Medaka: University of Tokyo 5'-SAGE

Description

This track shows the start sequence tags of mRNA transcripts determined by 5'-end Serial Analysis of Gene Expression (5'-SAGE) sequencing. These 5'-SAGE tags are composed of 19 bases from the 5'-end of a cDNA. See the Human tag pages for more details on 5'-SAGE sequencing.

5'-SAGE libraries

The 5'-SAGE tag features are represented as small boxes. Clicking on the feature brings up a menu with information about this tag and a link to this more detailed description.

Alignments

The 5'-SAGE tags were aligned to the unmasked genome sequence using Exonerate. The hits were filtered using the following strategy:

Credits

The 5'-SAGE libraries were produced at the University of Tokyo and Bioinformatics Institute. The data was mapped and analyzed using code from the EnsEMBL project.

References

Hashimoto,S., Ahsan,B., Takeda,H., Morishita,S. and Kohara,Y.
Submission of 356,693 entries (accession numbers ACAAA0000001-ACAAA0356693) to the DDBJ/EMBL/GenBank databases on 14 November 2006.

Kasahara,M., Naruse,K., Sasaki,S., Nakatani,Y., Qu,W., Ahsan,B., Yamada,T., Nagayasu,Y., Doi,K., Kasai,Y., Jinbo,T., Kobayashi,D., Shimada,A., Toyoda,A., Kuroki,Y., Fujiyama,A., Sasaki,T., Shimizu,A., Asakawa,S., Shimizu,N., Hashimoto,S., Yang,J., Lee,Y., Matsushima,K., Sugano,S., Sakaizumi,M., Narita,T., Ohishi,K., Haga,S., Ohta,F., Nomoto,H., Nogata,K., Morishita,T., Endo,T., Shin-i,T., Takeda,H., Morishita,S. and Kohara,Y.
_The medaka draft genome : new insights into vertebrate genome evolution_ /Unpublished (2006)/

Hashimoto,S., Suzuki,Y., Kasai,Y., Morohoshi,K., Yamada,T., Sese,J., Morishita,S., Sugano,S. and Matsushima,K.
5'-end SAGE for the analysis of transcriptional start sites
Nat. Biotechnol. 22, 1146-1149 (2004)

Slater,G.S. and Birney,E.
Automated generation of heuristics for biological sequence comparison
BMC Bioinformatics 6(1), 31 (2005).

Links