1. Figures and Table for Supplemental material Kemin Zhou Nov 20, 2011

2. Transcription overlap Number of genes per congregation GenomeAgabi2Aspca3Spoth2Lacbi2Aspac1 %Multi genes13.538.163.044.563.9 %Genes in Cong.25.463.587.471.890.9 Count Fig S1

3. Fig S2 Relative Expression Level of Minor Isoforms Count Agabi2 0.00.40.8 0 500 1500 Aspca3 0.00.40.8 0 2000 6000 Spoth2 0.00.40.8 0 2000 6000 Lacbi2: Sanger+454 0.00.40.8 0 200 400 600 Lacbi2 0.00.40.8 0 10000 30000 Aspac1 0.00.40.8 0 20000 40000

4. 100200300400 0.25 0.30 0.35 0.40 0.45 0.50 SOM (std/mean) Average EST Length (nt) Agabi2 Aspca3 Aspac1 Spoth2 Lacbi2 Fig S3

5. Agabi2 NAG Fig S4 NAG

6. Aspca3 Fig S5 NAG

7. Lacbi2 Fig S6 NAG

8. Spoth2 Fig S7 NAG

9. Aspac1 Fig S8 NAG

10. AS Category Fraction of Total Fig S9 0.00 0.01 0.02 0.03 0.04 CE CE_AD CE_AA CE_ADAA CEorAAend ME Other

11. A B E D C Fig S10 Intron Length (nt) Frequency Intron Length (nt) Major: Expression Level > median of complete models Major isoform of AS All: Intron from partial + complete models

12. 2.6E-09 0.02163 0.95605 0.41517 5.1E-05 0.11912 0.32093 0.03850 0.00014 6.6E-06 0.68033 0.00084 0.02261 0.53449 0.05320 0.07668 0.11337 0.77613 0.01756 0.02417 Fig S11 Fraction