I. Intron Isoform events The line lists the intron isoform 1 along with phase information for isoform 1, and intron isoform 2 along with phase information, and the modularity of the event. 1. IDB60048-2419-2656 inCDS, p0 IDB60048-2419-2670 inCDS, p0 2 2. IDB60053-2809-2951 inCDS, p0 IDB60053-2809-2979 inCDS, p0 1 3. IDB60569-5047-5551 inCDS, p0 IDB60569-5047-5369 inCDS, p0 0 4. IDB61174-2669-2846 inCDS, p1 IDB61174-2669-2851 inCDS, p1 2 5. IDB61288-609-961 inCDS, p2 IDB61288-867-961 inCDS, p2 0 6. IDB61881-22656-23413 inCDS, p0 IDB61881-22656-23218 inCDS, p0 0 7. IDB61889-2236-20417 inCDS, p1 IDB61889-2251-20417 inCDS, p1 0 8. IDB62198-11006-13732 inCDS, p0 IDB62198-11099-13732 inCDS, p0 0 9. IDB62268-125-305 inCDS, p1 IDB62268-107-305 inCDS, p1 0 10. IDB62268-125-305 inCDS, p1 IDB62268-104-305 inCDS, p1 0 11. IDB62773-4084-4913 inCDS, p2 IDB62773-4084-4916 inCDS, p2 0 12. IDB62858-147-1786 inCDS, p2 IDB62858-147-1792 inCDS, p2 0 13. IDB62896-9257-9333 inCDS, p1 IDB62896-9257-9384 inCDS, p1 0 14. IDB62953-12628-12932 inCDS, p0 IDB62953-12628-12935 inCDS, p0 0 15. IDB62966-2430-3366 inCDS, p2 IDB62966-2430-3363 inCDS, p2 0 16. IDB63000-168-3955 inCDS, p1 IDB63000-171-3955 inCDS 0 17. IDB63028-8076-8154 unknown IDB63028-8076-8157 unknown 0 18. IDB63069-2524-3623 inCDS, p2 IDB63069-2524-3626 inCDS, p2 0 19. IDB63069-3853-4549 inCDS, p0 IDB63069-3853-4552 inCDS, p0 0 20. IDB63110-5446-5639 inCDS, p2 IDB63110-5409-5639 inCDS, p1 1 21. IDB63571-20124-20504 inCDS, p1 IDB63571-20124-20507 inCDS, p1 0 22. IDB64070-55-1298 inCDS, p0 IDB64070-66-1298 inCDS, p2 2 23. IDB64141-151-2279 inCDS, p0 IDB64141-210-2279 inCDS, p2 2 24. IDB64181-12784-17724 inCDS, p2 IDB64181-12784-17709 inCDS, p2 0 25. IDB64203-9912-16743 inCDS, p1 IDB64203-9912-16678 inCDS, p1 2 26. IDB64224-35156-35715 inCDS, p0 IDB64224-35156-35808 inCDS, p0 0 27. IDB64344-6501-6598 unknown 1 IDB64344-6501-6601 unknown 1 28. IDB64760-5533-6219 inCDS, p1 IDB64760-5533-6225 inCDS, p1 0 29. IDB64773-5569-6477 inCDS, p0 IDB64773-5569-7067 inCDS, p0 2 30. IDB64775-33924-34260 inCDS, p1 IDB64775-33924-34257 inCDS, p1 0 31. IDB64798-8608-8711 inCDS, p0 IDB64798-8608-8714 inCDS, p0 0 32. IDB65132-215-796 inCDS, p1 IDB65132-215-793 inCDS, p1 0 33. IDB66108-3934-6491 inCDS, p2 IDB66108-3855-6491 inCDS, p1 1 34. IDB66163-3316-4613 inCDS, p2 IDB66163-3307-4613 inCDS, p2 0 35. IDB66178-2529-3721 inCDS, p1 IDB66178-2529-3724 inCDS, p1 0 36. IDB66209-11182-11702 inCDS, p1 IDB66209-11251-11702 inCDS, p1 0 37. IDB66277-31150-32691 inCDS, p1 IDB66277-31150-32727 inCDS, p1 0 38. IDB62268-104-305 inCDS, p1 IDB62268-107-305 inCDS, p1 0 39. IDB66069-32854-33952 unknown IDB66069-32885-33952 unknown 1 II. Intron retention event Retained intron is IDB63867-17164-17241 (mod 0; inCDS; p2) with the 5' and 3' flanking exons as IDB63867-17066-17163 (inCDS, p0) & IDB63867-17242-17371 (inCDS, p2) III. Simple Cassette Exon Events. The lines list the modularity of the event, the intron 5' to cassette exon along with phase information, the intron 3' to the cassette exon along with phase information, and the covering intron (that causes the isoform event) along with phase information. 1. 0 IDB60346-2175-2378 inCDS, p1 IDB60346-2535-3111 inCDS IDB60346-2175-3111 inCDS, p1 2. 2 IDB60569-2880-3134 inCDS, p0 IDB60569-3227-3493 inCDS, p2 IDB60569-2880-3493 inCDS, p0 3. 0 IDB61221-167108-169705 inCDS, p1 IDB61221-169763-184646 inCDS, p1 IDB61221-167108-184646 inCDS, p1 4. 1 IDB61264-138-19118 inCDS, p2 IDB61264-19183-23533 inCDS, p0 IDB61264-138-23533 inCDS, p2 5. 0 IDB61415-11141-24932 inCDS, p1 IDB61415-24993-30892 inCDS, p1 IDB61415-11141-30892 inCDS, p1 6. 0 IDB61473-40035-41057 inCDS, p1 IDB61473-41220-43038 inCDS, p1 IDB61473-40035-43038 inCDS, p1 7. 1 IDB61736-6373-6479 inCDS, p1 IDB61736-6595-7145 inCDS, p2 IDB61736-6373-7145 inCDS, p1 8. 0 IDB61774-42115-42297 inCDS, p2 IDB61774-42346-44352 inCDS, p2 IDB61774-42115-44352 inCDS, p2 9. 1 IDB61905-3754-9201 inCDS, p0 IDB61905-9332-25125 inCDS, p1 IDB61905-3754-25125 inCDS, p0 10. 0 IDB62093-115-1244 inCDS, p1 IDB62093-1515-2997 inCDS, p1 IDB62093-115-2997 inCDS, p1 11. 0 IDB62161-7176-9318 inCDS, p1 IDB62161-9397-9756 inCDS, p1 IDB62161-7176-9756 inCDS, p1 12. 0 IDB62198-14595-15328 inCDS, p0 IDB62198-15422-20873 inCDS, p0 IDB62198-14595-20873 inCDS, p0 13. 2 IDB62325-712-1122 inCDS, p1 IDB62325-1233-2160 inCDS, p0 IDB62325-712-2160 inCDS, p1 14. 0 IDB62419-85-1354 inCDS, p0 IDB62419-1478-1926 inCDS, p0 IDB62419-85-1926 inCDS, p0 15. 0 IDB63531-92-489 inCDS, p0 IDB63531-601-860 inCDS, p0 IDB63531-92-860 inCDS, p0 16. 0 IDB63562-4212-4291 inCDS, p0 IDB63562-4442-4758 inCDS, p0 IDB63562-4212-4758 inCDS, p0 17. 0 IDB63610-466-822 inCDS, p0 IDB63610-934-1270 inCDS, p0 IDB63610-466-1270 inCDS, p0 18. 2 IDB63867-62-541 inCDS, p1 IDB63867-616-3088 inCDS, p0 IDB63867-62-3088 inCDS, p1 19. 0 IDB64065-1208-1635 inCDS, p1 IDB64065-1681-2213 inCDS, p1 IDB64065-1208-2213 inCDS, p1 20. 0 IDB64070-1931-2044 inCDS, p0 IDB64070-2231-3321 inCDS, p0 IDB64070-1931-3321 inCDS, p0 21. 0 IDB64123-4696-6959 inCDS, p0 IDB64123-7074-12313 inCDS, p0 IDB64123-4696-12313 inCDS, p0 22. 0 IDB64125-2416-11572 inCDS, p1 IDB64125-11627-49806 inCDS, p1 IDB64125-2416-49806 inCDS, p1 23. 0 IDB64203-9912-16678 inCDS, p1 IDB64203-16817-18293 inCDS, p2 IDB64203-9912-18293 inCDS, p1 24. 1 IDB64203-9912-16743 inCDS, p1 IDB64203-16817-18293 inCDS, p2 IDB64203-9912-18293 inCDS, p1 25. 0 IDB64224-46489-47566 inCDS, p0 IDB64224-47759-49719 inCDS, p0 IDB64224-46489-49719 inCDS, p0 26. 2 IDB64244-142-4028 inCDS, p0 IDB64244-4175-5771 inCDS, p2 IDB64244-142-5771 inCDS, p0 27. 0 IDB64313-7737-8040 inCDS, p1 IDB64313-8119-8956 inCDS, p1 IDB64313-7737-8956 inCDS, p1 28. 0 IDB64321-31788-32253 inCDS, p1 IDB64321-32380-33155 inCDS, p1 IDB64321-31788-33155 inCDS, p1 29. 0 IDB64798-12494-13045 inCDS, p0 IDB64798-13193-13465 inCDS, p0 IDB64798-12494-13465 inCDS, p0 30. 0 IDB64798-3492-3725 inCDS, p0 IDB64798-3780-3938 inCDS, p0 IDB64798-3492-3938 inCDS, p0 31. 0 IDB64817-15981-18914 inCDS, p1 IDB64817-19059-21047 inCDS, p1 IDB64817-15981-21047 inCDS, p1 32. 2 IDB65129-2992-3435 unknown IDB65129-3546-4765 unknown IDB65129-2992-4765 unknown 1 33. 0 IDB65170-14729-15473 inCDS, p0 IDB65170-15567-17145 inCDS, p0 IDB65170-14729-17145 inCDS, p0 34. 0 IDB66019-3600-6552 inCDS, p2 IDB66019-6646-9507 inCDS, p2 IDB66019-3600-9507 inCDS, p2 35. 0 IDB66052-12112-12824 unknown IDB66052-12912-15087 unknown IDB66052-12112-15087 unknown 36. 0 IDB66102-63221-67095 unknown IDB66102-67168-72866 unknown IDB66102-63221-72866 unknown 37. 2 IDB66159-1961-2265 unknown IDB66159-2310-3024 unknown IDB66159-1961-3024 unknown 38. 0 IDB66163-4668-5181 inCDS, p2 IDB66163-5218-6173 inCDS, p2 IDB66163-4668-6173 inCDS, p2 39. 0 IDB66171-498-2357 inCDS, p2 IDB66171-2415-8478 inCDS, p2 IDB66171-498-8478 inCDS, p2 40. 0 IDB66171-11329-11440 inCDS, p1 IDB66171-11588-12722 inCDS, p1 IDB66171-11329-12722 inCDS, p1 41. 0 IDB66171-12821-13122 notCDS IDB66171-13231-13970 notCDS IDB66171-12821-13970 notCDS 42. 0 IDB66190-119-4389 unknown IDB66190-4447-5853 unknown IDB66190-119-5853 unknown 43. 0 IDB66198-24551-27175 inCDS, p1 IDB66198-27257-35406 inCDS, p1 IDB66198-24551-35406 inCDS, p1 44. 0 IDB66203-14471-15428 inCDS, p0 IDB66203-15792-17375 inCDS, p0 IDB66203-14471-17375 inCDS, p0 45. 0 IDB66205-197-1162 inCDS, p0 IDB66205-1244-1471 inCDS, p0 IDB66205-197-1471 inCDS, p0 46. 2 IDB66232-179-2282 inCDS, p1 IDB66232-2405-2746 inCDS IDB66232-179-2746 inCDS, p1 47. 0 IDB61221-145282-166939 inCDS, p1 IDB61221-167108-169705 inCDS, p1 IDB61221-169763-184646 inCDS, p1 IDB61221-145282-184646 inCDS, p1 The last ENTRY is cassette exon with 2 exons and hence 3 flanking introns and one covering intron. IV. Alternating Exon Events. A pair of lines indicate the splice patterns for the occurrence of each of the two alternating exons. The modularity of the component cassette exon event is given in each line - note that effective modularity of each of the event is 0. Each line lists the intron 5' to the cassette exon along with the phase information, the intron 3' to the cassette exon along with the phase information, and the covering intron (which causes the isoform) along with the phase information. 1a. 2 IDB60543-1994-6073 inCDS, p0 IDB60543-6241-8037 inCDS, p2 IDB60543-5675-8037 inCDS 1b. 2 IDB60543-1994-5507 inCDS, p0 IDB60543-5675-8037 inCDS IDB60543-1994-6073 inCDS, p0 2a. 1 IDB61276-9350-17458 inCDS, p1 IDB61276-17577-21501 inCDS, p2 IDB61276-9350-17737 inCDS, p1 2b. 1 IDB61276-9350-17737 inCDS, p1 IDB61276-17856-21501 inCDS, p2 IDB61276-17577-21501 inCDS, p2 3a. 1 IDB64127-21176-23313 inCDS, p0 IDB64127-23417-42392 inCDS, p1 IDB64127-23192-42392 inCDS, p1 3b. 1 IDB64127-21176-23100 inCDS, p0 IDB64127-23192-42392 inCDS, p1 IDB64127-21176-23313 inCDS, p0 4a. 1 IDB64780-4657-4785 inCDS, p2 IDB64780-4862-5375 inCDS, p0 IDB64780-4657-5118 inCDS, p2 4b. 1 IDB64780-4657-5118 inCDS, p2 IDB64780-5195-5375 inCDS, p0 IDB64780-4862-5375 inCDS, p0 5a. 2 IDB66048-48814-72392 inCDS, p1 IDB66048-72473-74775 inCDS, p0 IDB66048-68272-74775 inCDS, p0 5b. 2 IDB66048-48814-68191 inCDS, p1 IDB66048-68272-74775 inCDS, p0 IDB66048-48814-72392 inCDS, p1 6a. 0 IDB66098-17180-20393 inCDS, p1 IDB66098-20550-23607 inCDS, p1 IDB66098-19961-23607 inCDS, p1 For the last entry, the corresponding alternating exon was not observed as conserved in mouse; the exon 20394-20549 alternates with 19796-19960 with the pattern of introns as 6b. 0 IDB66098-17180-19795 inCDS, p1 IDB66098-19961-23607 inCDS, p1 IDB66098-17180-20393 inCDS, p1