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Protocols

SUBA3 specifications

Information


Unique identifier OMICS_02987
Name SUBA3
Alternative name SUBcellular localisation database for Arabidopsis proteins
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Version 4.0
Content license CC Attribution
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Documentation


Publications for SUBcellular localisation database for Arabidopsis proteins

SUBA3 citations

 (22)
library_books

Classification and phylogenetic analyses of the Arabidopsis and tomato G type lectin receptor kinases

2018
BMC Genomics
PMCID: 5889549
PMID: 29625550
DOI: 10.1186/s12864-018-4606-0

[…] llowed by chromosome 4 (eight members), chromosome 5 (three members), chromosome 2 (two members) and chromosome 3 (one member) (Additional file ).Arabidopsis G-LecRKs localization was predicted using SUBA3 [, ]. This tool predicted all Arabidopsis proteins to be localized at the plasma membrane, consistent with the existence of a TM domain. SUBA predictions were further investigated with TargetP 1 […]

library_books

Nictaba Homologs from Arabidopsis thaliana Are Involved in Plant Stress Responses

2018
Front Plant Sci
PMCID: 5767604
PMID: 29375596
DOI: 10.3389/fpls.2017.02218

[…] nts were obtained using EMBOSS Water. Prediction of the presence of a signal peptide was conducted using Phobius and SignalP 4.1 (; ), whereas the presence of a NLS was predicted by NucPred (). Using SUBA3, protein subcellular localization was predicted (). BLASTn and tBLASTn searches against the expressed sequence tag (EST) database were performed using the NCBI website. Using the eFP browser () […]

call_split

Highly Efficient Single Step Enrichment of Low Abundance Phosphopeptides from Plant Membrane Preparations

2017
Front Plant Sci
PMCID: 5632542
PMID: 29042862
DOI: 10.3389/fpls.2017.01673
call_split See protocol

[…] Bioinformatics analysis was performed with Perseus, Microsoft Excel, SigmaPlot. Annotations were extracted from MapMan (), subcellular locations were obtained from SUBA3 (). […]

library_books

Global Analysis of Membrane associated Protein Oligomerization Using Protein Correlation Profiling*

2017
PMCID: 5672003
PMID: 28887381
DOI: 10.1074/mcp.RA117.000276

[…] aracterized in previous work on the oligomerization state of soluble proteins in the cytosol () or chloroplast () (B). Based on the current subcellular localization predictions from SUBAcon (Version: SUBA3) (), our proteomic data set included many uncharacterized cytosolic, chloroplast, and mitochondrial proteins. The largest enrichment was in endomembrane-localized proteins, with 65% analyzed for […]

library_books

The pentatricopeptide repeat protein MTSF2 stabilizes a nad1 precursor transcript and defines the 3΄ end of its 5΄ half intron

2017
Nucleic Acids Res
PMCID: 5449624
PMID: 28334831
DOI: 10.1093/nar/gkx162

[…] r 3 months (Figure ). Additionally, mtsf2 plants showed deformed and dark green rosette leaves and were late flowering but remained fertile (Figure ).The Arabidopsis subcellular database SUBA (http://suba3.plantenergy.uwa.edu.au/) strongly supported the mitochondrial localization of the MTSF2 protein. To verify the cellular distribution of MTSF2, a GFP translational fusion comprising the complete […]

library_books

Skewing in Arabidopsis roots involves disparate environmental signaling pathways

2017
BMC Plant Biol
PMCID: 5286820
PMID: 28143395
DOI: 10.1186/s12870-017-0975-9

[…] obable skew gene candidates (HPSGC).The 11 HPSGC are involved in many different processes and were subjected to a thorough literature and expression map search using many available databases, such as Suba3, TAIR, and the Arabidopsis eFP browser [–]. These genes were searched with the goal of finding associations with cell expansion, division, auxin transport, or any process involved with root trop […]


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SUBA3 institution(s)
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, Australia; Department of Genetics and Physiology, Biocenter Oulu, University of Oulu, Finland
SUBA3 funding source(s)
ARC Centre of Excellence in Plant Energy Biology (CE140100008)

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