ASSETs (Alternative Splicing Sequence Enriched Tags)

 

 

              This page provides the supplementary information of the article

           Akira Watahiki, Kazunori Waki, Norihito Hayatsu, Toshiyuki Shiraki, Shinji Kondo, Mari Nakamura,

Daisuke Sasaki, Takahiro Arakawa, Jun Kawai, Matthias Harbers, Yoshihide Hayashizaki & Piero Carninci

Libraries enriched for alternative splicied exons reveal splicing patterns in melanocytes and melanomas

in Nature Methods December 2004, Volume 1 No 3 pp233 – 239 Link to the paper

 

 

Correspondence should be addressed to

Matthias Harbers matthias.harbers@dnaforminc.com or Piero Carninci rgscerg@gsc.riken.jp

 

 

                      Abstract

          

It is becoming increasingly clear that alternative splicing enables the complex development and homeostasis of higher organisms. To gain a better understanding of how splicing contributes to regulatory pathways, we have developed an alternative splicing library approach for the identification of alternatively spliced exons and their flanking regions by alternative splicing sequence enriched tags sequencing. Here, w have applied our approach to mouse melan-c melanocyte and B16-F10Y melanoma cell lines, in which 5,401 genes were found to be alternatively spliced. These genes include those encoding important regulatory factors such as cyclin D2, Ilk, MAPK12, MAPK14, RAB4, melastatin 1 and previously unidentified splicing events for 436 genes. Real-time PCR further identified cell line–specific exons for Tmc6, Abi1, Sorbs1, Ndel1 and Snx16. Thus, the ASL approach proved effective in identifying splicing events, which suggest that alternative splicing is important in melanoma development.

 

                      Supplementary information

 

Information of ASSETs and ESTs

 

 

1.     ASSETs L1 ( xls / txt / html )

2.     ASSETs L2 ( xls / txt / html )

3.     ASSETs L3 ( xls / txt / html )

4.     ESTs G2 (melanocyte) ( xls / txt / html )

5.     ESTs G3 (melanoma) ( xls / txt / html )

6.     GO (gene ontology) identification ( xls / txt / html )

 

Alignments and Annotations of ASSETs

                                  Alignments are calculated by MAP program link

                                  Full length references are FANTOM2 clones link

(Some alignments are under adjustment)

 

Download ASSETs sequence DATA

 

 

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