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

AT1G53160.2

Common Name

F12M16.2, FTM6, SPL4

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: 174aa MW: 20119.6 Da PI: 10.1381

Description

squamosa promoter binding protein-like 4

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT1G53160.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	134.9	2.6e-42	54	129	2	77
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 Cqv++C+ad++eak yhrrhkvCevh+ka++v++sgl+qrfCqqCsrfh+l+efDe+krsCrrrLa+hnerrrk++ AT1G53160.2 54 CQVDRCTADMKEAKLYHRRHKVCEVHAKASSVFLSGLNQRFCQQCSRFHDLQEFDEAKRSCRRRLAGHNERRRKSS 129 **************************************************************************87 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF037575	1.4E-65	1	141	IPR017238	Squamosa promoter-binding protein
Gene3D	G3DSA:4.10.1100.10	3.7E-33	49	115	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	31.958	51	128	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	4.05E-38	53	131	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	6.1E-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:0009908	Biological Process	flower development
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: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:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0020148	anatomy	shoot apical meristem
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: 174 aa Download sequence Send to blast
MEGKRSQGQG YMKKKSYLVE EDMETDTDEE EEVGRDRVRG SRGSINRGGS LRLCQVDRCT 60 ADMKEAKLYH RRHKVCEVHA KASSVFLSGL NQRFCQQCSR FHDLQEFDEA KRSCRRRLAG 120 HNERRRKSSG ESTYGEGSGR RGINGQVVMQ NQERSRVEMT LPMPNSSFKR PQIR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	2e-51	40	127	1	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	261375_at	0.0
Expression Atlas	AT1G53160	-
AtGenExpress	AT1G53160	-
ATTED-II	AT1G53160	-

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 rib meristem and inter-primordial tissue of the inflorescence apex. {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
MP00634	PBM	Transfer from PK22320.1	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT1G53160.2

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

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT1G53160

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AJ011631	0.0	AJ011631.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 4.
GenBank	BT002856	0.0	BT002856.1 Arabidopsis thaliana clone RAFL15-05-B10 (R20352) putative transcription factor (At1g53160) mRNA, complete cds.
GenBank	BT004391	0.0	BT004391.1 Arabidopsis thaliana clone U20352 putative transcription factor (At1g53160) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_175723.1	1e-125	squamosa promoter binding protein-like 4
Refseq	NP_974014.1	1e-125	squamosa promoter binding protein-like 4
Swissprot	Q9S7A9	1e-126	SPL4_ARATH; Squamosa promoter-binding-like protein 4
TrEMBL	A0A178WEY0	1e-124	A0A178WEY0_ARATH; Squamosa promoter-binding-like protein
STRING	AT1G53160.2	1e-125	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT1G53160.2
Entrez Gene	841749
iHOP	AT1G53160
wikigenes	AT1G53160

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] Li J,Brader G,Palva ET The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense. Plant Cell, 2004. 16(2): p. 319-31 [PMID:14742872] 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] 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] Sunkar R,Zhu JK Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell, 2004. 16(8): p. 2001-19 [PMID:15258262] 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] Cai X, et al. A putative CCAAT-binding transcription factor is a regulator of flowering timing in Arabidopsis. Plant Physiol., 2007. 145(1): p. 98-105 [PMID:17631525] 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] 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] Torti S, et al. Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering. Plant Cell, 2012. 24(2): p. 444-62 [PMID:22319055] Kim MH,Sonoda Y,Sasaki K,Kaminaka H,Imai R Interactome analysis reveals versatile functions of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 in RNA processing within the nucleus and cytoplasm. Cell Stress Chaperones, 2013. 18(4): p. 517-25 [PMID:23334891] 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] Hyun Y, et al. Site-directed mutagenesis in Arabidopsis thaliana using dividing tissue-targeted RGEN of the CRISPR/Cas system to generate heritable null alleles. Planta, 2015. 241(1): p. 271-84 [PMID:25269397] 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]