. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell, 2009. 138(4): p. 750-9 [PMID:19703400] Yu N, et al. Temporal control of trichome distribution by microRNA156-targeted SPL genes in Arabidopsis thaliana. Plant Cell, 2010. 22(7): p. 2322-35 [PMID:20622149] Chen X, et al. SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development. J Integr Plant Biol, 2010. 52(11): p. 946-51 [PMID:20977652] 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] Gou JY,Felippes FF,Liu CJ,Weigel D,Wang JW Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor. Plant Cell, 2011. 23(4): p. 1512-22 [PMID:21487097] Li S,Yang X,Wu F,He Y HYL1 controls the miR156-mediated juvenile phase of vegetative growth. J. Exp. Bot., 2012. 63(7): p. 2787-98 [PMID:22268150] Yu S, et al. Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors. Plant Cell, 2012. 24(8): p. 3320-32 [PMID:22942378] Stief A, et al. Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors. Plant Cell, 2014. 26(4): p. 1792-1807 [PMID:24769482] Cui LG,Shan JX,Shi M,Gao JP,Lin HX The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants. Plant J., 2014. 80(6): p. 1108-17 [PMID:25345491] Yu ZX, et al. Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors. Mol Plant, 2015. [PMID:25355059] 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] Morea EG, et al. Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC Plant Biol., 2016. 16: p. 40 [PMID:26841873] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] 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] Mahmood K,Xu Z,El-Kereamy A,Casaretto JA,Rothstein SJ The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin Biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses. Front Plant Sci, 2016. 7: p. 1548 [PMID:27790239] Mao YB, et al. Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance. Nat Commun, 2017. 8: p. 13925 [PMID:28067238] Nguyen ST,Greaves T,McCurdy DW Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module. Plant Physiol., 2017. 173(3): p. 1676-1691 [PMID:28082719] 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] Dotto M,Gómez MS,Soto MS,Casati P UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. Plant Cell Environ., 2018. 41(6): p. 1394-1406 [PMID:29447428] He J, et al. Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana. PLoS Genet., 2018. 14(4): p. e1007337 [PMID:29672610]