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

AT3G51060.1

Common Name

AtSTY1, F24M12.100, SRS1, STY1

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

SRS

Protein Properties

Length: 370aa MW: 38352.1 Da PI: 7.5014

Description

Lateral root primordium (LRP) protein-related

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G51060.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF702	230.4	3.1e-71	138	286	2	153
DUF702 2 rsgtasCqdCGnqakkdCaheRCRtCCksrgfdCathvkstWvpaakrrerqqqlaaasskaaasaaeaaskrkrelkskkqsalsstklssaeskke 99 +sg++sCqdCGnqakkdC+h+RCRtCCksrgf+C+thv+stWvpaakrrerqqqla+ + +++ + e+ +kr+re+ +++s+l +t+++s++ AT3G51060.1 138 GSGGVSCQDCGNQAKKDCSHMRCRTCCKSRGFECSTHVRSTWVPAAKRRERQQQLATVQPQTQLPRGESVPKRHRENLPATSSSLVCTRIPSHS---G 232 57899***************************************************99999999********************9995...7 PP DUF702 100 letsslPeevsseavfrcvrvssvddgeeelaYqtavsigGhvfkGiLydqGle 153 le+ ++P+evss+avfrcvrvssv+dgeee+aYqtavsigGh+fkGiLyd G+ AT3G51060.1 233 LEVGNFPAEVSSSAVFRCVRVSSVEDGEEEFAYQTAVSIGGHIFKGILYDLGPG 286 8999**********************************************85 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF05142	1.2E-64	141	285	IPR007818	Protein of unknown function DUF702
TIGRFAMs	TIGR01623	4.7E-27	143	185	IPR006510	Zinc finger, lateral root primordium type 1
TIGRFAMs	TIGR01624	1.0E-26	238	285	IPR006511	Lateral Root Primordium type 1, C-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0009851	Biological Process	auxin biosynthetic process
GO:0009938	Biological Process	negative regulation of gibberellic acid mediated signaling pathway
GO:0010051	Biological Process	xylem and phloem pattern formation
GO:0010252	Biological Process	auxin homeostasis
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048479	Biological Process	style development
GO:0048480	Biological Process	stigma 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
GO:0046982	Molecular Function	protein heterodimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000015	anatomy	cotyledon primordium
PO:0000017	anatomy	vascular leaf primordium
PO:0000018	anatomy	ovule primordium
PO:0000019	anatomy	gynoecium primordium
PO:0004704	anatomy	sepal primordium
PO:0020020	anatomy	nucellus

Sequence ? help Back to Top
Protein Sequence Length: 370 aa Download sequence Send to blast
MAGFFSLDGG GGGGGGGGNN QEDHRSNTNP PPPVSEAWLW YRNPNVNANA NTNVNANAPS 60 SSNAALGTLE LWQNHNQQEI MFQHQQHQQR LDLYSSAAGL GVGPSNHNQF DISGETSTAG 120 AGRAAAMMMI RSGGSGGGSG GVSCQDCGNQ AKKDCSHMRC RTCCKSRGFE CSTHVRSTWV 180 PAAKRRERQQ QLATVQPQTQ LPRGESVPKR HRENLPATSS SLVCTRIPSH SGLEVGNFPA 240 EVSSSAVFRC VRVSSVEDGE EEFAYQTAVS IGGHIFKGIL YDLGPGSSGG GGYNVVAAGE 300 SSSGGGGAQQ LNLITAGSVT VATASSSTPN LGGIGSSSAA AATYIDPAAL YPTPINTFMA 360 GTQFFPNPRS

Sequence ? help Back to Top

Protein Sequence Length: 370 aa Download sequence Send to blast

MAGFFSLDGG GGGGGGGGNN QEDHRSNTNP PPPVSEAWLW YRNPNVNANA NTNVNANAPS  60
SSNAALGTLE LWQNHNQQEI MFQHQQHQQR LDLYSSAAGL GVGPSNHNQF DISGETSTAG  120
AGRAAAMMMI RSGGSGGGSG GVSCQDCGNQ AKKDCSHMRC RTCCKSRGFE CSTHVRSTWV  180
PAAKRRERQQ QLATVQPQTQ LPRGESVPKR HRENLPATSS SLVCTRIPSH SGLEVGNFPA  240
EVSSSAVFRC VRVSSVEDGE EEFAYQTAVS IGGHIFKGIL YDLGPGSSGG GGYNVVAAGE  300
SSSGGGGAQQ LNLITAGSVT VATASSSTPN LGGIGSSSAA AATYIDPAAL YPTPINTFMA  360
GTQFFPNPRS

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	240255587	0.0
Expression Atlas	AT3G51060	-
AtGenExpress	AT3G51060	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the apical parts of the developing gynoecium. Detected throughout the youngest flower primordium. Later relocalizes towards the regions of the presumptive sepal anlagen and remains in sepal primordia until just after their emergence. Also observed on the abaxial side of the young floral meristem. Present in the newly arisen gynoecial primordium. Restricted to the apical parts of the carpels as the open-ended gynoecial cylinder elongates vertically. In the apical regions of the gynoecium, confined to a zone in the interphase between the style and the stigma and fades out later. Within the gynoecium, accumulates in ovule primordia, and, as the ovules developed, restricted to the epidermis of the developing funiculi, to the outer, but not the inner, integuments and to the tip of the nucellus. Also present in the cell layer of the septum that faces the ovary. In the embryo, detected in the cotyledon primordia during late globular to mid heart stage. In addition, transiently expressed in petal and stamen primordia and in the tapetum of the anthers. {ECO:0000269\|PubMed:12361963}.
Uniprot	TISSUE SPECIFICITY: Expressed in flowers, seeds and seedlings. {ECO:0000269\|PubMed:12361963}.

Functional Description ? help Back to Top
Source	Description
TAIR	A member of SHI gene family. Arabidopsis thaliana has ten members that encode proteins with a RING finger-like zinc finger motif. Despite being highly divergent in sequence, many of the SHI-related genes are partially redundant in function and synergistically promote gynoecium, stamen and leaf development in Arabidopsis. STY1/STY2 double mutants showed defective style, stigma as well as serrated leaves. Binds to the promoter of YUC4 and YUC8 (binding site ACTCTAC)
UniProt	Transcription activator that binds DNA on 5'-ACTCTAC-3' and promotes auxin homeostasis-regulating gene expression (e.g. YUC genes), as well as genes affecting stamen development, cell expansion and timing of flowering. Synergistically with other SHI-related proteins, regulates gynoecium, stamen and leaf development in a dose-dependent manner, controlling apical-basal patterning. Promotes style and stigma formation, and influences vascular development during gynoecium development. May also have a role in the formation and/or maintenance of the shoot apical meristem (SAM). {ECO:0000269\|PubMed:12361963, ECO:0000269\|PubMed:16740145, ECO:0000269\|PubMed:16740146, ECO:0000269\|PubMed:18811619, ECO:0000269\|PubMed:20154152, ECO:0000269\|PubMed:22318676}.

Function -- GeneRIF ? help Back to Top
STY1 and related genes promote normal development of the style and affect apical-basal patterning of the gynoecium through regulation of auxin homeostasis. [PMID: 16740145] results suggest that reduced auxin concentrations cause the sty1-1 sty2-1 phenotype, that STY1 induces auxin biosynthesis [PMID: 18811619] Induction of the transcriptional activator DORNROSCHEN-LIKE (DRNL) activates the transcription of STY1 and other SHI/STY family members and that this activation is dependent on a functional GCC box. [PMID: 21976484] STY1 induces the transcription of 16 additional genes independently of protein translation. [PMID: 22318676]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00613	PBM	24477691	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G51060.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Regulated by ESR1 and ESR2. {ECO:0000269\|PubMed:21976484}.

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	AT1G59500(A), AT2G23170(A), AT4G01500(A), AT4G27260(A), AT4G37390(A), AT5G11320(A), AT5G54510(A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin, gibberellin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT3G51060

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: Gynoecia with aberrant style morphology. The double mutant sty1-1 and sty2-1 has a reduction in the amount of stylar and stigmatic tissues and decreased proliferation of stylar xylem, as well as shorter siliques and rosette and cauline leaves with a higher degree of serration. Hypersensitive to 1-N-naphthylphtalamic acid (NPA), but restored by exogenous application of auxin. {ECO:0000269\|PubMed:12361963, ECO:0000269\|PubMed:16740145, ECO:0000269\|PubMed:16740146, ECO:0000269\|PubMed:18811619}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G51060

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT029509	0.0	BT029509.1 Arabidopsis thaliana At3g51060 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_190675.4	0.0	Lateral root primordium (LRP) protein-like protein
Swissprot	Q9SD40	0.0	SRS1_ARATH; Protein SHI RELATED SEQUENCE 1
TrEMBL	A0A178VGX9	0.0	A0A178VGX9_ARATH; STY1
STRING	AT3G51060.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM3419	28	64
Representative plant	OGRP1872	11	40

Link Out ? help Back to Top
Phytozome	AT3G51060.1
Entrez Gene	824270
iHOP	AT3G51060
wikigenes	AT3G51060

Publications ? help Back to Top
Fridborg I,Kuusk S,Robertson M,Sundberg E The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley. Plant Physiol., 2001. 127(3): p. 937-48 [PMID:11706176] Kuusk S,Sohlberg JJ,Long JA,Fridborg I,Sundberg E STY1 and STY2 promote the formation of apical tissues during Arabidopsis gynoecium development. Development, 2002. 129(20): p. 4707-17 [PMID:12361963] Castelli V, et al. Whole genome sequence comparisons and "full-length" cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res., 2004. 14(3): p. 406-13 [PMID:14993207] Sohlberg JJ, et al. STY1 regulates auxin homeostasis and affects apical-basal patterning of the Arabidopsis gynoecium. Plant J., 2006. 47(1): p. 112-23 [PMID:16740145] Kuusk S,Sohlberg JJ,Magnus Eklund D,Sundberg E Functionally redundant SHI family genes regulate Arabidopsis gynoecium development in a dose-dependent manner. Plant J., 2006. 47(1): p. 99-111 [PMID:16740146] Ståldal V,Sohlberg JJ,Eklund DM,Ljung K,Sundberg E Auxin can act independently of CRC, LUG, SEU, SPT and STY1 in style development but not apical-basal patterning of the Arabidopsis gynoecium. New Phytol., 2008. 180(4): p. 798-808 [PMID:18811619] Alvarez JP,Goldshmidt A,Efroni I,Bowman JL,Eshed Y The NGATHA distal organ development genes are essential for style specification in Arabidopsis. Plant Cell, 2009. 21(5): p. 1373-93 [PMID:19435933] Trigueros M, et al. The NGATHA genes direct style development in the Arabidopsis gynoecium. Plant Cell, 2009. 21(5): p. 1394-409 [PMID:19435937] Eklund DM, et al. The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis. Plant Cell, 2010. 22(2): p. 349-63 [PMID:20154152] Zawaski C, et al. SHORT INTERNODES-like genes regulate shoot growth and xylem proliferation in Populus. New Phytol., 2011. 191(3): p. 678-91 [PMID:21564099] Eklund DM, et al. Expression of Arabidopsis SHORT INTERNODES/STYLISH family genes in auxin biosynthesis zones of aerial organs is dependent on a GCC box-like regulatory element. Plant Physiol., 2011. 157(4): p. 2069-80 [PMID:21976484] St The Arabidopsis thaliana transcriptional activator STYLISH1 regulates genes affecting stamen development, cell expansion and timing of flowering. Plant Mol. Biol., 2012. 78(6): p. 545-59 [PMID:22318676] Baylis T,Cierlik I,Sundberg E,Mattsson J SHORT INTERNODES/STYLISH genes, regulators of auxin biosynthesis, are involved in leaf vein development in Arabidopsis thaliana. New Phytol., 2013. 197(3): p. 737-50 [PMID:23293954] 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] Estornell LH,Landberg K,Cierlik I,Sundberg E SHI/STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis. Front Plant Sci, 2018. 9: p. 150 [PMID:29491878]