| 155 | | This track displays the medaka expression profile by showing mapped 5’end tag of an expressed Gene. Details of each tag can be found by clicking on each viewed rectangle on this track. |
| 156 | | |
| 157 | | Given the limited availability of expressed gene tags (EST) and |
| 158 | | full-length enriched cDNA sequences, a considerable amount of 5’-end |
| 159 | | serial analysis of gene expression (5’SAGE) data, the 19-20 5’-end |
| 160 | | bases of mRNAs, have been collected, to detect transcription start |
| 161 | | sites (TSSs) and subsequently protein-coding regions were predicted |
| 162 | | from the TSSs by using GENSCAN. In all, 1,186,742 5’SAGE tags were |
| 163 | | collected from a mixture of cDNA from 0- to 7-day-old day old medaka |
| 164 | | embryos and adult body tissues. Of these, 841,235(70.9%) were aligned |
| 165 | | to unique positions in the medaka draft genome, but most of them were |
| 166 | | duplicates and were expressed from 344,266 transcription start sites. |
| 167 | | Stated another way, multiple tags are often derived from one locus, |
| 168 | | and the frequency approximates the expression level of the gene |
| 169 | | encoded at that locus. From these TSSs, 20,141 genes were predicted, |
| 170 | | and individual predicted genes were supported by the evidence of some |
| 171 | | 5’SAGE tags, which was effective in reducing the false-positive |
| 172 | | ratio of predicted genes. These evidence-based predicted medaka genes |
| 173 | | were compared with human genes comprehensively, and about 57.7% of |
| 174 | | the predicted medaka genes have human orthologues, and 21.6% of the |
| 175 | | genes constitute medaka-human reciprocally best 1:1 orthologue pairs, |
| 176 | | indicating that medaka could serve as a model system for humans. |
| 177 | | |
| | 155 | This track displays the medaka expression profile by showing mapped 5’end tag of an expressed Gene. |
| | 156 | The positions of individual 5’SAGE tags are illustrated by red boxes. The label associated with each 5’SAGE tag is of the form S_F (L0, L1), where S indicates whether the tag is derived from the sense (+) or the antisense strand (-), F is the frequency of occurrences of the tag in the collection from a mixture of cDNA, and L0 (L1, resp.) is the number of loci where the tag is aligned to the genome with no mismatch (with one mismatch). Tags are aligned to unique positions if L0=1, or L0=0 and L1=1. For example, a tag labeled with +_5(1,3) is aligned uniquely to the plus strand of the position, it is observed five times in the tag collection, and it is also aligned to three other locations with one mismatch. A tag with -_1(0,1) fails to map to the genome with no mismatch but maps uniquely to the minus strand of the position with one mismatch. The figure displays a large number of 5’SAGE tags are observed in both strands. |
