sp|Q2LAE1|ASHH2_ARATH ----> Histone-lysine N-methyltransferase ASHH2

Intron 1 GTGACTGTTC ... GGTGTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	16.73	234	47	73.4
A2	21.8	269	75	36.4
A3	17.76	250	54	43.2
A4	18.33	205	46	37.1
A5	31.63	67	31	8.6
A6	14.29	12	2	2.3
A7	19.1	72	17	8.5
A8	8.82	31	3	7.7
A9	8.33	44	4	6.9
A10	16.28	72	14	14.6

>TRINITY_DN116217_c0_g2_i3 from sample A1 / Example spliced isoform

GCTGTCTTGACAATCGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAA
GAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATT
CTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGT
ATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACC
AGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTA
ATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCA
GGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACA
AGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGT
GTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCT
GCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGG
TACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATA
TTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAA
GATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTAT
CATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGA
ATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCT
GAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGG
CACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAA
CTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTG
AAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAA
GCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAA
GAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCAT
TCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCA
ACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCC
GCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACAT
CCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGG
CCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTC
TTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCA
GAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCT
TAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCAC
CTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTG
GTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTG
TACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTA
GTAAGCATGCTTGTAAGCTT

>TRINITY_DN116217_c0_g2_i1 from sample A1 / Example unspliced isoform:

GAAAAATGCTGATTATAAATTTAAGTTGGCCATAATACAGTATTCCTAATATGACTAGTTTGTATATATTTGGTAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTA
ACCAGCGGGTAATGTGATTTTTCCTAAGTTCAATTGCTCCTTTAAGGACTGTTGCTACATTCCAACTTTATTCCTGACACTTATATGTTCATAAATTTTTTTAAACTCAATATCCATAGTATGTATTTTGCAGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGG
TTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGgtgactgttcttttggatcccaatgtagttttctctgaataactagaatgaagctatgttcttttttgcagggcatagttctaaaattgttaagggttatgttttaagtcagcaattttattttatgattacattaatattttatgatga
tggacggttagttttctaagaatagaagtgtgtatccattcgaaaatgcaaaattgtttcacctatctcttcatatcatatttatttgagttagaaggtaacatgcttcacatcttggtaacgtttctcttggtgatgtaggttttagattttcacaatactttatctttctattcatatgatatttgggttagaagata
acaagcttaaaatcttgacaatgtttcttttggtgttgcagGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTGCAGCTCAATCATTTGACTTGTTTGAGCTTTAATGTCTTTAAATTTTTGTTTGTTTCCTTAAAT
TGCACGAAACATGGAAACAGGTACAAGTTTTTGAAATGGGTATGCTGTAGAAATGTGACCTTCCAAAATTTGGAAATATGGTATATAAAAAATACAAAAAAATATAAATATTTTAAGCAAATAGATATTTATTTAAAAAAAATAAGAGCAACACACATAAGCACATAAGAAAATAAGAACAATACACATAAATGAAATAG
GAACAATACACATTAGAAAATAAGAACAATATACATAAATGACA

Intron 2 GTGCGTTAAT ... TGTGGCCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	12.32	50	5	9
A2	15.49	41	7	8
A3	19.34	21	5	5
A4	16.37	19	4	3
A5	35.06	3	1	2
A6	19.3	81.5	11	28
A7	16.84	104	15	27
A8	18.84	185.5	29	57
A9	17.6	96	4	37
A10	13.46	71	4	18

>TRINITY_DN35843_c0_g2_i3 from sample A9 / Example spliced isoform

TCGGGGACCAATTGCCAATGCCAAGCTGTCTTGACAATCGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGG
CGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGG
AGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTG
GACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACC
AAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTT
CCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGG
GAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCA
ATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAAC
CATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGAT
GATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGG
AAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACG
CTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATG
GTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGA
GGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATT
GTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTA
AGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAA
GAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGC
ATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAA
ACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACC
TATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGG
TTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGAC
AATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAA
AATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTG
ATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTT
GATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACT
GGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATC
TAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTG
AATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATT
TTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCT
GTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGGTAGGTAAAGGTGTACCGACCTGTCTGTCTATTTGATGTTCAAAAGGCAATTCTTCTCTTTTTTTATTCCCCCTCCCTTT
TTTTAGTTAAGGGGTTGTGGGGTGTGTTGTAATATAGAGACCTGTAGTGAGGCAGGAATACAGCAAAAATATGGTTTACATTCTTCCAATGTTTTCTCTTTCATCTCAAAAGGCATGTAATAATCTTTGTTGAAGTCCTCGGCAGTATTTGCAATATTGGTTTAATGATGCTGTTTATATTTAGGTAGATTATTGCTATA
ATTAGACACACATTTTCTCTGCAGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTT
ATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCA
GGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGTAAGCTTTTGCAATTAATACCTGATGATTGAAGGCATATGCAGCAAATTGTGTATTGTA
AGTCTATATGTAACTTGTACTTTAGATTTAAAAATGGTCCTTCTTTCAGGATAATGTTAATCTAGATTGTCCAGTGTAGGAATCTATTATTTTGAGTAGGAATATGCTGGAGGTTAAAGATGTCCATTG

>TRINITY_DN35843_c0_g2_i2 from sample A9 / Example unspliced isoform:

TCGGGGACCAATTGCCAATGCCAAGCTGTCTTGACAATCGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGG
CGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGG
AGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTG
GACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACC
AAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTT
CCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGG
GAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCA
ATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAAC
CATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGAT
GATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGG
AAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACG
CTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATG
GTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGA
GGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATT
GTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTA
AGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAA
GAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGC
ATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAA
ACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACC
TATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGG
TTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGAC
AATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAA
AATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTG
ATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTT
GATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACT
GGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATC
TAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTG
AATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATT
TTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCT
GTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGGTAGGTAAAGGTGTACCGACCTGTCTGTCTATTTGATGTTCAAAAGGCAATTCTTCTCTTTTTTTATTCCCCCTCCCTTT
TTTTAGTTAAGGGGTTGTGGGGTGTGTTGTAATATAGAGACCTGTAGTGAGGCAGGAATACAGCAAAAATATGGTTTACATTCTTCCAATGTTTTCTCTTTCATCTCAAAAGGCATGTAATAATCTTTGTTGAAGTCCTCGGCAGTATTTGCAATATTGGTTTAATGATGCTGTTTATATTTAGGTAGATTATTGCTATA
ATTAGACACACATTTTCTCTGCAGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGgtgcgttaataaagacttttttgttacatttgacatgcaatactcttatgatagaaatgttgttttaaaagttatcattaggttagacatatcacaatttttc
tttgcagttatcttctacactgttgcatcctagatggtatatataagatgtttgagtagtatactattttgagccagtgtataatgtgatgcatatagtattgtaacatagaaaatgttcttaaagcagtctccatattttgggtgagttgtgttaacccactacaagaatcacttacaaggatggtttattgttaggtg
tattttttttcctgtgattcttgagagatctcagatacttcagccttacatgtaggggattctctttgcttcagttgacattgtataatttgtattcaattgcatgaaatagttctgcagatttggctatttgttagtctgccacttccatagagtaacatgatcagatttttatccacattttagtcagagtgattgga
tattaagtgcagaaacatgtaacataaatgttttgtcggtatgaaatgatcattctgaattgagctctacttttaagtagtatttttaaactgttttccaatggatatgaagctccttcaaattgtggttactctgctttctttttttaatagccattagacaattgattaggttttgttgtcttcatgcactggactac
tctaatacttatcctcttttgtggcccagAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAA
ATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATA
ACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGTAAGCTTTTGCAATTAATACCTGATGATTGAAGGCATATGCAGCAAATTGTGTATTGTAAGTCTATATGTAACTTGTACTTTAGATTTAAAAATGGTCCTTCTTTCAGGATAATGTTAATCTAGATT
GTCCAGTGTAGGAATCTATTATTTTGAGTAGGAATATGCTGGAGGTTAAAGATGTCCATTG

Intron 3 GTAATGTGAT ... TATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	21.5	157	29	57
A2	22.77	212	34	91
A3	19.47	211	38	64
A4	24.76	155	37	65
A5	24.05	60	12	26
A6	23.08	5	3	0
A7	20.53	60	7	24
A8	20	22	3	8
A9	15.32	47	9	8
A10	11.52	96	6	19

>TRINITY_DN116217_c0_g2_i3 from sample A1 / Example spliced isoform

GCTGTCTTGACAATCGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAA
GAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATT
CTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGT
ATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACC
AGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTA
ATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCA
GGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACA
AGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGT
GTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCT
GCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGG
TACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATA
TTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAA
GATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTAT
CATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGA
ATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCT
GAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGG
CACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAA
CTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTG
AAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAA
GCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAA
GAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCAT
TCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCA
ACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCC
GCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACAT
CCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGG
CCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTC
TTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCA
GAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCT
TAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCAC
CTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTG
GTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTG
TACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTA
GTAAGCATGCTTGTAAGCTT

>TRINITY_DN116217_c0_g2_i1 from sample A1 / Example unspliced isoform:

GAAAAATGCTGATTATAAATTTAAGTTGGCCATAATACAGTATTCCTAATATGACTAGTTTGTATATATTTGGTAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTA
ACCAGCGGgtaatgtgatttttcctaagttcaattgctcctttaaggactgttgctacattccaactttattcctgacacttatatgttcataaatttttttaaactcaatatccatagtatgtattttgcagTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGG
TTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGGTGACTGTTCTTTTGGATCCCAATGTAGTTTTCTCTGAATAACTAGAATGAAGCTATGTTCTTTTTTGCAGGGCATAGTTCTAAAATTGTTAAGGGTTATGTTTTAAGTCAGCAATTTTATTTTATGATTACATTAATATTTTATGATGA
TGGACGGTTAGTTTTCTAAGAATAGAAGTGTGTATCCATTCGAAAATGCAAAATTGTTTCACCTATCTCTTCATATCATATTTATTTGAGTTAGAAGGTAACATGCTTCACATCTTGGTAACGTTTCTCTTGGTGATGTAGGTTTTAGATTTTCACAATACTTTATCTTTCTATTCATATGATATTTGGGTTAGAAGATA
ACAAGCTTAAAATCTTGACAATGTTTCTTTTGGTGTTGCAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTGCAGCTCAATCATTTGACTTGTTTGAGCTTTAATGTCTTTAAATTTTTGTTTGTTTCCTTAAAT
TGCACGAAACATGGAAACAGGTACAAGTTTTTGAAATGGGTATGCTGTAGAAATGTGACCTTCCAAAATTTGGAAATATGGTATATAAAAAATACAAAAAAATATAAATATTTTAAGCAAATAGATATTTATTTAAAAAAAATAAGAGCAACACACATAAGCACATAAGAAAATAAGAACAATACACATAAATGAAATAG
GAACAATACACATTAGAAAATAAGAACAATATACATAAATGACA

Intron 4 GTAATGTGAT ... GGTGTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	38.02	97	29	90
A2	36.65	70	34	47
A3	38.66	73	38	54
A4	37.17	71	37	47
A5	42.31	15	12	10
A6	37.5	5	3	3
A7	34.62	17	7	11
A8	39.39	10	3	10
A9	33.33	18	9	9
A10	36.23	22	6	19

>TRINITY_DN107667_c0_g2_i5 from sample A5 / Example spliced isoform

TCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGC
GATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGT
GGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGA
GGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGA
AAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGG
GAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAG
GAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAG
GATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGC
ACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGA
ACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACG
ACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGT
CAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATT
GAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACA
GCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACT
CCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCC
TAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAA
GGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGT
AAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGA
CTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAA
AAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCA
AATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAA
CATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTAC
CTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTT
TATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGA
ACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGG
ATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATG
GCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAG
AGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAA
TAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAG
ATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTT
GCATGACGG

>TRINITY_DN107667_c0_g2_i4 from sample A5 / Example unspliced isoform:

TCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGC
GATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGT
GGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGA
GGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGA
AAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGG
GAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAG
GAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAG
GATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGC
ACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGA
ACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACG
ACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGT
CAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATT
GAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGgtaatgtgatttttcctaagttcaattgctcctttaaggactgttgctacattccaactttattcctgacacttatatgttcataaatttttttaaactcaatatccatagtatgtattttgcagtttcaaaagagatcata
tgcaaatgttgggtggttccgttgtgggaagaaaggttttggtttgcaggttttggaggatgttccatgtggcacttttatcatagaatatgtcggagaggtgactgttcttttggatcccaatgtagttttctctgaataactagaatgaagctatgttcttttttgcagggcatagttctaaaattgttaagggttat
gttttaagtcagcaattttattttatgattacattaatattttatgatgatggacggttagttttctaagaatagaagtgtgtatccattcgaaaatgcaaaattgtttcacctatctcttcatatcatatttatttgagttagaaggtaacatgcttcacatcttggtaacgtttctcttggtgatgtaggttttagat
tttcacaatactttatctttctattcatatgatatttgggttagaagataacaagcttaaaatcttgacaatgtttcttttggtgttgcagGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTG
TAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGAC
TGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTC
TGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAA
TGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTG
CAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGA
GGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTA
GTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCT
TTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCA
TAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATAT
TATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAG
CCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACA
TGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCT
GTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGAT
TGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGA
TGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACG
AAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAG
GAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAAT
ATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGG

Intron 5 GTAGGTAAAG ... CTATAATTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	60	60	13
A2	57.95	37	51	15
A3	43.18	50	38	12
A4	51.22	40	42	13
A5	60.71	11	17	5
A6	60.5	94	144	29
A7	56.9	153	202	55
A8	58.76	252	359	59
A9	65.45	104	197	25
A10	55.14	83	102	15

>TRINITY_DN99234_c0_g2_i1 from sample A4 / Example spliced isoform

GAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGT
TGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACAGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGAT
CTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAG
TCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGG
GTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATTAAGCAAGAT
GCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGC
AGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGG
GAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAG
GTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGA
TGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCAT
GGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAAT
GATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAAC
TATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTG
GTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCAC
AGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTAC
TCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTC
CTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGA
AGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAG
TAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGG
ACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAA
AAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTC
AAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAA
ACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTA
CCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGT
TTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGG
AACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAG
GATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCAT
GGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATA
GAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAA
ATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGACACACATTTTCTCTGCAGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCT
TCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAA
TTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAA
CATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAG

>TRINITY_DN99234_c0_g2_i11 from sample A4 / Example unspliced isoform:

GAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGAGGAGGGAGGGAGTGT
TGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACAGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTTAGGTCAATGCCGGAT
CTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAAGTTCAGAGACAGGAG
TCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCGAGTCTCCGAGTAAGG
GTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGAGCGATTAAGCAAGAT
GCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCGGTGTCTTGATGAGGC
AGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCATTGCTTAAAGGCAGGG
GAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACTAATGCAGAAGAACAG
GTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGTAGAGAAAGTAGAAGA
TGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAAAACCACGGAAAGCAT
GGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCCAACTGTGACAAAAAT
GATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAAC
TATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGGTAATGTGATTTTTCCTAAGTTCAATTGCTCCTTTAAGGACTGTTGCTACATTCCAAC
TTTATTCCTGACACTTATATGTTCATAAATTTTTTTAAACTCAATATCCATAGTATGTATTTTGCAGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCGGAGAGGTGACTGTTCTTTTGG
ATCCCAATGTAGTTTTCTCTGAATAACTAGAATGAAGCTATGTTCTTTTTTGCAGGGCATAGTTCTAAAATTGTTAAGGGTTATGTTTTAAGTCAGCAATTTTATTTTATGATTACATTAATATTTTATGATGATGGACGGTTAGTTTTCTAAGAATAGAAGTGTGTATCCATTCGAAAATGCAAAATTGTTTCACCTAT
CTCTTCATATCATATTTATTTGAGTTAGAAGGTAACATGCTTCACATCTTGGTAACGTTTCTCTTGGTGATGTAGGTTTTAGATTTTCACAATACTTTATCTTTCTATTCATATGATATTTGGGTTAGAAGATAACAAGCTTAAAATCTTGACAATGTTTCTTTTGGTGTTGCAGGTCTTAGATATGAAGGAACATAATG
CACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATA
AAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGT
TGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGG
AGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACA
AGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGA
ACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAA
GCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAA
ATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAG
GAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATA
GTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGA
GAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAA
TCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATC
ATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGC
ATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTA
CCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGC
CAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAA
TGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGgtaggtaaaggtgtaccgacctgtctgtctatttgatgttcaaaaggcaattcttctctttttttattccccctccctttttttagttaaggggttgtggggtgtgttgtaatatagagacctgtagtgaggcaggaatacagcaaaa
atatggtttacattcttccaatgttttctctttcatctcaaaaggcatgtaataatctttgttgaagtcctcggcagtatttgcaatattggtttaatgatgctgtttatatttaggtagattattgctataattagACACACATTTTCTCTGCAGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTC
TTCCAGCAGTCAAGCTTCAAGATAATTAGGTGCGTTAATAAAGACTTTTTTGTTACATTTGACATGCAATACTCTTATGATAGAAATGTTGTTTTAAAAGTTATCATTAGGTTAGACATATCACAATTTTTCTTTGCAGTTATCTTCTACACTGTTGCATCCTAGATGGTATATATAAGATGTTTGAGTAGTATACTATT
TTGAGCCAGTGTATAATGTGATGCATATAGTATTGTAACATAGAAAATGTTCTTAAAGCAGTCTCCATATTTTGGGTGAGTTGTGTTAACCCACTACAAGAATCACTTACAAGGATGGTTTATTGTTAGGTGTATTTTTTTTCCTGTGATTCTTGAGAGATCTCAGATACTTCAGCCTTACATGTAGGGGATTCTCTTTG
CTTCA

Intron 6 GTAGGTAAAG ... TTCTCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.11	73	60	18.2
A2	50	51	51	20.2
A3	41.76	53	38	11.3
A4	46.67	48	42	10.6
A5	60.71	11	17	4
A6	59.75	97	144	35.3
A7	54.89	166	202	47.3
A8	58.85	251	359	70
A9	62.74	117	197	32.2
A10	52.31	93	102	16.7

>TRINITY_DN116217_c0_g2_i6 from sample A1 / Example spliced isoform

AGGTTATGTATTTCTAAAATTGTTTTTAAAATCTACTAATGACCCAAAGCAGATGAACTTCAGAGATCTCATTCTTCCCCAAGATGCAGTTTTTGCCTGTTTCAGTAAATGCAAAAGTGAAGTGTATAGCACACTTGAAAATTTCAGTAGCTTACCCAGACACATTTTCTTTTGCTTTCCACTTTCTCCTACTTAATTTA
TAACTATGTTGCAAAAGAGTAGATGATTCCCATATTGTTTTTGTGATAGATTTGACACCTAAGCCTGTTTCTCTTGTTCTTTGTTTAGTTGTTAATAACTTGTTCTTATGTGGTTTGGAATCTTTGACTTTCAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAG
TGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATC
TGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAG
AGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCA
GATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTT
TCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAA
AACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAA
CAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCA
TGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGAC
CAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACA
ACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAG
GCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCT
ATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTCTTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATG
AATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATG
TGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTG
GGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGG
AGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGT
ATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGC
CTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGTAAGCTT

>TRINITY_DN116217_c0_g2_i7 from sample A1 / Example unspliced isoform:

GCTGTCTTGACAATCGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAA
GAACCCGAGGAGGAGGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATT
CTGCAGATAATTTTAGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGT
ATTGACAATAGGAAGTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACC
AGAGGAGGTGTCCGAGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTA
ATGGATATTGTGGAGCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCA
GGAGATGATCGCCGGTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACA
AGCACATAAGTCATTGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGT
GTTCGCCGAGAACTAATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCT
GCTCTGTCAAAGGTAGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGG
TACAGAGCCGGAAAAACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATA
TTTCTGAGATTTCCAACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAA
GATGGCAGCAGTGGTTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTAT
CATAGAATATGTCGGAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGA
ATGGTGAAGTTTGCATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCT
GAGCCAATAGTTCTGACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGG
CACTGCTAAGAAGCTGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAA
CTGCTGCATCGGGTGATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTG
AAGATTTTGCATATTTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAA
GCAAACACAGGGTGGATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAA
GAATATTTGAGCATGATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCAT
TCCAGCATTTCAGAGGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCA
ACTTAACACAGTTACAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCC
GCAGGCCAATTGAGAACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACAT
CCATTTGCTTCGGCTTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGG
CCTTTCACCACCACATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTAATAATCAGGATCTATCCCCAAATCTAAGTGCACAGGATTCTGTTCGTC
TTAATTCAAATTGTGATACTGAAAATCAGTCAGCAAAAACATGCATTTTAGATGGCTTGTCTAGCCAAATGTCATGTCCTGTTGACGGCAACACTGCTAGCCATGCATCTATGAATACAGCCATTGATTGTAGTTCTCAAAGATCTAGTCCATTGTGCATGGCAGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCA
GAAACGGTAGCTTCCTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCT
TAGGACTGATAGAGATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCAC
CTCCTGTGGAAGGAGGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGgtaggtaaaggtgtaccgacctgtctgtctatttgatgttcaaaaggcaattcttctctttttttattccccctccctttttttagttaaggggttgtggggtg
tgttgtaatatagagacctgtagtgaggcaggaatacagcaaaaatatggtttacattcttccaatgttttctctttcatctcaaaaggcatgtaataatctttgttgaagtcctcggcagtatttgcaatattggtttaatgatgctgtttatatttaggtagattattgctataattagacacacattttctctgcag


TGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCA
TTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCT
GTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGTAAGCTT

Intron 7 GTAATAATCA ... TGCATGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	62.54	59	109	88
A2	66.32	32	59	67
A3	68.09	30	57	71
A4	79.23	19	76	69
A5	62.03	15	25	24
A6	62.96	30	44	58
A7	67.53	50	105	103
A8	59.32	84	105	140
A9	61.88	69	108	116
A10	63.1	50	86	85

>TRINITY_DN116251_c1_g1_i2 from sample A2 / Example spliced isoform

CGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGA
GGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTT
AGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAA
GTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCG
AGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGA
GCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCG
GTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCAT
TGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACT
AATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGT
AGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAA
AACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCC
AACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGG
TTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCG
GAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGC
ATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCT
GACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGC
TGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGT
GATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATAT
TTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTG
GATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCAT
GATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGA
GGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTA
CAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAG
AACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGC
TTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCAC
ATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTCCTCAAATAATAATCAT
TCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAGATTCCCATTCTAGTCA
TGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGAGGTCGATCTTCAGATA
TTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAACAATCATTCTTTGAAGT
AAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGATATTTGTTTGCATATT
TTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGTAAGCTTTTGCAATTAA
TACCTGATGATTGAAG

>TRINITY_DN116251_c1_g1_i6 from sample A2 / Example unspliced isoform:

CGTGACTTCCTTAAAGAAGCGTGGCCGTCTTCGCCCGTTGCTGTCTTGAGCTGCGGTGCAGTGGGCGTGGTTTTTCCGTCGTCGTCGCTTCGGCTATTTACTTAACCGTCTAAATTAAGGAATTTTATTTTGTTTTGATTTAAGTATTTAGAGGAGCTGAGGCGGAGGGAGAGCAGAAGCGAGGAAGAACCCGAGGAGGA
GGAGGGAGGGAGTGTTGAACGGAGCCATGCGATGACCAGGCGGCCCATCGAACCCAAAACACACCAATATTCTCTCAAATTAATGAAAAATCATCACAAGAGATTCCCTCTGAGCCCTATATCCTAGAGCGCCCGAGGTCACGGGTTCGAAACTGTGGAAGGAGAAAAACAAATTTGTACAGAATTCTGCAGATAATTTT
AGGTCAATGCCGGATCTCGAACCCGTTCGTGGCATGGCTAACGGGGGTCCGCTCGGGCCGCGATTTGGCGGCGATCGCCGAAGGCCGGGAATGCCAGAGTCGTCGGTTTTCGCCTGCGACCGGTCGGAGACTTGCAATGGGGAACCGAACGGACAGTCCGTGGACCGCCGGCAGAAGGCGTTAGGTATTGACAATAGGAA
GTTCAGAGACAGGAGTCGAATTGGCGGGGAGGTCTCGGGTTCGAATCTACCCAAGGTGAGCCATTCCAAATTGGAGAAAGCGTGCCGGAAGTTAAAGGGCGGAGTGGTGAAGCCGACGGAGTTGGTAATGAGGCTTGTTCAGCTGGTTAAAGGTTCAAAACCAAGGAAATGTCTAGATTTGGTACCAGAGGAGGTGTCCG
AGTCTCCGAGTAAGGGTAAGAAGAGGAGGAAAAATATCGAAAGCGAGAGCGAAGCCTGTGGTTTTACGGGGTCCGGCGAAGGGGTGGCTGTAGGCTTTCGTGAACAGATGGCAGGAGCCGATATGGAAGCCTCCGATTTTGGTAATAATAAGGCTGGGAGTTCCTCGATGGATTTTTCACAGATTAATGGATATTGTGGA
GCGATGAAGCAAGATGCGATTGCCAATGGGGAAGCTCACAGAGAAATTACAGAAGAAGGTAAGAAATCTAAGAAATATAGAGCTACAATGAAATCGGTCATGGGCAGTGTGGAGGAAAAGAGCGAACCGAAACGCACTAGGAAAGGGAAGGTGCAATGTGGGGAAAGTTTAGGATCACATGAAGCAGGAGATGATCGCCG
GTGTCTTGATGAGGCAGATAGAGAGGGCAGGAATAACAAGAGAAAGAGACACAGGAATTCAGGCAATGCGGTTGCAGATATGGTCGGAAGTAAAGTAACAGGATCTATAGCTGATGATGTTTCATCGACATTGAAATTAACTGATCCTTTTGGCAAAAGCCAATTGGCAAATGAAGACACATCACAAGCACATAAGTCAT
TGCTTAAAGGCAGGGGAAGTAAAATAACAGGATCTACAACTGATGATGTTTCGTCGACATTGAAATTTACCGAACCTGTCAACAAAAGGCATCTATCTAAACAAGACATGTCGCAAGAGAATAAATTGTTGCTTAAAGGCAGGGGGAGACCCAAGAAAGAACCATTGAGCAACAAGAGGACTAAGTGTTCGCCGAGAACT
AATGCAGAAGAACAGGTTGCATTAAAAGGCACCACGGAAAATGGATTTTTGGAAAAGCATAAGATGGGAAAAGCGAAGCGAGTGAAAGCTACATCAGACGAGTCGAAGATCAATGGATTCTATAGTCCTTCGAAGGAGAAGGGAACTTTCACTTATGCTGATGATATTGGGCCTTTGGGAGAAGCTGCTCTGTCAAAGGT
AGAGAAAGTAGAAGATGGTTTTGATGGGGAACAACAAGCAACTTTGACTCATGATAAGACTATTGCTGCTGCTGATCTTCCTATGGTTGAAGGGATAATCGTTCACAAGAGTAGCCCAACTGTTGGGGAGGATGTATCCAGTGTGCTAACTGAGGCTGAAGGAAACAAAGACCCAAAAGGTCTTGGTACAGAGCCGGAAA
AACCACGGAAAGCATGGGTTTCATGCGACGACTGTAAAAAATGGCGTCACATATCAGTGGAACTAGCTGATCATATAGAAACAACGGGGTCTAGATGGTCTTGCCGTGATAACTTAGACAAGGATTTTGCTGATTGTTCCGTACCACAAGAAAAGTCCAACGCTGAAATCAATGCCGAACTCAATATTTCTGAGATTTCC
AACTGTGACAAAAATGATAATGCAGATGGTCAGGTTGATTCAAAGGCTCTTCACAGGGAATCTAATGAAGTGCGTCAGAAAAATGAAAATGTATGGACACATATTTCTCACAGCGTTTATAAGCACAGGAGCCGAAAGGCTCAAACTATTGACGAGATAATGGTCTGTCAGTGCAAGCCTCCTGAAGATGGCAGCAGTGG
TTGTGGGGATGGATGCTGGAACCGTTTATTGAATATTGAATGTGTTCCTGGCACATGTCCTTGCGGAGATCAGTGTTCTAACCAGCGGTTTCAAAAGAGATCATATGCAAATGTTGGGTGGTTCCGTTGTGGGAAGAAAGGTTTTGGTTTGCAGGTTTTGGAGGATGTTCCATGTGGCACTTTTATCATAGAATATGTCG
GAGAGGTCTTAGATATGAAGGAACATAATGCACGTCAACAAGAGTATGCAAAGCGAAATCAAAAGCATTTCTACTTTATGACACTAAATAGTAATGAGGTTATTGATGCATGTGTAAAAGGAAACCTTGGACGGTATATAAACCACAGCTGCAATCCTAATTGTCAAACGGAGAAGTGGACAGTGAATGGTGAAGTTTGC
ATTGGCTTCTTTGCACTCAGAGATCTTATAAAGGGTGAAGAGGTAACATTTGATTACAATTATGTACGGTTTTTAGGTTCAGCAGCCAAAAAATGTGAGTGTGGTTTTGCTGACTGTAGAGGTTTTATTGGTGGGGATCCTACTACTCCCCAAAATGTGGTAAGTGGGTCGGAAATAGAAGATCCTGAGCCAATAGTTCT
GACCGAAGAATGTGAGGACTTGGCTATGGTTGTTGATATTATCAAGCCATCTCAAGTTGGGAAATTGCAAGATTTCTCTGAAGCTAAGATTCAGATATCTGAAAGGCTTCACTCTGATTCAATAGCAAAAAAAGGGCTTTCTAGTCCTAGTAACGAGGATAAGAATAGTAACGATGAAAATAAAGGCACTGCTAAGAAGC
TGAAACGGTCCAAAGCAGTTTCAACAGTGGAGAAACACATTAGTTCGAGTGCAAAAAGGCTAACAATTAATACAAGTGAGCGTTTCGAAGGAGTGGAAGAGAAGCTTAACGAAATGCTGGATGTGAGTGGTGGAATCGCTAAGCGAAGGGATGTTGCAAAGCATTATTTAAAGCTTTTGGTTTTAACTGCTGCATCGGGT
GATGCTAGTGGTGAGGCATCTGGCAGTACAAGAGATCTTTCAATGGTGTTGGATGCTTTACTCAAAACAGAATCACGTACTGTGTTGATGGATATTGCAGATAAGAACGGTCTGCAGTTGCTTCATAATTTGATTAAGCAGCACAGTAAAGATTACAGAAAAACTCCTATTATTCGCAAACTTCTGAAGATTTTGCATAT
TTTTGCATTGAAGAAAGTCATCACATCAGAACAGATCAACTCTATTCCTTCACGCAAAGGAGTTGAAAGCTTTGAAGAGTCCATTTGTTCCCTCACTTTTCACGCTGACAAGGAGGTGAAGATTGCATCTCGTCTAATCAGAGAGGACTGGGGTATTTCACCTATTGGAAAGTCACTAGAAGGAAAGCAAACACAGGGTG
GATCTCGGGCTACAAAAAGCTACAATTCAAGCTGGAGAAAGGACAAGTTTCCTCCGAATGGAAGAGCATCATCTGTAAACAGATTCAAAGTTCCAGGAAAACATGTGGAAGGTAGTATTACAGATGGTGGACAAGATATAGTAGAAAAAGGTGATATTCAGGTTAGAGATGAAAAAACAAAGAAAAGAATATTTGAGCAT
GATGGTGAATGGAATTCTTCAAATCAACAAATTTCTTCCAGGAAGGGTAAAGAGAAAAGTAATTTAGAGGAGCCAAGGCAGTTCCCACAAAATGAGAAACAATGTTTGGATTCTTTGTCAAAAGATCCTTTGCTTGGAGATCCTTCAAATGTTCTGGAAGACAATGGCTGTGGACCTTTTTCTCATTCCAGCATTTCAGA
GGGAGGAAAGTGGACCCAAGGTTCAAGGAGGAACATCCATTACAACACTGGTAGAGGGCATCCTAGGTACTATTCATCTAGCAGGAGTACTCCTTGGCATGATACACCGCCTCATAAAACTGGACCAAGCCCTGCAGCTAACCCAAACATGTTAGACAGGAAAATTGAACCACAGCACGGGGCCCAACTTAACACAGTTA
CAACAACGAACTCCAACCAACCTCTGAATAGTTTATCAGCACCAACATTGGTGGGAACTGTTTCAAGTTTGCCACAAGGAAATGGAGTTGTAGATAGACCAACCGGAGATATATTATTTCCGAATACGAATGAGGCAATTGGTGTACCTCTTGAAGTGTTTGATTATGTTCATGGCTTAACATTCCGCAGGCCAATTGAG
AACAAAGCTACTAGAGGTCATCATCCAAGAGAAGTTGGGGGAGTAGCGAGTGCCACTCCTTGCCGTATCCCATGTGAGCACTTCTCAATGCAACCGACAACAAATACAATGCAGCCATTTCATGGTTCAGGAGGCCCAGCTTCTGTTTATGGTTTTCCTCTTGATCCTGCTGCACATAATTCACATCCATTTGCTTCGGC
TTTGACAGCACCAGTCCGAGGTCCATCGAATCTACATTCAGGAATCAGGCCACCTCAATTCCACCATCTGTCTCAGTTGCAAGCCAATCAAATACATAGGCATCGTTTCATACATGGATCTGAAAAGAGCGATTGGGCTGTAGTGGAACAAAATAATATACTGGAACCAGAGCCTCCTGTTCCAGGCCTTTCACCACCAC
ATTTGCCAGAAGGAAACTCAGTTCATTATCATTCTCCTTTCGGTCCCGTTCATGAAATAAACAAAATGCGTGATATGTTTGCTAAAAAGGATTTACCCTATAAGAGAGATAGCTGTTCAATATTACGAAACAATGgtaataatcaggatctatccccaaatctaagtgcacaggattctgttcgtcttaattcaaattgt
gatactgaaaatcagtcagcaaaaacatgcattttagatggcttgtctagccaaatgtcatgtcctgttgacggcaacactgctagccatgcatctatgaatacagccattgattgtagttctcaaagatctagtccattgtgcatggcagGTGTTTGTCTGAATCTAGATGGGAAGCATTTTGCAGAAACGGTAGCTTC
CTCAAATAATAATCATTCAAAGTTTAGTTACCCTTGTGACTTGAAGGGGGCTAGGCAAAACAATTTTTCTTCAAAACATGACGTGAAAGTTGAAGCATGTGGACCAATTATTGATGGACAGAACTTTATTCGCAATGGAGAACATAGAGAAATCAGTAAATTTTCAAACAAATCAATTGAGAGTCTTAGGACTGATAGAG
ATTCCCATTCTAGTCATGACAAAGGTATGCCAAGGAGTTTTGATGCAGCAGGTAGAAACTTGGAAATTCAACAGAAATACCCATCGAATAAGGTGCTTGGGTATGTTGAAGACGAAAGCACTGATCGAGGCACTCAAGATACAAAAATAGATAGAGATTCCTGTCCAGATGGAGAAAAGTATGCACCTCCTGTGGAAGGA
GGTCGATCTTCAGATATTGGAAAACTTGAATGATTTGAATTGTTGTTCCAAATTTAATTGCTGGGCTCGGTACTATAAAATGTGGATTATTATGCAGGGAGTTGAAGCATGCAGGAAGTCCATTTCTTCCAGCAGTCAAGCTTCAAGATAATTAGAGGGAGTTGTCAATCTCTCAAGTTCCTTTTGGTAGATGTCACAAC
AATCATTCTTTGAAGTAAAACTCAGTATTGTAACTGGGTACTTCCATCTTTGTAATTTATACTCACAGATGTACCAAGTGCATTATGATGAAATAATGTATTTCATTTCGGAATATACAATGGAAAATTTAGATCGAGATCAAAGTTGCATGACGAGTATTTGAGATGCTTCATTCGTTGCCATTGTACACGATTTTAGA
TATTTGTTTGCATATTTTTTAATCCATTGAGAAGTTCCCAAATCCTTATTGTTGTGCAGGATGCACCTATTCATATCATGCTGTGAATATCGCTTCTGCCTATTATGAGCTCTGGTATGCGAAATAACATAGTGAATATGTATTATTTTTAGCAAATCCTAATAATGAATTGGAGGAATCTTCTTAGTAAGCATGCTTGT
AAGCTTTTGCAATTAATACCTGATGATTGAAG