sp|Q7Y0S0|URED_ARATH ----> Urease accessory protein D

Intron 1 GTATGTTTTT ... ATATTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	21	14
A2	100	0	14	6
A3	100	0	15	12
A4	100	0	9	3
A5	75	1	3	3
A6	76	3	3	16
A7	100	0	20	21
A8	89.83	3	22	31
A9	100	0	24	11
A10	95.45	1	30	12

>TRINITY_DN48409_c0_g1_i7 from sample A10 / Example spliced isoform

CTAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCA
AAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGG

>TRINITY_DN48409_c0_g1_i12 from sample A10 / Example unspliced isoform:

CGGGAATGGTAATGTAAACTCTATGTTGATTCAGCTTTGAGGATGAATAACAAGTTATAGAAAACAAACCTGTAAGTTTTAAGACCATGGCAATGCAATGAACTGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTCCTATCGCGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGA
CGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCA
AACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCT
CAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGT
TTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAA
TAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTTTGAAGCACTTCTACCGCAAGCAAAAA
AATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGC
ATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATG
AGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTC
CATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAG
AGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGgtatgtttttctccctttcagtttttttaaactctttttgtaacttgaatccttctttatttgact
agccaacaaattaagaacatcgactaaaatgaaaaagttcagccaatcctagaaattgaagcatttatagcattactgggactgtgtaagtggaagtggcttttaattaggtttttttgtgttacagcctggggtggaagagatgtcagatgtaatgttaataaactaaaataagaaaaggttgacatccaaacatgtaa
tgtttcaaaagaaaagattattataatgtaaaataaataaactagcatagatccatcttaaccctaaattttcagtcattttatatttacttaacaaaggaacagggaatataatggaaatttgattcccacccagtgatcagtcttctacaagagattctttcactttcaccctattcaaagaggggttgaaactttat
tgaagcaaaagagtggaaacaatagcttgctgtcatgctcacagtactttgcccatgtgcagggattttgattgcagtattacatctctacatttgccataatccttatgctaaccattttgtctttgttttgttttgatattttcagCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATT
CTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGTCAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTATACGTTTGGCTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTT
GGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCATGAAGTTATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTC
GGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTG
GGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGT
GAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCTAT

Intron 2 GTGCAATTCA ... CCACTGCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	81.39	6	26	26.5
A2	68.3	8	15	19.5
A3	62.33	7	16	7.2
A4	55.56	12	8	22
A5	80.65	3	16	9
A6	55.56	14	10	25
A7	61.34	44	54	85.7
A8	63.4	32	41	69.8
A9	65.44	22	27	56.3
A10	59.2	32	30	62.8

>TRINITY_DN118518_c10_g1_i6 from sample A3 / Example spliced isoform

CGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCA
TCCGTCCATGAGGTTCTATTGTGCTCTGACCCCACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGT
TGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGGTATGTGCCCTTTTCAACACTGCCCA
ATATCACCATAACAGAATTAAGGGCTATACTTTGAGCTGCTGCACAAATGATATGATTATTTTTCATCAGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCA
AGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAG

>TRINITY_DN118518_c10_g1_i8 from sample A3 / Example unspliced isoform:

AACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGACCC
CACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCG
CCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGgtgcaattcaaaccatttgttctt
ttatgaattctgtttttctgttttattttgatgcaagcacgatcaaatgggtttggtgtagccaacagggtgttagttcactggtgaggttgacaaagtactagctccgatccaagaaacccagacctggtattcgcctgtaggcatcattcccgaacctgcctccccctcagccctctcactcgtggccaattacagaa
cgtgtgttagaaatagagtatatacaactagttctcagtatttcagggtattctttggatactttctctgaaataggatgcctgctcatgctgggaagattgggcctgtgtcctccgcatgagtactgctgcataacgagagttaagtttgctctgttgtgtggtgtagccctttggggtgtgtttttgaagcacttcta
ccgcaagcaaaaaaatggggatttggtttaatagttagagagaatagcaattatcgttggtcacaagatgattgcatatccacttctcacaagtactcagattatacacagtctccatttccaaggaggaactgtagatatgacagtagggtttcaattaagcagatatcgatactcacctatggtgctcaattcttttt
gaggtgcggttgcatctaaattgcatgttacctgattggggcatatctcataagtataaaaacttagaactaggttcgcctgtggaactaatttttttcccatctaatccataagaattgggtagagcattaatcctcccaaataaactggttggctttgacatcacaaaatcccttattaccatccctaaaggttaaat
caaatcaccaatgagattgggatctcggctttctgtgtattttgcatttgaactcataagctagtaacgtcatatacaggtctacaagtcagcgggagggaagtgctcagagcagttctttgaagtatgttctgaacagttcttcaaaaccctagttctgttccaatgcatacttttcaacgaagatgtttttcctcagc
ttatgttctattccatgtgctgtgctgtaggctcaagtaggaagtaatgctcttttagctattcttccagacccagtgacatgcttttccactgccagATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTT
TGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

Intron 3 GTCATTTGTG ... GATCATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	73.33	6	12	21
A2	69.23	2	4	5
A3	76.92	3	11	9
A4	61.3	7	9	13
A5	30.3	3.5	1	2
A6	48	13	9	15
A7	61.29	18	11	46
A8	50.95	39.5	26	56
A9	46.05	19.5	7	26
A10	58.33	10	6	22

>TRINITY_DN106907_c1_g2_i17 from sample A4 / Example spliced isoform

GGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAG
ACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGT
AACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAA
GTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAA
GATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACT
CAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTT
TCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGA
GGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCA
GATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTT
GTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAG
AACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATA
CGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

>TRINITY_DN106907_c1_g2_i19 from sample A4 / Example unspliced isoform:

ACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTTCTCTGGCCCCACTTATTTATCAAGCAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTG
GACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTT
GTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAG
TAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGG
TTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTAT
TCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAAT
TATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCAT
AAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGA
ACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCT
CTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATT
GTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCT
GGTAGTTTTGGGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATTACTGGGACTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGT
TACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTTACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATT
TGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAAATTTATTGAAGCAAAAGAGTAGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGTCCATGTGCAGGGATTTTGATTGCAGTATTACATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTG
TCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGgtcatttgtgaactctaattactctctttgtttcttttaaatgtctttaccattttatcttttggtcaaatatttattgcaaagaaacatatgccttttcccttta
tacatttggcttcggtaattttcctccaactttcaatgtatttttcaaatgctctcttctttgaaaggcagttcatccgctgacaatatgctatggatctaatattgctttggttaaagatgtgaccagatatattagggcacgttctaaccatggctgtgtaaagctttgttcactttgattttttaatgcatgaagtt
atttcctcgaaaagagaagaagtccatccataacttgccgatttgatcatgtagACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTAC
TTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAA
AAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

Intron 4 GTATGTTCTG ... TGTGCTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	41.69	18.2	6	19.5
A2	32.26	26	9	15.5
A3	54.96	10.1	13	11.2
A4	76.48	4.3	14	14
A5	91.11	1	10	10
A6	43.78	14.9	7	16
A7	42.52	56.6	30	52.4
A8	27.23	51.3	11	26.8
A9	21.86	57.7	3	27.9
A10	35.91	64.1	26	44.8

>TRINITY_DN126904_c0_g1_i7 from sample A1 / Example spliced isoform

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCT
GGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCT
TTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTG
TTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTA
CAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCAC
TTCTACCGCAAGCAAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTC
TTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGT
TAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATA
TTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGG
ATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTA
AGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCT

>TRINITY_DN126904_c0_g1_i3 from sample A1 / Example unspliced isoform:

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCT
GGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCT
TTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTG
TTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTA
CAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCAC
TTCTACCGCAAGCAAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTC
TTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTATTTTTTTTGCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGT
TAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAgtatgttctgaacagttcttcaaaaccctagttctgttccaatgcatacttttcaacgaagatgtttttcc
tcagcttatgttctgttccatgtgctgtgctgtagGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGG
GATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGA
GAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTA
CATCTATTGGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATGTTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATC
TAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCTATATTTTGGTTATGATGCTGTGATTGGGGGTATTTATTGTGCCAGGTTTGTTTGTGACTTAAACGTGGTCCTAATTGCATGAAATAGCCTACTTATGCATATGTGACAACTCAT
AAAGGTCGAACAAGTCTTTGAGGGAATTTGAATTCTGACGAAGGATAACACCACCCTCTTTTACTGACCAACCAAACTCTTATTAAGCGTTAACCAATTTTTTAATAACTTTTAAGCTAAAGTTCATTTTTTTTAATATAATATGTTCAGAGCTTGCAAGCTCACTTCACTACATACATTGGTGCATCACTCCCATCAAG
CGTTAACCAATTTTTTAATAACTTTTAAGTTAAAGTTCTTTTTCAGGCCTTGCAACCTCACTTCTACATACATTTGCGATGGATGCATGCTAATTCAGTAGAGCTTAAGAAATACATCTATTTGATTACATTGACAAGTACAAAGATTAACATGATGTATACGATTAACATGATGTATTGTATAAGTGGGTAATATGATC
A

Intron 5 GTGCAATTCA ... TGTGCTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	60.66	14.6	25.6	19.4
A2	52.03	14	15	15.4
A3	80.43	3.6	16	11.2
A4	57.42	8	7.6	14
A5	92.86	1	16	10
A6	41.14	18	9.2	16
A7	52.6	47	52	52.4
A8	46.26	38	38.8	26.8
A9	44.52	33.4	25.6	28
A10	46.38	42.4	28.6	44.8

>TRINITY_DN106907_c1_g2_i4 from sample A4 / Example spliced isoform

TGTAAACTCTATGTTGATTCAGCTTTGAGGATGAATAACAAGTTATAGAAAACAAACCTGTAAGTTTTAAGACCATGGCAATGCAATGAACTGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTCCTATCGCGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTA
TAATTTTTTTTATGTATATATGTTTTCTATTGTTCTCTGGCCCCACTTATTTATCAAGCAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGG
CGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAA
CTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGT
ACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGA
TTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGA

>TRINITY_DN106907_c1_g2_i19 from sample A4 / Example unspliced isoform:

ACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTTCTCTGGCCCCACTTATTTATCAAGCAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTG
GACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTT
GTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAG
TAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGgtgcaattcaaaccatttattcttttatgaattctgttttgctgttttattttgatgcaagcacgatcaaatggg
tttggtgtagccaacaggatgttagttcactggggaggttgacaaagtactagctccgatccaagaaacccagacctggtattcgcctgtaggcatcattcccgaacctgcctccccctcagccctctcactcgtggccaattacagaacgtgtgttagaaatagagtatatacaactagttctcagtatttcagggtat
tctttggatactttctctgaaataggatgcctgctcatgctgggaagattgggcctgtgtcctccgcatgagtactgctgcataacgagagttaagtttgctctgttgtgtggtgtagccctttggggtgtgtttctgaagcacttctaccgcaagcaaaaaaatggggatttggtttaatagttagagagaatagcaat
tatcgttggtcacaagatgattgcatatccacttctcacaagtactcagattatacacagtctccatttccaaggaggaactgtagatatgacagtagggtttcaattaagcagatatcgatactcacctatggtgctcaattctttttgaggtgcggttgcatctaaattgcatgttacctgattggggcatatctcat
aagtataaaaacttagaactaggttcgcctgtggaactaatttttttcccatctaatccataagaattgggtagagcattaatcctcccaaataaactggttggctttgacatcacaaaatcccttattaccatccctaaaggttaaatcaaatcaccaatgagattgggatctcggctttctgtgtattttgcatttga
actcataagctagtaacgtcatatacaggtctacaagtcagcgggagggaagtgctcagagcagttctttgaagtatgttctgaacagttcttcaaaaccctagttctgttccaatgcatacttttcaacgaagatgtttttcctcagcttatgttctgttccatgtgctgtgctgtagGCTCAAGTAGGAAGTAATGCT
CTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATT
GTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCT
GGTAGTTTTGGGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATTACTGGGACTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGT
TACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTTACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATT
TGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAAATTTATTGAAGCAAAAGAGTAGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGTCCATGTGCAGGGATTTTGATTGCAGTATTACATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTG
TCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGTCAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTA
TACATTTGGCTTCGGTAATTTTCCTCCAACTTTCAATGTATTTTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTTGGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCATGAAGTT
ATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTAC
TTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAA
AAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

Intron 6 GTCATTTGTG ... GATCATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	73.33	6	12	21
A2	69.23	2	4	5
A3	76.92	3	11	9
A4	61.22	7.3	9	14
A5	29.29	3.7	1	2
A6	48	13	9	15
A7	61.29	18	11	46
A8	50.63	40	26	56
A9	44.99	20.3	7	26
A10	58.33	10	6	22

>TRINITY_DN43985_c4_g1_i19 from sample A6 / Example spliced isoform

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTAC
AGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGTCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCA
TACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAG
AATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

>TRINITY_DN43985_c4_g1_i15 from sample A6 / Example unspliced isoform:

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGAC
TGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAACAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTT
ACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATTTGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAACTTTATTGAAGCAAAAGAGTGGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGCCCATGTGCAGGGATTTTGATTGCAGTATTA
CATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTGTCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGgtcatttgtgaactctaattactctctttgtttcttttaaatgtctttaccattttatcttttggt
caaatatttattgcaaagaaacatatgccttttccctttatacgtttggcttcaaatgctctcttctttgaaaggcagttcatccgctgacaatatgctatggatctaatattgctttggttaaagatgtgaccagatatattagggcacgttctaaccatggctgtgtaaagctttgttcactttgattttttaatgca
tgaagttatttcctcgaaaagagaagaagtccatccataacttgccgatttgatcatgtagACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCA
GTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAA
ATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

Intron 7 GTACTTCTCT ... AATTGGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20.16	17	6	2.6
A2	50.45	10	10	10.4
A3	29.14	12	5	5
A4	25	9	6	0
A5	41.8	11	7	8.8
A6	25.46	10	3	4
A7	24.17	29	12	6.6
A8	19.01	32	7	8.2
A9	19.81	37	9	9.4
A10	17.78	46	5	15.2

>TRINITY_DN100249_c0_g1_i2 from sample A5 / Example spliced isoform

CGGGAATGGTAATGTAAACTCTATGTTGATTCAGCTTTGAGGATGAATAACAAGTTATAGAAAACAAACCTGTAAGTTTTAAGACCATGGCAATGCAATGAACTGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTCCTATCGCGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAAATGCCACCGA
CGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCA
CCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATAC
GACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTT
ATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATA
CAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTTTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTT
GGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGG

>TRINITY_DN100249_c0_g1_i4 from sample A5 / Example unspliced isoform:

CGGGAATGGTAATGTAAACTCTATGTTGATTCAGCTTTGAGGATGAATAACAAGTTATAGAAAACAAACCTGTAAGTTTTAAGACCATGGCAATGCAATGAACTGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTCCTATCGCGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAAATGCCACCGA
CGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCA
CCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATAC
GACCGACCAAGgtacttctcttcagttcacatgaatggaattgagggtttctaaggcataaagggtttcattccctcttcatctcatttgaataaattggacagGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGTTAGTATAAATACCATAACAATAATACAA
TATATTTTGGCTCTGTAAGTATCTGGGGATTTTTCTAAGATTTCTCTGTGGGTTGGTCAGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACG
ATCAAATGGGTTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTAT
TTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTTTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGA
GAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGG

Intron 8 GCTCAAGTAG ... CCACTGCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	84.87	4.2	18.2	29.4
A2	70.54	10.9	25	27.2
A3	76.45	3.4	9.3	15
A4	55	10.2	4.8	20.2
A5	53.85	3	1	6
A6	69.02	9.2	15.6	25.1
A7	66.19	37.4	56.1	90.7
A8	71.55	27.9	50.4	90.8
A9	77.88	18.9	55.7	79.8
A10	75.08	22.7	61.9	75.4

>TRINITY_DN48869_c0_g3_i13 from sample A7 / Example spliced isoform

GACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATAT
GTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGTACTTCTCTTCAGTTCACATGAATG
GAATTGAGGGTTTCTAAGGCATAAAGGGTTTCATTCCCTCTTCATCTCATTTGAATAAATTGGACAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

>TRINITY_DN48869_c0_g3_i1 from sample A7 / Example unspliced isoform:

CTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGgctcaagtaggaagtaatgctcttttagctattcttccagacccagtgacgtgcttttcc
actgccagATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

Intron 9 GTATGTGCCC ... TTGTAACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.44	15	12	5.6
A2	50	12	12	5.2
A3	54.55	10	12	7
A4	23.53	13	4	5.6
A5	33.33	6	3	1
A6	25	9	3	3
A7	29.82	40	17	2.6
A8	19.23	63	15	8.4
A9	39.06	39	25	7.6
A10	23.6	68	21	2.2

>TRINITY_DN118518_c10_g1_i2 from sample A3 / Example spliced isoform

CGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCA
TCCGTCCATGAGGTTCTATTGTGCTCTGACCCCACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGT
TGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCAC
AAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAA
ACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAA
ACTAAAATAAGAAAAGGTTGAC

>TRINITY_DN118518_c10_g1_i13 from sample A3 / Example unspliced isoform:

AACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGACCC
CACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCG
CCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTGTTCTT
TTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAA
CGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTTTGAAGCACTTCTA
CCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTT
GAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAAT
CAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACATGCTTTTCCACTGCCAGATATTCGC
AGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGgtatgtgcccttttcaacactgcccaatatcaccataacaga
attaagggctatactttgagctgctgcacaaatgatatgattatttttcatcagatcacgttaattacacctagaacaagctttggccctcaactctatgagtgaatgctcctggtgacgagggtatagatcaaactaagtgtacttgctttctgctcacttgtaaccagACACAGCTGGAGCAAGGTGCTGGCTATTCT
GTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGA
CTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTT
TATATTTACTTAACA

Intron 10 GTATGTTTTT ... ATATTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	96.39	0.7	21	14
A2	92.34	0.8	13.3	6
A3	85.95	2.5	15.7	12
A4	67.7	2.8	7	3
A5	55.55	2	1.7	3
A6	63.95	5	1	16
A7	89.87	2.3	16.7	21
A8	78.38	7.2	18	31
A9	81.68	4	21.3	11
A10	81.98	4.3	19.2	12

>TRINITY_DN106907_c1_g2_i17 from sample A4 / Example spliced isoform

GGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAG
ACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGT
AACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAA
GTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAA
GATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACT
CAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTT
TCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGA
GGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCA
GATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTT
GTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAG
AACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATA
CGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

>TRINITY_DN106907_c1_g2_i19 from sample A4 / Example unspliced isoform:

ACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTTCTCTGGCCCCACTTATTTATCAAGCAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTG
GACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTT
GTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAG
TAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGG
TTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTAT
TCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAAT
TATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCAT
AAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGA
ACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCT
CTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATT
GTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCT
GGTAGTTTTGGGgtatgtttttctcccgttcagtttttttaaactctttttgtaacttgaatccttctttatttgactagccaacaaattaagaacatcgactaaaatgaaaaagttcagccaatcctagaaattgaagcatttatagcattactgggactgtgtaagtggaagtggcttttaattaggtttttttgtgt
tacagcctggggtggaaggagatgtcagatgcaatgttaataaactaaaataagaaaaggttgactccaaacatgtaatgtttcaaaagaaaagattattataatgtaaaataaataaactagcatagatccatcttaaccctaaattttcagtcattttacatttgcttaacaaaggaacagggaatataatggaaatt
tgattctcacccagtgatcagtcttctaccagagattctttcactttcaccctattcaaagaggggttgaaaatttattgaagcaaaagagtagaaacaatagcttgctgtcatgctcacagtactttgtccatgtgcagggattttgattgcagtattacatctctacgtttgccataatccttatgctaaccattttg
tctttgttttgttttgatattttcagCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGTCAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTA
TACATTTGGCTTCGGTAATTTTCCTCCAACTTTCAATGTATTTTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTTGGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCATGAAGTT
ATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTAC
TTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAA
AAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

Intron 11 GTATGTGCCC ... TTGTAACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	37.09	16.2	13	6
A2	46.67	12	15	6
A3	49.6	9.2	11	7
A4	30	11.8	4	6
A5	20	6	2	1
A6	22.5	10.6	3	3
A7	19.02	42.8	17	3
A8	15.42	69.6	15	10
A9	28.65	44.2	25	10
A10	13.35	75.6	21	2

>TRINITY_DN126904_c0_g1_i7 from sample A1 / Example spliced isoform

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCT
GGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCT
TTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTG
TTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTA
CAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCAC
TTCTACCGCAAGCAAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTC
TTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGT
TAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATA
TTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGG
ATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTA
AGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCT

>TRINITY_DN126904_c0_g1_i13 from sample A1 / Example unspliced isoform:

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTA
TTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGT
CACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCA
AACCATTTGTTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGT
GGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTT
CTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGT
GCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTATTTTTTTTGCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATC
CCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGA
TGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGT
GAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGgtatgtgcccttttcaacactgcccaatatcaccataacagaattaagggctatactttgagctgcagcacaaatgatatggttatttatggtctcatgttagtcctcatttaaatattcat
cagatcacgttaattacacctagaacaagctttggccctcaactctatgagtgaatgctcctggtgacgagggtatagatcaaactaagtgtacttgctttctgctcacttgtaaccagACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTG
GGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGG
GGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCT

Intron 12 GTATGTTTTT ... GATCATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	65.63	11	21	21
A2	79.91	2.3	13.2	5
A3	45.88	14.7	15.8	9
A4	52.77	9.2	6.5	14
A5	42.13	2.3	1.3	2
A6	31.95	16.5	0.5	15
A7	47.66	34	15.8	46
A8	35.5	66.3	17	56
A9	36.38	40.8	20.7	26
A10	30.84	43.2	16.7	22

>TRINITY_DN43985_c4_g1_i12 from sample A6 / Example spliced isoform

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGGTATGTGCCCTTTTCAACACTGCCCAATATCACCATAACAGAATTAAGGGCTATACTTTGAGCTGCAGCACAAATGATATGGTTATTTATGGTCTCATGTTAGTCCTCATTTAAATATTCATCAGATCACGTTAATTACACCTAGAA
CAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGACCAAAGTTGGAACCCACACGGA
AGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGTCCTATGGTAAGGGATTATTGCATTGTGAAGTAATTCAAAAGAGGTTTGTAAACG
GAAGTCCATATTTTATAATCAGTGCCTGCATCAGAACTTTTCATAAACCCCAATTCAAACAATCATTTAAAAAACGTTTCTTTTTCAGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGG
GAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATA
GGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

>TRINITY_DN43985_c4_g1_i6 from sample A6 / Example unspliced isoform:

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGgtatgtttttctccctttcagtttttttaaactctttttgtaacttgaatccttctttatttgactagccaacaaattaagaacatcgactaaaatgaaaaagttcagccaatcctagaaattgaagcatttatagcatcactgggac
tgtgtaagtggaagtggcttttaattaggtttttttgtgttacagcctggggtggaaggagatgtcagatgcaatgttaataaactaaaataagaaaaggttgactccaaacatgtaatgtttcaaaagaaaagattattataatgtaaaacaaataaactagcatagatccatcttaaccctaaattttcagtcatttt
acatttgcttaacaaaggaacagggaatataatggaaatttgattctcacccagtgatcagtcttctaccagagattctttcactttcaccctattcaaagaggggttgaaactttattgaagcaaaagagtggaaacaatagcttgctgtcatgctcacagtactttgcccatgtgcagggattttgattgcagtatta
catctctacgtttgccataatccttatgctaaccattttgtctttgttttgttttgatattttcagcttgaacaataatatgaaagattgcaagtgttgtgaagcagtctacctcattcttttttacatgactggtcatttgtgaactctaattactctctttgtttcttttaaatgtctttaccattttatcttttggt
caaatatttattgcaaagaaacatatgccttttccctttatacgtttggcttcaaatgctctcttctttgaaaggcagttcatccgctgacaatatgctatggatctaatattgctttggttaaagatgtgaccagatatattagggcacgttctaaccatggctgtgtaaagctttgttcactttgattttttaatgca
tgaagttatttcctcgaaaagagaagaagtccatccataacttgccgatttgatcatgtagACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCA
GTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGTAAGGGATTATTGCATTGTGAAGTAATTCAAAAGAGGTTTGTAAACGGAAGTCCATATTTTATAATCAGTGCCTGCATCAGAACTTTTCATAAACCCCAATTCAAACAATCATTTAAAAAACGTTTCTTTTTCAGGATATTGGTTTGGTGGTTCGTATAGTAG
CAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTA
ACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

Intron 13 GTATGTTTTT ... GATCATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	65.63	11	21	21
A2	74.72	3.2	13.4	5
A3	47.18	13.8	15.6	9
A4	51.24	9.6	7.2	13
A5	37.98	3.2	1.8	2
A6	31.28	17.8	1.2	15
A7	46.32	36.6	17	46
A8	34.79	69.8	18.4	56
A9	35.75	42.8	21.6	26
A10	30.17	48.6	20.2	22

>TRINITY_DN106907_c1_g2_i5 from sample A4 / Example spliced isoform

GGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAG
ACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGT
AACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAA
GTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAA
GATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACT
CAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTT
TCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGA
GGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGA
GCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATT
CGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATT
GGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAG
TGAACATTTTGGATGCAG

>TRINITY_DN106907_c1_g2_i19 from sample A4 / Example unspliced isoform:

ACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTTCTCTGGCCCCACTTATTTATCAAGCAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTG
GACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTT
GTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTCGTCCCAAG
TAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTATTCTTTTATGAATTCTGTTTTGCTGTTTTATTTTGATGCAAGCACGATCAAATGGG
TTTGGTGTAGCCAACAGGATGTTAGTTCACTGGGGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTAT
TCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAAT
TATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCAT
AAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGA
ACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTGTTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTAATGCT
CTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATT
GTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGCTAGCAATGCT
GGTAGTTTTGGGgtatgtttttctcccgttcagtttttttaaactctttttgtaacttgaatccttctttatttgactagccaacaaattaagaacatcgactaaaatgaaaaagttcagccaatcctagaaattgaagcatttatagcattactgggactgtgtaagtggaagtggcttttaattaggtttttttgtgt
tacagcctggggtggaaggagatgtcagatgcaatgttaataaactaaaataagaaaaggttgactccaaacatgtaatgtttcaaaagaaaagattattataatgtaaaataaataaactagcatagatccatcttaaccctaaattttcagtcattttacatttgcttaacaaaggaacagggaatataatggaaatt
tgattctcacccagtgatcagtcttctaccagagattctttcactttcaccctattcaaagaggggttgaaaatttattgaagcaaaagagtagaaacaatagcttgctgtcatgctcacagtactttgtccatgtgcagggattttgattgcagtattacatctctacgtttgccataatccttatgctaaccattttg
tctttgttttgttttgatattttcagcttgaacaataatatgaaagattgcaagtgttgtgaagcagtctacctcattcttttttacatgactggtcatttgtgaactctaattactctctttgtttcttttaaatgtctttaccattttatcttttggtcaaatatttattgcaaagaaacatatgccttttcccttta
tacatttggcttcggtaattttcctccaactttcaatgtatttttcaaatgctctcttctttgaaaggcagttcatccgctgacaatatgctatggatctaatattgctttggttaaagatgtgaccagatatattagggcacgttctaaccatggctgtgtaaagctttgttcactttgattttttaatgcatgaagtt
atttcctcgaaaagagaagaagtccatccataacttgccgatttgatcatgtagACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTAC
TTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAA
AAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAG

Intron 14 GTTAGTATAA ... GGTTGGTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	31.46	17.2	4.8	8.1
A2	17.37	10.9	1.4	2.3
A3	28.72	14.1	0.1	5.7
A4	0	6	1.2	0
A5	30.26	6.1	1.2	2.7
A6	1.82	7.2	0.3	0.2
A7	13.18	25.3	2.2	3.8
A8	24.63	34.8	1.8	12
A9	22.43	36.5	5.7	10.5
A10	13.21	48	6.7	7.3

>TRINITY_DN126904_c0_g1_i7 from sample A1 / Example spliced isoform

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCT
GGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCT
TTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTG
TTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTA
CAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCAC
TTCTACCGCAAGCAAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTC
TTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGT
TAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATA
TTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGG
ATCGCATGCAATCTTTTCACGTGCTAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCGTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTA
AGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCT

>TRINITY_DN126904_c0_g1_i9 from sample A1 / Example unspliced isoform:

TATCAAACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGATTCTA
TTGTGCTCTGGCCCCACTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGT
CACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGgttagtataaataccataacaataatacaatatattttggctctgtaagtatctggggatttttctaagatttctctgtgggttg
gtcagGGGGACTCAGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTGCAATTCAAACCATTTGTTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAA
AGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCCCTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGA
AGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTAGCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAATGGGGGTTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACT
CAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATATCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAAATGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTT
TCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGA
GGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGA
GCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATT
CGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCAGTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATT
GGGCCTTTTATAGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATGTTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAG
TGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCTATATTTTGGTTATGATGCTGTGATTGGGGGTATTTATTGTGCCAGGTTTGTTTGTGACTTAAACGTGGTCCTAATTGCATGAAATAGCCTACTTATGCATATGTGACAACTCATAAAGGTCG
AACAAGTCTTTGAGGGAATTTGAATTCTGACGAAGGATAACACCACCCTCTTTTACTGACCAACCAAACTCTTATTAAGCGTTAACCAATTTTTTAATAACTTTTAAGCTAAAGTTCATTTTTTTTAATATAATATGTTCAGAGCTTGCAAGCTCACTTCACTACATACATTGGTGCATCACTCCCATCAAGCGTTAACC
AATTTTTTAATAACTTTTAAGTTAAAGTTCTTTTTCAGGCCTTGCAACCTCACTTCTACATACATTTGCGATGGATGCATGCTAATTCAGTAGAGCTTAAGAAATACATCTATTTGATTACATTGACAAGTACAAAGATTAACATGATGTATACGATTAACATGATGTATTGTATAAGTGGGTAATATGATCA

Intron 15 GTAAGGGATT ... TCTTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	42.86	12	10	8
A2	33.33	10	3	7
A3	29.73	13	6	5
A4	48.39	8	14	1
A5	28.57	5	3	1
A6	28.3	19	9	6
A7	36.28	72	59	23
A8	33.06	82	47	34
A9	24.24	50	25	7
A10	28.76	54.5	35	9

>TRINITY_DN43985_c4_g1_i15 from sample A6 / Example spliced isoform

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGAC
TGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAACAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTT
ACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATTTGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAACTTTATTGAAGCAAAAGAGTGGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGCCCATGTGCAGGGATTTTGATTGCAGTATTA
CATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTGTCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGT
CAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTATACGTTTGGCTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTTGGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCA
TGAAGTTATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCA
GTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAA
ATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

>TRINITY_DN43985_c4_g1_i6 from sample A6 / Example unspliced isoform:

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGAC
TGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAACAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTT
ACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATTTGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAACTTTATTGAAGCAAAAGAGTGGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGCCCATGTGCAGGGATTTTGATTGCAGTATTA
CATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTGTCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGT
CAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTATACGTTTGGCTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTTGGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCA
TGAAGTTATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCA
GTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGgtaagggattattgcattgtgaagtaattcaaaagaggtttgtaaacggaagtccatattttataatcagtgcctgcatcagaacttttcataaaccccaattcaaacaatcatttaaaaaacgtttctttttcagGATATTGGTTTGGTGGTTCGTATAGTAG
CAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAAATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTA
ACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

Intron 16 GTATGTGCCC ... TATTCATCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	59.09	9	13	4
A2	78.95	4	15	3
A3	64.71	6	11	3
A4	57.14	3	4	0
A5	50	2	2	0
A6	42.86	4	3	3
A7	65.38	9	17	1
A8	62.5	9	15	1
A9	60.98	16	25	3
A10	50	21	21	5

>TRINITY_DN43985_c4_g1_i15 from sample A6 / Example spliced isoform

CCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCACTTAT
TTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGACAGTATTCATCCGTCCATGAGATTCTATTGTGCTCTGGCCCCA
CTTATTTATCAAACAAATGCCAACCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCC
CGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTG
CTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACA
AGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTCCTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTG
TTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGAC
TGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGGAGATGTCAGATGCAATGTTAATAAACTAAAATAAGAAAAGGTTGACTCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAACAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTT
ACATTTGCTTAACAAAGGAACAGGGAATATAATGGAAATTTGATTCTCACCCAGTGATCAGTCTTCTACCAGAGATTCTTTCACTTTCACCCTATTCAAAGAGGGGTTGAAACTTTATTGAAGCAAAAGAGTGGAAACAATAGCTTGCTGTCATGCTCACAGTACTTTGCCCATGTGCAGGGATTTTGATTGCAGTATTA
CATCTCTACGTTTGCCATAATCCTTATGCTAACCATTTTGTCTTTGTTTTGTTTTGATATTTTCAGCTTGAACAATAATATGAAAGATTGCAAGTGTTGTGAAGCAGTCTACCTCATTCTTTTTTACATGACTGGTCATTTGTGAACTCTAATTACTCTCTTTGTTTCTTTTAAATGTCTTTACCATTTTATCTTTTGGT
CAAATATTTATTGCAAAGAAACATATGCCTTTTCCCTTTATACGTTTGGCTTCAAATGCTCTCTTCTTTGAAAGGCAGTTCATCCGCTGACAATATGCTATGGATCTAATATTGCTTTGGTTAAAGATGTGACCAGATATATTAGGGCACGTTCTAACCATGGCTGTGTAAAGCTTTGTTCACTTTGATTTTTTAATGCA
TGAAGTTATTTCCTCGAAAAGAGAAGAAGTCCATCCATAACTTGCCGATTTGATCATGTAGACCAAAGTTGGAACCCACACGGAAGCATATAATGGACAAAATTAGGGAGAGAAATTCGGAGTTGTTTGGCGGTCCATTACAGAACTCAAATACTCATGCTAAGAAAGCAAAGCTCGACGAAAGCAAAGCATCAGAAGCA
GTTCTACTTGCCTCATGTAGTGCATTTGGCCCTATGGATATTGGTTTGGTGGTTCGTATAGTAGCAACTACCACTGAATCAGTTTACAAATTCTTCAGAGAACATCTTACATCTATTGGGCCTTTTATTGGGACATGCCCATACGGGGGAAAGACGATTACCTAATGCATATTTTAACAAGTACAAGAACGCATGGCAAA
ATTGTAAAAGATACTACACAAATAAAATGTTTTTGTGTTGTCTTTTGAAATTGTAATATGCCTAACTTAAATAGAAAAGCTTTGGAGAATAATAAGATGAACATGGATCTAATAAAGTGAACATTTTGGATGCAGAATGAGAATGATAGGCATTCCTTGCAGTGATGCAAATACATCTAACAGTTTATGAAAGCT

>TRINITY_DN43985_c4_g1_i10 from sample A6 / Example unspliced isoform:

CTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTATTTTTTTTGCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACAAAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCA
TTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGTATGTTCTGAACAGTTCTTCAAAACCCTAGTTCTGTTCCAATGCATACTTTTCAACGAAGATGTTTTTCCTCAGCTTATGTTCTATTCCATGTGCTGTGCTGTAGGCTCAAGTAGGAAGTA
ATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAG
CCATTGTTTCTTGACTCGgtatgtgcccttttcaacactgcccaatatcaccataacagaattaagggctatactttgagctgcagcacaaatgatatggttatttatggtctcatgttagtcctcatttaaatattcatcagATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTTTATGAGTGAATGCTC
CTGGTGACGAGGGTACAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGG

Intron 17 GTCTACAAGT ... CCACTGCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	74.47	6	5	30
A2	72.41	8	14	28
A3	66.67	7	12	16
A4	48.94	12	3	20
A5	50	3	0	6
A6	52.54	14	6	25
A7	58.88	44	34	92
A8	65.78	32	29	94
A9	72.33	22	32	83
A10	64.44	32	39	77

>TRINITY_DN48869_c0_g3_i13 from sample A7 / Example spliced isoform

GACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATAT
GTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGTACTTCTCTTCAGTTCACATGAATG
GAATTGAGGGTTTCTAAGGCATAAAGGGTTTCATTCCCTCTTCATCTCATTTGAATAAATTGGACAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

>TRINITY_DN48869_c0_g3_i5 from sample A7 / Example unspliced isoform:

GACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATAT
GTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGTACTTCTCTTCAGTTCACATGAATG
GAATTGAGGGTTTCTAAGGCATAAAGGGTTTCATTCCCTCTTCATCTCATTTGAATAAATTGGACAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGgtctacaagtcagcgggagggaagtgctcagagcagttctttgaagctcaagtaggaagtaatgctcttttagctattcttccagacccagtgacgtgcttttccactgccagATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCAC
AAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

Intron 18 GTGCAATTCA ... CCACTGCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	82.35	6	26	30
A2	72.88	8	15	28
A3	69.4	7	16	15.8
A4	53.85	12	8	20
A5	78.57	3	16	6
A6	55.56	14	10	25
A7	62.35	44	54	91.8
A8	67.72	32	41	93.3
A9	71.43	22	27	83
A10	62.57	32	30	77

>TRINITY_DN118518_c10_g1_i6 from sample A3 / Example spliced isoform

CGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCA
TCCGTCCATGAGGTTCTATTGTGCTCTGACCCCACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGT
TGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGGTATGTGCCCTTTTCAACACTGCCCA
ATATCACCATAACAGAATTAAGGGCTATACTTTGAGCTGCTGCACAAATGATATGATTATTTTTCATCAGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCA
AGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGCTTGAACAATAATATGAAAG

>TRINITY_DN118518_c10_g1_i13 from sample A3 / Example unspliced isoform:

AACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGACCC
CACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCG
CCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGgtgcaattcaaaccatttgttctt
ttatgaattctgtttttctgttttattttgatgcaagcacgatcaaatgggtttggtgtagccaacagggtgttagttcactggtgaggttgacaaagtactagctccgatccaagaaacccagacctggtattcgcctgtaggcatcattcccgaacctgcctccccctcagccctctcactcgtggccaattacagaa
cgtgtgttagaaatagagtatatacaactagttctcagtatttcagggtattctttggatactttctctgaaataggatgcctgctcatgctgggaagattgggcctgtgtcctccgcatgagtactgctgcataacgagagttaagtttgctctgttgtgtggtgtagccctttggggtgtgtttttgaagcacttcta
ccgcaagcaaaaaaatggggatttggtttaatagttagagagaatagcaattatcgttggtcacaagatgattgcatatccacttctcacaagtactcagattatacacagtctccatttccaaggaggaactgtagatatgacagtagggtttcaattaagcagatatcgatactcacctatggtgctcaattcttttt
gaggtgcggttgcatctaaattgcatgttacctgattggggcatatctcataagtataaaaacttagaactaggttcgcctgtggaactaatttttttcccatctaatccataagaattgggtagagcattaatcctcccaaataaactggttggctttgacatcacaaaatcccttattaccatccctaaaggttaaat
caaatcaccaatgagattgggatctcggctttctgtgtattttgcatttgaactcataagctagtaacgtcatatacaggtctacaagtcagcgggagggaagtgctcagagcagttctttgaagctcaagtaggaagtaatgctcttttagctattcttccagacccagtgacatgcttttccactgccagATATTCGC
AGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGGTATGTGCCCTTTTCAACACTGCCCAATATCACCATAACAGA
ATTAAGGGCTATACTTTGAGCTGCTGCACAAATGATATGATTATTTTTCATCAGATCACGTTAATTACACCTAGAACAAGCTTTGGCCCTCAACTCTATGAGTGAATGCTCCTGGTGACGAGGGTATAGATCAAACTAAGTGTACTTGCTTTCTGCTCACTTGTAACCAGACACAGCTGGAGCAAGGTGCTGGCTATTCT
GTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGA
CTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTT
TATATTTACTTAACA

Intron 19 GTATGTTCTG ... CCACTGCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80.49	4	6	27
A2	56.21	11.3	9	20
A3	76.92	3	13	7
A4	64.29	10	14	22
A5	76	3	10	9
A6	64.89	8.7	7	25
A7	61.07	36.7	30	85
A8	59.71	27.3	11	70
A9	60.52	18.7	3	54
A10	67.31	21.7	26	63

>TRINITY_DN48869_c0_g3_i12 from sample A7 / Example spliced isoform

CAGTATTCATCCGTCCATGAGGTCCTATCGCGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCCGCGCAAACTCCAACTGGGCG
CATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTTCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCCACCAAGGCTGTGTC
GTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAATATTCGCAGAGACAAATATTT
AATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

>TRINITY_DN48869_c0_g3_i11 from sample A7 / Example unspliced isoform:

GACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTCTCTGGCCCCACTTATTTATCAAACAAATGCCACCCACGTCATGTTTTATCATTTTGTTTGTGTATATAT
GTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTTTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGTACTTCTCTTCAGTTCACATGAATG
GAATTGAGGGTTTCTAAGGCATAAAGGGTTTCATTCCCTCTTCATCTCATTTGAATAAATTGGACAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGGTGCAATTCAAACCATTTGTTCTTTTATGAATTCTGTTTTTCTGTTTTATTTTGATGCAAGCACGATCAAATGGGTTTGGTGTAGCCAACAGGGTGTTAGTTCACTGGTGAGGTTGACAAAGTACTAGCTCCGATCCAAGAAACCCAGACCTGGTATTCGCCTGTAGGCATCATTCCCGAACCTGCCTCCCC
CTCAGCCCTCTCACTCGTGGCCAATTACAGAACGTGTGTTAGAAATAGAGTATATACAACTAGTTCTCAGTATTTCAGGGTATTCTTTGGATACTTTCTCTGAAATAGGATGCCTGCTCATGCTGGGAAGATTGGGCCTGTGTCCTCCGCATGAGTACTGCTGCATAACGAGAGTTAAGTTTGCTCTGTTGTGTGGTGTA
GCCCTTTGGGGTGTGTTTCTGAAGCACTTCTACCGCAAGCAAAAAAATGGGGATTTGGTTTAATAGTTAGAGAGAATAGCAATTATCGTTGGTCACAAGATGATTGCATATCCACTTCTCACAAGTACTCAGATTATACACAGTCTCCATTTCCAAGGAGGAACTGTAGATATGACAGTAGGGTTTCAATTAAGCAGATA
TCGATACTCACCTATGGTGCTCAATTCTTTTTGAGGTGCGGTTGCATCTAAATTGCATGTTACCTGATTGGGGCATATCTCATAAGTATAAAAACTTAGAACTAGGTTCGCCTGTGGAACTAATTTTTTTCCCATCTAATCCATAAGAATTGGGTAGAGCATTAATCCTCCCAAATAAACTGGTTGGCTTTGACATCACA
AAATCCCTTATTACCATCCCTAAAGGTTAAATCAAATCACCAATGAGATTGGGATCTCGGCTTTCTGTGTATTTTGCATTTGAACTCATAAGCTAGTAACGTCATATACAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAgtatgttctgaacagttcttcaaaaccctagttctgttccaatg
catacttttcaacgaagatgtttttcctcagcttatgttctattccatgtgctgtgctgtaggctcaagtaggaagtaatgctcttttagctattcttccagacccagtgacgtgcttttccactgccagATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGT
GGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCG

Intron 20 GTGCAATTCA ... TCATATACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	83.56	4.2	25.8	16.3
A2	53.17	12.2	15	11.7
A3	58.46	10.4	16	11.6
A4	75.95	2.6	7.8	9.2
A5	100	0	16	2.4
A6	56.4	5.6	9.5	4.9
A7	58.42	29.2	52.8	26.6
A8	57.85	24.7	39.7	26.1
A9	47.14	27.4	26.2	20.6
A10	45.78	33.6	29.2	24.9

>TRINITY_DN118518_c10_g1_i2 from sample A3 / Example spliced isoform

CGCTCTTGCCCCACTTATTTATCAAACGATTCCCACAGATGCCACCGACGTCATATTTTATAATTTTTTTTATGTATATATGTTTGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGCGCGCAAACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCA
TCCGTCCATGAGGTTCTATTGTGCTCTGACCCCACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGT
TGCGGGCAGGTCTGCTGTCACGAGCCTCTTCGCCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTT
CAACAAAGGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACGTGCTTTTCCACTGCCAGATATTCGCAGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCAC
AAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGCATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAA
ACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTAAGTGGAAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAA
ACTAAAATAAGAAAAGGTTGAC

>TRINITY_DN118518_c10_g1_i12 from sample A3 / Example unspliced isoform:

AACGATTCCCACAAATGCCACCGACGTCATATTTTATCATTTTTTTATGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTCAAGACCACGGCAATGGCAATGAACTTGGACAAATCTGCGCAGACTCCAACTGGGCGCATTGTGATCCAGACAGTATTCATCCGTCCATGAGGTTCTATTGTGCTCTGACCC
CACTTATTTATCAAACAAATGCCACTCACGTCATGTTTTATCATTTTGTTTGTGTATATATGTTGGACGAACCTGTAAGTTTCATGGATCTGTGAAGACCATGGCAATGGCAATGAACTTGGACAAATCTGCGCAAACTCCAACTGGGCGCATTGTGATTCAGAAAGTTGCGGGCAGGTCTGCTGTCACGAGCCTCTTCG
CCCGATATCCTCTCAAATTTATACGACCGACCAAGGCTGTGTCGTCCCAAGTAGACGTAGTATGGATCTACACTGTGTCCTTCGGCGGAGGCATTGTAACGGGGGACTCGGTTCATTACACAATTGCTGTTGGAGAGGGTTGTACTGCGGTTTTGACTACTCAGGCTTCAACAAAGgtgcaattcaaaccatttgttctt
ttatgaattctgtttttctgttttattttgatgcaagcacgatcaaatgggtttggtgtagccaacagggtgttagttcactggtgaggttgacaaagtactagctccgatccaagaaacccagacctggtattcgcctgtaggcatcattcccgaacctgcctccccctcagccctctcactcgtggccaattacagaa
cgtgtgttagaaatagagtatatacaactagttctcagtatttcagggtattctttggatactttctctgaaataggatgcctgctcatgctgggaagattgggcctgtgtcctccgcatgagtactgctgcataacgagagttaagtttgctctgttgtgtggtgtagccctttggggtgtgtttttgaagcacttcta
ccgcaagcaaaaaaatggggatttggtttaatagttagagagaatagcaattatcgttggtcacaagatgattgcatatccacttctcacaagtactcagattatacacagtctccatttccaaggaggaactgtagatatgacagtagggtttcaattaagcagatatcgatactcacctatggtgctcaattcttttt
gaggtgcggttgcatctaaattgcatgttacctgattggggcatatctcataagtataaaaacttagaactaggttcgcctgtggaactaatttttttcccatctaatccataagaattgggtagagcattaatcctcccaaataaactggttggctttgacatcacaaaatcccttattaccatccctaaaggttaaat
caaatcaccaatgagattgggatctcggctttctgtgtattttgcatttgaactcataagctagtaacgtcatatacagGTCTACAAGTCAGCGGGAGGGAAGTGCTCAGAGCAGTTCTTTGAAGCTCAAGTAGGAAGTAATGCTCTTTTAGCTATTCTTCCAGACCCAGTGACATGCTTTTCCACTGCCAGATATTCGC
AGAGACAAATATTTAATGTAGCTTCAGATGCCAACTTAGTTCTGGTTGACTGGCTGACCAGTGGCCGTCACAAGCGGGGTGAAATTTGGGATTTTGAGCAGTACAAGAGCACAAACAATATTTATTTGGACGGACATCAGCCATTGTTTCTTGACTCGACACAGCTGGAGCAAGGTGCTGGCTATTCTGTTGTGGATCGC
ATGCAATCTTTTCACGTGATAGCAATGCTGGTAGTTTTGGGGTATGTTTTTCTCCCTTTCAGTTTTTTTAAACTCTTTTTGTAACTTGAATCCTTCTTTATTTGACTAGCCAACAAATTAAGAACATCGACTAAAATGAAAAAGTTCAGCCAATCCTAGAAATTGAAGCATTTATAGCATCACTGGGACTGTGTAAGTGG
AAGTGGCTTTTAATTAGGTTTTTTTGTGTTACAGCCTGGGGTGGAAGAGATGTCAGATGTAATGTTAATAAACTAAAATAAGAAAAGGTTGACATCCAAACATGTAATGTTTCAAAAGAAAAGATTATTATAATGTAAAATAAATAAACTAGCATAGATCCATCTTAACCCTAAATTTTCAGTCATTTTATATTTACTTA
ACA