Genome / Gene Models
The current genome assembly displayed at OsGDB is version
Release 7.
Annotated gene models are
Release 7. For more information see
Data & Methods.
More about the genome...
Oryza sativa (ssp. japonica) genome at OsGDB
| Chr |
Length (bp) |
Chromosome Map |
Gene Models |
| 1 | 43,270,923 | 8,023 |
| 2 | 35,937,250 | 6,656 |
| 3 | 36,413,819 | 7,022 |
| 4 | 35,502,694 | 6,179 |
| 5 | 29,958,434 | 5,485 |
| 6 | 31,248,787 | 5,467 |
| 7 | 29,697,621 | 5,185 |
| 8 | 28,443,022 | 4,866 |
| 9 | 23,012,720 | 3,928 |
| 10 | 23,207,287 | 4,067 |
| 11 | 29,021,106 | 4,695 |
| 12 | 27,531,856 | 4,580 |
| 13 | 633,585 | 0 |
| 14 | 592,136 | 0 |
| Total: |
|---|
| 14 | 374,471,240 | 66,338 |
Alignments to Genome
OsGDB displays high quality spliced alignments for EST, cDNA, PUT, and model species proteins. The current alignment database version is
OsGDB187. For more information see
Data & Methods.
More about alignments...
- Transcript sequences displayed at OsGDB were aligned to genomic sequence using GeneSeqer, which performs a consensus spliced alignment on ESTs and cDNA, providing both cognate and non-cognate alignments for improved gene prediction (Brendel et al., 2004).
- Related-species predicted proteins were aligned to genomic sequence using GenomeThreader (Gremme et al., 2005).
- Microarray probes (if any) were matched to the PUT assembly sequence using Vmatch and then coordinately transfered to genomic location.
Search / Download
Search or download any sequence from OsGDB using
Search / Download links at left. Complete datasets can also be downloaded from the
OsGDB Download page or by
ftp.
More about search / download...
| Resource |
Description |
| Search by ID / Keyword |
Search for any OsGDBgene or aligned sequence by ID or keyword, and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format).
|
| Download Region Data |
For any specified genomic region, download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format).
|
| Download All |
Download bzip2 files and MySQL tables representing complete OsGDB dataset |
| ftp download |
Download all OsGDB data via ftp |
Note: sequences displayed here may not reflect the latest Oryza sativa (ssp. japonica) sequence count at PlantGDB, which can be viewed on our download page.
Tools
Sequence analysis tools accessed from the
Genome Context View menu use the current genomic region as input. Or, to access the same tools without a genomic context, use OsGDB left menubar Tools links.
More about tools...
Online Analytical Tools - Description
| Name |
Description |
Source/Version |
| BLAST |
Use BLASTn, BLASTp, tBLASTn and tBLASTx to match a query sequence to OsGDB sequences.
BLAST-able datasets include Oryza sativa (ssp. japonica) genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences. |
NCBI Blastall 2.2.18 |
| GeneSeqer |
Spliced alignment of user-specified transcript datasets to genomic DNA from any region in OsGDB. User can specify splice site model and stringency level. |
Brendel Group (Oct 2008) |
| GenomeThreader |
Spliced alignment of user-specified protein datasets to genomic DNA from any region in OsGDB. User can specify splice site model and stringency level. |
GenomeThreader Home Page |
Gene Structure Annotation
Help annotate the
Oryza sativa (ssp. japonica) genome using our yrGATE gene structure annotation tool (
see Overview), aided by
GAEVAL tables that flag problematic gene models.
Video demo: QuickTime
Flash
Custom Track Display
Distributed Annotation Service (DAS) (
see Overview) is available for displaying remotely served genome alignments at OsGDB, as well as for displaying selected OsGDB tracks on a different genome browser (e.g. Ensembl, GBrowse).
How to use DAS...
To add a DAS track to OsGDB using our DAS client, first select desired genome coordinates above and click "Go", then select menu item "Configure -> Add Track" and paste in the appropriate DAS URL.
To view OsGDB tracks in another genome browser (e.g. Ensembl, Gbrowse) using our DAS server, first find the appropriate xDAS Server URL on our DAS overview page, then follow instructions on the remote browser website for adding the remote track. NOTE: DAS service available for certain tracks only.
For more details, refer to DAS section in our Genome Browser help pages.
Additional custom track display features are under development.
Annotated Protein Alignments
A searchable table of splice-aligned, annotated protein models from one or more related species. Select from the left menu under Gene Annotations -> Splice-Aligned Proteins.
Support
Genome browser video demo: QuickTime
Flash
For help pages and tutorials focusing on genome browser features and gene annotation, see side bar.