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Gramene Transposable Element Annotation Project
Gramene is a comparative mapping resource for grains. Part of this lab's responsibility for the Transposable Element project is to make the discovered elements public. We have chosen Gramene to be the repository for this information in addition to Genbank.
Support: NSF
Personnel and Curation Responsibilities:
Principle Coder: Gregory Wilson
Publications:
None yet.
Annotation Process
Because some transposable elements occur in large copy numbers (>500), an automated annotation process is needed. Well defined elements (like the "MITEs") allow for quick annotation. Elements that have hyper-variable regions pose more of a challenge. The general flow is as follows:
- Publicly available concensus sequences for transposable elements are obtained.
- The Gramene genetic dataset is blasted with an E-value cutoff of 1E-10.
- Elements found that are greater than 70% of the concensus length are automatically accepted and displayed.
- Elements that are less than 70% but greater than 50% of the concensus length are placed in a manual curation queue.
- Elements that are less than 50% of the concensus length are discarded.
ELEMENTS CURRENTLY ANNOTATED
| Name | Class | Family |
|---|
| ID-1 | Type 2 | Tourist |
| ID-2 | Type 2 | Tourist |
| ID-3 | Type 2 | Tourist |
| ID-4 | Type 2 | Tourist |
| Centre | Type 2 | Tourist |
| Buhui | Type 2 | Tourist |
| Lier | Type 2 | Tourist |
| Casin | Type 2 | Tourist |
| Susu | Type 2 | Tourist |
| Stola | Type 2 | Tourist |
| Wuji | Type 2 | Tourist |
| Stone | Type 2 | Tourist |
| Helia | Type 2 | Tourist |
| Youren | Type 2 | Tourist |
| Os0594-RC1564 | Type 2 | Tourist |
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| Name | Class | Family |
|---|
| mPing | Type 2 | PIF |
| Pangrangja | Type 2 | ? |
| | | |
| Cloud | Type 2 | Mutator |
| ECR | Type 2 | Mutator |
| | | |
| Stow-OS20 | Type 2 | Stowaway |
| Os1288 | Type 2 | Stowaway |
| | | |
| Delay | Type 2 | hAT |
| Os0411 | Type 2 | hAT |
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Project Website: http://www.botany.uga.edu/rice/index.html
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