sp|F4JN26|MLH3_ARATH ----> DNA mismatch repair protein MLH3

Intron 1 GTAAAACAGA ... CTGAACAAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	75	14	51	33
A2	69.86	11	22	29
A3	74.55	7	23	18
A4	72.6	10	25	28
A5	61.9	4	5	8
A6	71.43	1	1	4
A7	87.5	2	13	15
A8	54.55	5	4	8
A9	80	1	3	5
A10	91.3	1	10	11

>TRINITY_DN125458_c3_g3_i1 from sample A1 / Example spliced isoform

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGA
GGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTC
GTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTG
TTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAAT
AAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGG
GAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGAT
TTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGA
GGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTA
TTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGA
TGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAA
ATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAA
GCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGT
CCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAA
CAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAA
CGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTAT
AAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAA
TTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAG
CTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCC
ATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCT
GGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAAT
GTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTAT
G

>TRINITY_DN125458_c3_g3_i8 from sample A1 / Example unspliced isoform:

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGC
GCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACT
TTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGC
CCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCA
GGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGT
ATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGA
CAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTG
TGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGgtaaaacagaaaaacaaagatactctgttatcatttttttcttttcaaaatgggccagaagtaacagggaacagtattctgctgcatccgaaagatgcacagggatttacacaagaaatt
agtcctttaggactgatgagtttgttttctgaacaaagTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATT
CAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATG
GACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAAT
CCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGC
GCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCC
CACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACA
GTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACG
ACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAA
GGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATT
CGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCT
CCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCAT
CAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGG
CATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAATGT
CCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTATG

Intron 2 GTAAACAGCG ... GAAGGAAAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	21	25	17
A2	41.07	33	23	23
A3	50.94	26	28	26
A4	55.06	20	26	23
A5	62.16	7	12	11
A6	63.64	2	4	3
A7	51.35	9	12	7
A8	0	1	0	0
A9	48.39	8	5	10
A10	44.44	10	10	6

>TRINITY_DN125458_c3_g3_i18 from sample A1 / Example spliced isoform

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGA
GGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTC
GTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTG
TTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAAT
AAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTGTATCCTTTGGGAAAATATTGTAGAATGTTTTGATTTCATGTGATGTTTTATACTGTTTGTAGCCTTGACTCTTATAGACATTAACTCTCACTTTGTTGATAAAACTCCCATTC
ACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTG
GAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAA
GGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGC
TGCATCCGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTT
CATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGC
TTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATG
ATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTC
TTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTT
AGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAAT
TTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAA
AAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAAT
GACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATC
TTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTT
TCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTG
TAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAA
CAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATA
AATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGG
ACATGTTCCATTTGAACAGTGATGTTCTCATTGTATG

>TRINITY_DN125458_c3_g3_i19 from sample A1 / Example unspliced isoform:

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGgtaaacagcggaattcatgccagcagaagcgaaggaaaagGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGC
GCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACT
TTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGC
CCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCA
GGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTGTATCCTTTGGGAAAATATTGTAGAATGTTTTGATTTCATGTGATGTTTTATACTGTTTGTAGCCTTGACTCTT
ATAGACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTC
GAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAA
TCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCT
TTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAA
TATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACT
TTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAAT
GAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAA
CATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAG
ATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGA
AGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAA
TTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAG
TTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAA
CTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAG
TGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTG
CTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAA
TTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTG
TATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAAC
TGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTATG

Intron 3 GTATCCTTTG ... ACTCTTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	38.02	18	9.3	13
A2	28.99	19	4.7	11
A3	26.91	27	13.4	7
A4	24.57	38	19.9	6.6
A5	21.02	16	7.1	2
A6	12.26	4	1.2	0
A7	18.14	12	2.5	3
A8	12.26	2	0.6	0
A9	43.55	1	0.6	1
A10	0	4	0	0

>TRINITY_DN125458_c3_g3_i20 from sample A1 / Example spliced isoform

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGC
GCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACT
TTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGC
CCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCA
GGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGT
ATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGA
CAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTG
TGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATTTACACAAGAAATT
AGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATT
CAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATG
GACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAAT
CCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGC
GCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCC
CACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACA
GTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACG
ACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAA
GGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATT
CGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGGTGTGTTTTTGGATTCTTACAACATGTTTTTATCTATGAAATTGCTTGCTTCTTTGCTTTGAGTACTTTAGCAGAAATCTGTGATTCTACAAAAAATGCAGGTGCAATGGGCTTATCCT
GTGTTGTGGTACATCACTTATTTTATTCCTTTCAGA

>TRINITY_DN125458_c3_g3_i19 from sample A1 / Example unspliced isoform:

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGC
GCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACT
TTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGC
CCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCA
GGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTgtatcctttgggaaaatattgtagaatgttttgatttcatgtgatgttttatactgtttgtagccttgactctt
atagACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTC
GAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAA
TCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCT
TTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAA
TATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACT
TTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAAT
GAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAA
CATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAG
ATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGA
AGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAA
TTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAG
TTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAA
CTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAG
TGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTG
CTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAA
TTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTG
TATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAAC
TGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTATG

Intron 4 GTGTGTTTTT ... TTCCTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	0.76	65.5	0	1
A2	2.73	35.6	1	1
A3	13.26	39.3	9	3
A4	0	12.9	0	0
A5	5.88	8	0	1
A6	6.46	43.5	0	6
A7	0.89	56	0	1
A8	1.14	44.4	0	1
A9	0	37.4	0	0
A10	0	29.9	0	0

>TRINITY_DN113647_c0_g1_i6 from sample A3 / Example spliced isoform

GCTGCCACTAACATTTAAACTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTA
TTGCTTTACATCGTGGCAGCGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTC
TCGCCTTCCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTG
GTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGC
AGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGT
TCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAAT
TGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTT
AAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGA
AGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATC
CGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTGTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTT
GATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTG
CTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATT
TGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAA
GATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTTAGACCA
CCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTC
TTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCA
AGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACAATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAG
TAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTG
TTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAA
AGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGG
TGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATG
GCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTG
TACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGT
TCCATTTGAACAGTGATGTTCTCATTGTATGGAAACAATCTGACTACTATTATTGATGTTTTATTAATTATTATAAAAAAAG

>TRINITY_DN113647_c0_g1_i13 from sample A3 / Example unspliced isoform:

TCCTGGAATGTGAAGAAGAATTGgtgtgtttttggattcttacaacatgtttttatctatgaaattgcttgcttctttgctttgagtactttagcagaaatctgtgattctacaaaaaatgcaggtgcaatgggcttatcctgtgttgtggtacatcacttattttattcctttcagATGCTTCCTTTTGGTGGGCTGCA
ATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGTATTCTTCCAATTTGACTATGGGCTTGGCTATAAGTTTGTTTCTGTCACCATTTTGCAGAAGACATAATTTTTATTTGAACAGATATGTGATATTTCTTTAAAATTGAGTACTATTTT
GCAG

Intron 5 GTACCTTGCA ... TTGGGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	49.43	26.1	21	29
A2	45.58	16.9	13.9	14
A3	49.87	32.4	27	37
A4	50.34	21.3	24	19
A5	46.67	9.8	7	10
A6	46.63	54.9	40	55
A7	47.74	81.6	67	80
A8	48	82.9	70.9	79.9
A9	50.83	67.3	61.9	75.9
A10	49.46	32.8	30	32

>TRINITY_DN119805_c0_g1_i6 from sample A2 / Example spliced isoform

CTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAG
CGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTT
TTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGTAATTCTTTAGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGA
CATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCA
AGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCA
CGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAA
AATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTG
GGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAA
TGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGAT
GCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTGTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGA
TGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAA
AGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCT
GAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATG
TCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTATTTAGACCACCCACCTT
TGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTC
AATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTC
AGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACAATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAA
AAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGAC
CAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGAC
ATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCC
ATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCT
GGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAAT
GTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTAT
GGAAACAATCTGACTACTATTATTGATGTTTTATTAATTATTATAAAAAAAGAGACAAATGTTTAAGTTTTACATAGTAGTTACTTTGAATATCT

>TRINITY_DN119805_c0_g1_i4 from sample A2 / Example unspliced isoform:

CTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAG
CGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTT
TTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTC
AAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAA
CGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTT
TGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAAT
CAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTA
TTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAG
AATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATT
TACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTGTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGAT
CGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCT
AGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCT
ACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGC
ATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTATTTAGACCACCCACCTTTGACCAATTCT
ATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATG
CAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACA
TACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACAATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAAC
CAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGC
AGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGA
AGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGgtaccttgcattttgggtgtagATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGAT
TTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCC
AAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCT
TTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGT
TCTCATTGTATGGAAACAATCTGACTACTATTATTGATGTTTTATTAATTATTATAAAAAAAGAGACAAATGTTTAAGTTTTACATAGTAGTTACTTTGAATATCT

Intron 6 GTAATCTATA ... GAGTTCTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.94	54	2.1	17
A2	31.67	41	8.7	19
A3	32.14	38	3.7	18
A4	27.5	29	6.8	11
A5	15.38	11	0	2
A6	33.33	2	0.1	1
A7	5.26	18	1.2	1
A8	0	7	0.5	0
A9	25	9	0.1	3
A10	8.33	11	0.4	1

>TRINITY_DN119805_c0_g1_i9 from sample A2 / Example spliced isoform

CTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAG
CGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTT
TTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTC
AAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAA
CGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTT
TGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAAT
CAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTA
TTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAG
AATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGTTGTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGA
CAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTC
ATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGA
AGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTG
CCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAG
ATTGATAACTTTTATTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTA
CAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCAT
TTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACAATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGC
CCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGT
TATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTT
GGCGCTACAAGATACTTTCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATT
CTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACT
AGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAA
AAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTT
CAAATTTAGTAAAATGGACATGTTCCATTTGAACAGTGATGTTCTCATTGTATGGAAACAATCTGACTACTATTATTGATGTTTTATTAATTATTATAAAAAAAGAGACAAATGTTTAAGTTTTACATAGTAGTTACTTTGAATATCT

>TRINITY_DN119805_c0_g1_i12 from sample A2 / Example unspliced isoform:

TCCCTTAACAGTTCAGAGCTGCTTATGGAAAATACATTTGTCTACAAAGTTAAAAGTATTCTGACTGTGGCGAAATTCACTTCATTTATCTCTTTATAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGgtaatctatacatttaattgct
tttttggtaatatttcattgtttttcaaatatgtaaggaattcgatagcttggatttctgagttctcagGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCA
TCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACA
GGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTGTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAG
CTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTT
GATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGA
TATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATA
GGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTATTTAGACCACCCACCTTTGACC
AATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCC
TTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGG
GAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACAATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAA

Intron 7 GTTCTTTATT ... ATGTGAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25.93	60	10.9	21
A2	24.9	36.2	8	12
A3	27.27	32	7.6	12
A4	14.29	30	7.4	5
A5	15.38	22	7.6	4
A6	0	3	1.4	0
A7	37.5	5	1.4	3
A8	0	3	0	0
A9	18.18	9	4.1	2
A10	6.67	14	4.8	1

>TRINITY_DN125458_c3_g3_i18 from sample A1 / Example spliced isoform

CAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTTACATCGTGGCAGCGTAATGTCATCT
GGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGA
GGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTC
GTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTG
TTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAAT
AAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTGTATCCTTTGGGAAAATATTGTAGAATGTTTTGATTTCATGTGATGTTTTATACTGTTTGTAGCCTTGACTCTTATAGACATTAACTCTCACTTTGTTGATAAAACTCCCATTC
ACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTG
GAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAA
GGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGC
TGCATCCGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTT
CATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGC
TTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATG
ATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTC
TTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTGTTT
AGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAAT
TTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAA
AAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAAT
GACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATC
TTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTT
TCTCAAAGTAAGACATCTGCGAGGAAGGCACATCAGCTCCATAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTG
TAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAGAATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAA
CAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCATGGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATA
AATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCCATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCCATTAGAAAGTTGACTTCCTAGAGAGTAGTTCAGTTTAATGCTTTATATTTAGTAGGTTTAGATGATTTAGAACTGAAAACTGTCAGGATTACAGGGCAACTTTCAAATTTAGTAAAATGG
ACATGTTCCATTTGAACAGTGATGTTCTCATTGTATG

>TRINITY_DN125458_c3_g3_i6 from sample A1 / Example unspliced isoform:

GCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAA
AGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGgttctttatttaaatgcacatattattttggcgatgctaaagtgcagacttttacattttctagagaacattgttctagcag
gtttctctaacaaagctatgctacatatgctataattcctgtaatcatattatataagctcattctctttgttttgtattttgaaatggatgaatgtgagcagCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAA
GAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGA
TAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAGAGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTAT
CAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTTCCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATAC
CGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAATGATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGG
GAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATTTACACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAA
TTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATT
AATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGA
GTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAACGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCA
ACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATT
GATAACTTTTGTTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAA
GTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTT
TCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATACAGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCA
GAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAATCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTAT
TGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGATGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTG

Intron 8 GTTAGAATTT ... TTTTGGATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20.54	31	8	4
A2	39.14	37.3	24	2
A3	19.14	17	4	7
A4	36.43	29.7	17	2
A5	24.48	9.3	3	0
A6	14.29	6	1	0
A7	26.32	31	11	0
A8	28.92	19.7	8	0
A9	18.27	31.3	7	0
A10	31.11	31	14	0

>TRINITY_DN109663_c1_g1_i8 from sample A4 / Example spliced isoform

CTAACATTTAAACTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTATTGCTTT
ACATCGTGGCAGCGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGTAAACAGCGGAATTCATGCCAGCAGAAGCGAAGGAAAAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTT
CCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGTACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAG
ACATGCAACTTCAAAACTTCACACTTTGGCTGAGCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGC
AAGGACATGGAACGACAGTTATTGCCCGTGACATTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGGTTCTTTATTTAAATGCACATATTATTTTGGCGATGCTAAAGTGCAGACTTTTACATTTTCTAGAGAACATTGTTCTAGCAGGTTTCTCTAACAAAGCTATGCTACATATGCTATAATTCCTGT
AATCATATTATATAAGCTCATTCTCTTTGTTTTGTATTTTGAAATGGATGAATGTGAGCAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGT
ACACTGAGCAGGATTTTTGGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTACATTAACTCTCACTTTGTTGATAAAACTCCCATTCACAAATTGCTGAAAAATTCATCAATCAG
AGTTGAAAGTATTTTAACTCCATCACAGAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGATTGGGCACCTATTATTT
CCTTTGTTGACAAAGTTATCCAGGACACTTGGAGAAAGCCTTTTGCTGATTTTTCACAAGGCATGACCAAAGGAACTTCAAGAACCAGTTCATCTCAAATCAAAAGAAAACCAGTGCCAAGAAAACGAAAAATCTGTCAGCAAATAGATCCAATATACCGTTCTCATTTTAAGGCTGAAGCATCAATGCCATCAGAGAAT
GATGGTTGTGTGCTTGCCATAGAAGAGTGCTACAAAAGAAGGCAAAGAGAGGTTTCAGAAGAGCCATTTACAGAAACTTCAGCTCTGCAGGTAAAACAGAAAAACAAAGATACTCTGTTATCATTTTTTTCTTTTCAAAATGGGCCAGAAGTAACAGGGAACAGTATTCTGCTGCATCCGAAAGATGCACAGGGATTTAC
ACAAGAAATTAGTCCTTTAGGACTGATGAGTTTGTTTTCTGAACAAAGTTTTAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGC
CAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATCATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGC
AGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCTCCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACA
GTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAATCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATT
TTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAGAAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTATTTAGACCACCCACCTTTGACCAATTCTATA
GAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAGAATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAG
CCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACCATTAGGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTTACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGGGAGATTCAAAAATCAAGTTGTTCAGAGGGAAACATAC
AGAATAAACGACAGATTGTGGAAAGCTTTGAGCAATCTGAACCTTTGCTTCTGCCAGATAACATGCACTCTTTGCCAGATGATGGAGATACCATGCTCAAGTGGATAACAGATGAAGTGCCACCTAGACCAGTTCCAGTGTCCGTCATTAAATGCCCAGAAGTTTTGCTAATGACAAGTAGATTAAAAGAGTGGAACCAA
TCACGTATAAGGCATGATTGTGATGATGACATTCTAGATGTTTCTTCGGGAGCCTTGTATTTAGCTAACAGTGGTTTGGTCCCCGAATCCATGAATAAAGATTGTTTAATGAAAGCAAAGGTTCTTCAACAACTAGACAGGAAATACATTGCTGTTATTGCCCAAGGAAATCTTGCTGTTATTGACCAGCATGCTGCAGA
TGAAAGAATTCGCTTAGAACAGCTCCGTAAAGAGGTTCTTGAAGGTGTAGGAAGGCAAAAAGTTACTGTCCTGGAATGTGAAGAAGAATTGATGCTTCCTTTTGGTGGGCTGCAATTACTTCAAAATTACAGTGAACAAATAGAGAATTGGGGTTGGCGCTACAAGATACTTTCTCAAACAGGAAGGCACATCAGCTCCA
TAGGAGTAGCTGTAAGGCCATCCTAACTGCGGTACCTTGCATTTTGGGTGTAGATTTGACAGCAGAGGACCTTTCCGAGTATATTCGACAGCTTGCTCAGACTGATGGGTCTTCAGCTGCTCCTCCAGCTGTTCTGCGTATTCTCAGCTCAAAGGCTTGTAGAGGTGCAATCATGTTTGGAGATTTGCTATTGCCATCAG
AATGTGCACTTCTGGTAGAGGAGTTAAAGAGAACATCTCTTTGTTTCCAGTGTGCTCATGGTCGGCCAACAACAGTTCCTCTAGTCAATCTAGAGGGTTTGCACAAGGAACTAGAAAAATTTGGGAACTCTGAAAGGGTACTAGACCAATCAGGAATAACAAATGGCAATGTTGCTAAGTATCCAAGCAAGTGCTGGCAT
GGACTTCAAAAGCATAGTGCAAACCTTGAGCGAACCAAAATGCGGTTAAATTGAAGCAGTTGAAGTTAATTTTAAATTTGAATATATTTTGAATAAGTATTATTCCGTGTCAGTTTCTGTATCATTATTAATCTGCCAGCAAAAAGCTAGTTGAGGATAAATGTGTACATTTACGAGTTATTCTTTGATGACAATGTCCC
ATTTCATAATTGATTCAATCTCAGATGTTTCTTGTGTCC

>TRINITY_DN109663_c1_g1_i17 from sample A4 / Example unspliced isoform:

TAAAGATGAAGAAAGCAATGGACATATGGGAATAGAGTGGGCAAATCAGGCTCCTGGCAGTGACTTAGGGATACTGGATAATATTATACAAAGTAAGTCCAAGACAATTTGTGATTCATTTCATGTTGATCATGATGAAGCTCGATCGCCAATTCTATTCAAATCTTGTAGTAGTGAGAAATTGGATGTGTCTTCAAATC
ATTCAGCTGCTGCAAAAATATCAATTGCCGTAATGCGACCTACTTTTAGCAATGAGAAGCTGCTGATAGGAGAAGATAACTTTCAGCAGGAAAATGGAGAATTCATTAATGCACAAGACGCTTGTTGCTCTGGAAAGCTTGATTCTAGCAGTAGTGATGGACTTTCATTCTCCACTAAAAATTTCCATTCATCTCTATCT
CCAATCAGTTATAAAAGGAGCCCACTAACCCGGAAATTGAGGGCCCATACATGGGAAAATGGTAACTTTAGTATTTGTAATGAACTAGATTGGGCCAGGACAGAAGAGTTATTGGGAAATGATTATTTGTTTTCTGAAGATATTCTACAGTCAAGAAATCCATATTCTGAATTAGATTCTTTGGAGAATAATGAGGGGAA
TCATTTGGTCAGAAAAAGATCTATCAGACTGGACCATGAAATGAAATCATTTGAAGATGAGTATGATCAGAAGCCAAGAAACATTGAGAAAATATATCTTGGTGCCAACTCAGACAAGCTCTTCAAAGATTCATGTCATAGGCTGCATTTTGAGGAAGCGCTAAACTCACAGCATATAAAATTCAGGACACATGGCAGAG
AAGGGTGGGATGTCACTGAAAGGCTGAACGGAAGTACAATTTATGAAGGTCAACCAGATACATCTTTGTCAAAGATGAGAGATTTTGGTAGTGTGGATTATCAGATTGATAACTTTTATTTAGACCACCCACCTTTGACCAATTCTATAGAAATGGTCCCACCTGTCTCCTTTTGCAGTGGCTCAGAAGATCATTATCAG
AATAACTTGGGGTTCAGATATGACATGGATGTAGAACGACAGAAATTTCATAAGGGTTCTCGCAAAGCTGTCAGAAGGAGAAGTCTATCTGCTCCACCGTTCTACAAGTCCCTGAGAAAATTTGGTCTTCACTTCAATCCTTTATGCAGCCTATCAACAGTTGCAAGAAATGACCAGCATTATTATGCCTGTGATAAACC
ATTAGgttagaatttgtgctcattgagagtttaaagtttaaaatggaaatgaacaaaaatcccatattgcacattttccagagctttagttgatagttgtaaaagagcaatatattggatttcatgagataatgtctactttttggatagGAGTTTCAGTTCCGCAGAATGATAAGGAAGCTATACAACTATCTGACCTT
ACGATGGAATCTCTTACAATGTCAAATTACCAGCCTGGTTTGGAGTCATTTTTCAGG

Intron 9 GTATCCTTTG ... TCCATCACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	72.09	12	7.3	31
A2	70.59	10	3	24
A3	40.63	19	12	13
A4	42.86	24	12.7	18
A5	47.06	9	4.3	8
A6	-1	0	0.7	0
A7	60	6	1.3	9
A8	-1	0	0.3	0
A9	66.67	1	0.3	2
A10	57.14	3	0	4

>TRINITY_DN113647_c0_g1_i5 from sample A3 / Example spliced isoform

GCTGCCACTAACATTTAAACTTTCACGTTCGACAAATCCTGAACCCACATTTTTGGTTCGGAATCTCGCTGTTACTCTCCCACAGTGGGTATCTGTTGTTGTGGCCAACACCGATCGACAAAATACCCAATCGTAATTGAATTTTGCTTTGCTAGCCTCCCGAGTCCCAACCGTGACCTGCATTTTTGGGTAGACGAGTA
TTGCTTTACATCGTGGCAGCGTAATGTCATCTGGGCTGGTTCCTTGTGGCTATGGAAGTTAACAGAGTCGGCAGGAATCGAACTCTTAATCTGGAATGAATTTTTCCGGTGGGCGATAACGCGAGGATTCAATCAATATACCATAGATGGGGTATATTTCTCGCCTTCCTGAGGCAGTTTTCAACTCTTTGCGCTCCAGT
ACAATTTTGTCAGATTTTGCACAGATTGTAGAGGAATTGGTATCGAACAGCATTGATGCTGGATCAACAAAGGTGCACGTTTCTGTAGATGTGGAAGCAAGCTATATCAAAGTGGAAGATGATGGGCATGGCATTAAGAGAGACGATTTGACGCTCCTTGGTGAAAGACATGCAACTTCAAAACTTCACACTTTGGCTGA
GCTTGATGCGGGGATAAGGACCTTAGGGTTTCGTGGAGAAGCATTAAGTTCTCTTTCTGATGTTGCTTTGCTTGAGGTGACTACAAGAGCACATGGAAATCCAAATAGTTACAAGAAAATAATAAAGGGTTGCAAGAGTCTGTCCCTTGGGCTTAGTGGCAGCAAGCAAGGACATGGAACGACAGTTATTGCCCGTGACA
TTTTTTACAGCCAACCAGTCCGAAGGAGGCTGTTTCAGTCAAGCCAAAGGAAGGTCCTGCAGTCTATAAGGGAATGTATTCTTCGCATTGCCCTTATTCATCCCCAGGTGGCATTTAGAGTCGTAGATATGGACAGGGAAGAGGAGTTGATTCACACTGTTCCTTCCACGTCACCCCTTTGTACACTGAGCAGGATTTTT
GGGAATGAGCTCACATGTGATTTGTGTGAAATAAATTTTGCCCAAGGGAAGTTAAGGCTTTCTGGATTTTTATCCAGTTCACCTCATCTACTGTCCTCAAAGGGGCTTCAGTATTTTTAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTT
TGAATCTAAGTTGTCCTCACTCGAGCTATGATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGG

>TRINITY_DN113647_c0_g1_i16 from sample A3 / Example unspliced isoform:

TTAATATATATGTTTCACCTGTGACCATTATTTTTCTGGTTTCATCTTGTTGTTTGATAGTAAGCTATTCTTTTAGTAAATGAATTTTCATTTCCTTTTGCAGGGGCTTCAGTATTTTTgtatcctttgggaaaatattgtagaatgttttgatttcatgtgatgttttatactgtttgtagccttgactcttatagaca
ttaactctcactttgttgataaaactcccattcacaaattgctgaaaaattcatcaatcagagttgaaagtattttaactccatcacagAATGATTTGGGGCGAATAAAGGGAGGAAATGAGAAGCCAGACAAGGATTCTTGTGAGAGGCATTCATATCCTGCATATATTTTGAATCTAAGTTGTCCTCACTCGAGCTAT
GATATCACATATGATCTATCAAAGACTATGGTGGAATTTAAGGTAAAATTTATTCTACTTTATTTTGACCTTATATGTGAAATATGTTCATTAAAAGGGAAGAATGTTTTGTGTCTTATTTTAATTTTCATGGATTTTCAATGCATAGGCTAAAT