ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

For each MSU locus, the corresponding Arabidopsis thaliana loci from orthology databases are reported, along with a percentage score, and columns of data for comparison with rice.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Users can search for At TAIR identifiers (AGIs) to find orthologous Rice loci.
  • Dropdown orthology can be viewed in Rice search results.
  • A spreadsheet of orthology can be obtained with "orthology summary". It shows the corresponding Arabidopsis loci, database scores, and comparable information for each rice locus.
Example: view ortholog summary for LOC_Os05g43480.1
Example: show orthology summaries for LOC_Os02g06480.1, LOC_Os08g06060.1, Q5VQF5

Coverage

  Total Exclusive Common
InParanoid 17899 6056 11843
Gramene 31188 19345 11843
Either 37244

Caution

Rice:
Arabidopsis thaliana:


Please note: While orthology reflects sequence homology conservation between Arabidopsis and rice, and ‘expressology’ involves both orthology and conserved expression, tissue equivalency determination is not always exact and can be difficult to establish between different species (as outlined in Patel et al., 2012). Thus, it is important to note this before assuming a direct conserved functional relationship between orthologues or expressologs.

Example

AT_AGIAT1G10950.1
MSU RGAP Putative Function Annotationstransmembrane nine 1
TAIR Model SequencesDNA 4776 bp; Upstream 1000 bp; CDS 1770 bp; Peptide 589 aa
RNA Tissue Data73 of 73
Developmental ExpressionSilique, Seed, Germination, Seedling, Leaf, Stem, Root, Flower
Stress ExpressionControl, Drought, Salt, Cold, Heat
Experimentally Shown Motifs
Predicted Locationsextracellular + 2 more from 4 preds
Experimentally Shown Locationsgolgi + 1 more from 3 refs
Experimentally Shown Phenotypes
ExpressologsLOC_Os02g34690 + 2 more
AT_AGIAT1G10950.1

System Information

Transcript of last update

Took 5 hours, 35 minutes, 12 seconds, 951 millis starting Thu, 7 Feb 2013 13:54:51 GMT:
Using /tmp/RiceDB/OrthologySummary_
Using /var/www/ricedb/Data/downloaded/OrthologySummary_
Updating orthology join table
Updating IDMAP
Updating orthology identifier summary
Updating orthology experimental localisation summary
Updating orthology predicted location summary
Updating orthology sequence summary
Updating orthology annotation summary
Adding orthology orthology column
Updating orthology RNA expression summary
Adding orthology expressolog column