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

AT3G57920.1

Common Name

SPL15, T10K17.130

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: 354aa MW: 39672.4 Da PI: 8.994

Description

squamosa promoter binding protein-like 15

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G57920.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	127.7	4.3e-40	58	135	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +CqvegC++dls++k y++rhkvC +hsk+++v+vsgl+qrfCqqCsrfh+lsefD ekrsCrrrLa hnerrrk+q+ AT3G57920.1 58 RCQVEGCRMDLSNVKAYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQP 135 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	8.7E-31	52	120	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	30.983	56	133	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	2.88E-37	57	137	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.0E-28	59	132	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:0008361	Biological Process	regulation of cell size
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0042127	Biological Process	regulation of cell proliferation
GO:0048653	Biological Process	anther development
GO:0005634	Cellular Component	nucleus
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:0000230	anatomy	inflorescence meristem
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:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009052	anatomy	flower pedicel
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:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 354 aa Download sequence Send to blast
MELLMCSGQA ESGGSSSTES SSLSGGLRFG QKIYFEDGSG SRSKNRVNTV RKSSTTARCQ 60 VEGCRMDLSN VKAYYSRHKV CCIHSKSSKV IVSGLHQRFC QQCSRFHQLS EFDLEKRSCR 120 RRLACHNERR RKPQPTTALF TSHYSRIAPS LYGNPNAAMI KSVLGDPTAW STARSVMQRP 180 GPWQINPVRE THPHMNVLSH GSSSFTTCPE MINNNSTDSS CALSLLSNSY PIHQQQLQTP 240 TNTWRPSSGF DSMISFSDKV TMAQPPPIST HQPPISTHQQ YLSQTWEVIA GEKSNSHYMS 300 PVSQISEPAD FQISNGTTMG GFELYLHQQV LKQYMEPENT RAYDSSPQHF NWSL

Sequence ? help Back to Top

Protein Sequence Length: 354 aa Download sequence Send to blast

MELLMCSGQA ESGGSSSTES SSLSGGLRFG QKIYFEDGSG SRSKNRVNTV RKSSTTARCQ  60
VEGCRMDLSN VKAYYSRHKV CCIHSKSSKV IVSGLHQRFC QQCSRFHQLS EFDLEKRSCR  120
RRLACHNERR RKPQPTTALF TSHYSRIAPS LYGNPNAAMI KSVLGDPTAW STARSVMQRP  180
GPWQINPVRE THPHMNVLSH GSSSFTTCPE MINNNSTDSS CALSLLSNSY PIHQQQLQTP  240
TNTWRPSSGF DSMISFSDKV TMAQPPPIST HQPPISTHQQ YLSQTWEVIA GEKSNSHYMS  300
PVSQISEPAD FQISNGTTMG GFELYLHQQV LKQYMEPENT RAYDSSPQHF NWSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	4e-28	53	132	5	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.34784	0.0	floral meristem

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145339622	0.0
Genevisible	251560_at	0.0
Expression Atlas	AT3G57920	-
AtGenExpress	AT3G57920	-
ATTED-II	AT3G57920	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Weak increase of expression during floral induction. {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.
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.

Function -- GeneRIF ? help Back to Top
SPL15 has a role in shoot maturation. [PMID: 18278578] Enhanced miR156b expression in sk156 leads to the mutant phenotype including carotenoid levels in the seed through suppression of SPL15 and other SPL target genes. [PMID: 22989211] SPL15 and the MADS-box protein SOC1 cooperate to promote transcription of their target genes. [PMID: 27134142]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00412	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G57920.1

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

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

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G57920

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY086384	0.0	AY086384.1 Arabidopsis thaliana clone 247919 mRNA, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_191351.1	0.0	squamosa promoter binding protein-like 15
Swissprot	Q9M2Q6	0.0	SPL15_ARATH; Squamosa promoter-binding-like protein 15
TrEMBL	A0A178V850	0.0	A0A178V850_ARATH; SPL15
STRING	AT3G57920.1	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	AT3G57920.1
Entrez Gene	824961
iHOP	AT3G57920
wikigenes	AT3G57920

Publications ? help Back to Top
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] 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] Usami T,Horiguchi G,Yano S,Tsukaya H The more and smaller cells mutants of Arabidopsis thaliana identify novel roles for SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes in the control of heteroblasty. Development, 2009. 136(6): p. 955-64 [PMID:19211679] 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] Deng W, et al. FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2011. 108(16): p. 6680-5 [PMID:21464308] Wei S, et al. Arabidopsis mutant sk156 reveals complex regulation of SPL15 in a miR156-controlled gene network. BMC Plant Biol., 2012. 12: p. 169 [PMID:22989211] 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]