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Alternative splicing visualization tool...
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Usage and Interpretation of ASIP Tables
Table list:
Maize Intron Retention. This table contains data derived from maize EST/TUG spliced alignments. Columns:
| Short name | Full name | Links to |
|---|---|---|
| TUG | Tentative Unique Gene (retaining an intron) | PlantGDB maize TUC/EST entry |
| EST | representative Expressed Sequence Tag | PlantGDB maize EST entry |
| len | length of the retained intron | |
| IntronBorder | 5' and 3' terminal sequences of the retained intron | full intron sequence |
| Dscore | GeneSeqer score for the intron donor site | |
| Ascore | GeneSeqer score for the intron acceptor site | |
| TugESTcnt | Total number of ESTs supporting intron retention/splicing (or splicing/retention when the alignment code contains R) | |
| MaxLibrary | major library source for the ESTs supporting the spliced transcript version (or intron retention when the alignment code contains R) | EST library source details |
| Alignment | alignment code | display of the alignment |
Example:
To view a schematic representation of the spliced alignments, click on the alignment code in the "Alignment" column, and a page similar to the following picture will be shown. Details of the alignments can be retrieved by clicking in the picture.
Conserved Intron Retention. This table contains data supporting conservation of intron retention between maize, rice, and Arabidopsis homologous genes. The examples include cases in which introns in homologous positions are retained in alternative transcripts in all species as well as cases in which intron retention was observed in all three species for a particular gene, but not in homologous positions. Columns:
| Short name | Full name |
| Query | maize TUG aligned against the rice genome |
| ZmOsSim | GeneSeqer similarity score of the maize TUG spliced alignment against the rice genome |
| ZmOsCov | GeneSeqer coverage score of the maize TUG spliced alignment against the rice genome |
| BAC | rice BAC containing the putative homologous gene of the maize query |
| osFrom | alignment start position on the BAC |
| osTo | alignment end position on the BAC |
| osClust | rice EST cluster ID |
| AtModel | Arabidopsis gene model matched to the same region |
| AtOsSim | GeneSeqer similarity score of the Arabidopsis protein to rice genome alignment |
| AtOsCov | GeneSeqer coverage score for the Arabidopsis protein to rice genome alignment |
| count | number of homologous rice BAC locations (note: may include the same genetic locus on different BACs) |
The "Query" and "AtModel" columns are searchable in the search box. Entries in the "Query" column are linked to pages showing the spliced alignment of rice ESTs, maize TUGs and Arabidopsis proteins to the rice genome (upper panel) and of Arabidopsis cDNAs and ESTs to the homologous Arabidopsis genome location (lower panel). The instances of intron retention are easily spotted. Example:
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