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Oryza
sativa

Triticum
aestivum

Zea
mays

Hordeum
vulgare

Where do plant proteins go?

Proteins in barley, wheat, rice and maize have specific functions and locations within the plant cell. They generate or are themselves products important for human use. In order to improve crops, protein function and location must be known. Protein subcellular location is an important clue to function and also to how proteins interact within the metabolic household. Subcellular location can be determined by fluorescent protein tagging or mass spectrometry detection in subcellular purifications as well as by prediction using protein sequence features. Location information helps represent plant cells as interacting protein networks that can be investigated for improving product generation in crops.

The compendium of crop Proteins with Annotated Locations (cropPAL) collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and maize proteomes. The data collection including metadata for proteins and studies can be accessed through the search portal. The reciprocal blast and EnsemblPLants homology tree allows the search for location data across the four crop species as well as compares it to Arabidopsis data from SUBA.

If you find this resource useful please cite cropPAL (PubMed, Plant Cell Physiol). Download the cropPAL data set from the ANDS web-based data discovery service RDA

Choose a crop at left then build a query with the questions below by pressing the → buttons.

... or try a quick text query:
Queries appear here....
Find proteins where the... (To start a query or add another filter to your query select a filter below and press the → button.)
Test for experimental (e.g. GFP or MS/MS) evidence of subcellular location.
... experimental location inferred by to be in
Many proteins have no experimental evidence for their subcellular location. Check what the predictors think.
... predicted location inferred by to be in
Find proteins where the... (To start a query or add another filter to your query select a filter below and press the → button.)
Search for or exclude proteins by keywords. A search will be conducted against the descriptions of proteins in the CropPAL database. The syntax of this search supports extended regular expressions (see this site for more information). Choosing matches will give you access to the match syntax of MySQL, e.g. entering +leaf –seed* in the keyword(s) box matches a description that contains leaf but that does not contain seed, seeds, or seedling etc.
... protein description keyword(s)
Filter for proteins based on various numeric data derived from sequence data. GRAVY is defined in Kyte J., Doolittle R.F.: Mol. Biol. 157:105-132(1982) "A simple method for displaying the hydropathic character of a protein" doi:10.1016/0022-2836(82)90515-0. PMID: 7108955.
... physical property of is ← Should be a number
Filter for proteins that are translated from genes on (or not on) a specific chromosome or assembly (or set of scaffolds!).
... gene model on chromosome
Search for proteins that are (or are not) in a list of Identifiers. Enter this list of Identifiers into the box below. Current Identifiers come from the following databases:
  • InterPro 473319
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  • GO 392236
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  • EMBL 233475
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  • UniProt 232269
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  • Proteomes 222192
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  • Pfam 216166
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  • EnsemblPlants 176994
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  • EnsemblPlantsGene 167603
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  • PROSITE 134197
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  • OMA 127441
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  • SUPFAM 115586
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  • Gene3D 113150
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  • ExpressionAtlas 69529
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  • RefSeq 67219
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  • UniGene 59395
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  • SMART 58845
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  • GeneID 58749
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  • Gramene 52082
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  • KEGG 50728
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  • MSU 47962
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  • InParanoid 45038
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  • PANTHER 41296
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  • HOGENOM 36987
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  • PRINTS 29124
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  • ProteinModelPortal 22047
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  • TIGRFAMs 20202
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  • KO 17314
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  • eggNOG 15801
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  • PRIDE 14805
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  • EC 11019
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  • Reactome 10474
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  • PIRSF 8859
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  • HAMAP 6345
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  • STRING 5133
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  • UniPathway 2729
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  • PIR 2465
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  • ProDom 2431
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  • SMR 2400
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  • CAZy 1864
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  • MEROPS 1614
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  • PaxDb 1557
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  • MaizeGDB 939
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  • Genevestigator 904
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  • PDBsum 640
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  • PDB 640
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  • BRENDA 422
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  • PeroxiBase 280
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  • IntAct 272
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  • Allergome 154
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  • BioCyc 144
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  • EvolutionaryTrace 137
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  • ProMEX 101
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  • SABIO-RK 76
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  • TCDB 52
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  • DIP 50
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  • MINT 40
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  • ChEMBL 31
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  • DNASU 15
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  • BindingDB 14
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  • PRO 10
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  • REBASE 10
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  • DisProt 5
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  • BioGrid 3
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  • MoonProt 2
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  • UCD-2DPAGE 1

You can use "wildcards" with "like" and "not like" e.g. GO:%.

... EnsemblPlants identifier(s), alias or protein sequence feature is the list of: (e.g. GO:0008270, IPR017986 etc.)
Find proteins with ... (To start a query or add another filter to your query select a filter below and press the → button.)

Reciprocal Blast

Search for or exclude proteins by keywords. A search will be conducted against the literature titles and abstracts in the SUBA database. The syntax of this search supports extended regular expressions (see this site for more information). Choosing matches will give you access to the match syntax of MySQL, e.g. entering +leaf –seed* in the keyword(s) box matches a title/abstract that contains leaf but that does not contain seed, seeds, or seedling etc.
... Arabidopsis orthologs with blast match score greater than ← must be a number and Arabidopsis consensus location in

EnsemblPlants Homology Tree

Search for proteins that are homologous to proteins from another Crop in a certain subcellular location. The homology types included are orthologs (any gene pairwise relation where the ancestor node is a speciation event) and paralogs (any gene pairwise relations where the ancestor node is a duplication event). For more specific classifications displayed in the query results please refer to: EnsemblPlants Protein trees
... any homology with identity greater than ← must be a number and type that have been experimentally localized in by MS/MS or GFP and has experimentally localized (by MS/MS or GFP) it in:
Find proteins where the... (To start a query or add another filter to your query select a filter below and press the → button.)
One aspect of CropPAL involves manual literature trawling for papers related to subcellular protein localization in Plants. Use this query component to extract localization calls by referenced papers. If you know of a publication that does not appear to be in the list, please inform Dr Cornelia Hooper (cornelia.hooper(at)uwa.edu.au).
... literature referenced location described in pubmed: ← Must be a PUBMED id
Search for proteins from publication year
... year of publication of localisation studies is between ← Should be a year and ← Should be a year
Search for or exclude proteins by keywords. A search will be conducted against the literature titles and abstracts in the SUBA database. The syntax of this search supports extended regular expressions (see this site for more information). Choosing matches will give you access to the match syntax of MySQL, e.g. entering +leaf –seed* in the keyword(s) box matches a title/abstract that contains leaf but that does not contain seed, seeds, or seedling etc.
... publication title or abstract of the localisation study the keyword(s)
... author's name like
... author's affiliation
... author's affiliation in
Search for proteins by author affiliation
... author's afflilation in