sp|Q9FJL0|SMC4_ARATH ----> Structural maintenance of chromosomes protein 4

Intron 1 GTTTATATTA ... TTTCTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.81	16	3	7
A2	10	9	1	1
A3	13.04	10	0	3
A4	17.65	14	2	4
A5	28.21	14	7	4
A6	20.97	49	4	22
A7	20.39	41	5	16
A8	19.05	51	7	17
A9	21.15	41	9	13
A10	20.63	25	3	10

>TRINITY_DN46675_c0_g1_i7 from sample A10 / Example spliced isoform

TTCCCATTTCCACAGCTATTGGTATTCCCAGGCAACCAAATCGTGGGATATTCTTATTGCAACTCTTGTTAAACTGTCTGCTTGTAATCAGGTTGAAGCCAGTCTACAGACAAAGCAATACTTGTCTGAGGCACGTATGAGTTTACAGGAGATGCTTCAAACCCTTAGTGTGCAAGAGAACACCCTTGCAACAATATCTG
TGGTCAGTGATGCAGCATATGCTTGGGGTATAATGGGTCGGTTTACAGAGATGATACATAAAAGTATTGAAGAAGACCCTCTGACAGTATTAAAACTACAATGCTTGTTTCTTAAGCTGCGATCTATGTTAGATATACCACTGCTACGGATATCACAAAGCAACAGCGCAGATCTGTTTTCTGTTTCTGAATATTACTCA
TCAGAACTTGTAACTTATGTGCGTACAGTACTGGAGATAATCCCTATCAATATTTTCAAAATCCTCAATGATATTGTTGCGAAGAAAACCAATAGGTTACATGACTTGCCGAGTCGTATTGAAAAAGCCAGTTTTCGTGAGTTTGCTCAGTTGGATGAGCGATATACTTTAGCAAAGGCGACACACAAATTAGCTGTTTT
CTCACAGGGAATACTGGCAATGTCAAAAACATTCATTGGGGTTATTGAGTTGGATCCTAGGCAACTGCTGGAGGATGGAATACGCAAGGAACTTGCAAGAGAAATTGAGAACACATTTAACAACTTCATTGTTTCCTCAGCTGTCCGAGCAGAAGAATTTGAAGAAAAGTTAGAGACTCTGTTGCTTTCAATACAATCAC
AACATCAATTAATGGAGTATTTTCAGGATTATGGTCATGTCCACGGTCATCAAATATGGCAAGAAGAGTCCATTCAAGTAGTCTCTCATCAGACGGAGCTGGAATGCAATGCATATCTCAAGAGGAAAACACAGGACTTGCGAAGTAGGTGCTTGAACATCAAGGATCTTTCAAGTGTGAGGACTTTTATTGGGCGATTG
CTGCAGCAAATTCTCCATTTGACTGATCCATCCCAGTCAATGTATCTTGCTCCTATGAGTGGGTGGTTTGATGCAGGAGGCAAAGAGTTGCTTGGTTTACGGTCTTTCAGATTGCTTGAATCCTGCTTAGGACCTGCAGGGATGACTGGCATTGATCGCCTCTTAAGTTTTATCATCACGAGAAGCCTTCAATGTGCACT
AATTGATCTACACAACCAGCTGGGTAAAAGCTATCTGGAGCAACTAGGAAGTCTGGATGCTGCATTAGCTCCACCTGCTTCAATCCCTCATTTGGGCGTTTCTGTTTATAAAAAGATTGAAATCATAAATTCAACATGGGAACCATGGGTTGAATGTTTGGCCCATATTGGGCAGCTACAATTATTGCGATGCTTGCTTG
CATCACAGTTAAGATCAGCATCTAAGGCAGAAGCAAGCACCATTTCATTTTCAGTAGAGGGGATTAATATTGCAGCAGTCCGTGAGATTAAGAGTTTTAACCAGAAAGGAAGCTCAGGAGTAGCATTGGAAGAGAAGCAAGAAGAAGTTAGAAGATATCTTAGAGAACTAAGAAAACAAGTGCATTTGTGTGGCTTCTAT
TCGCCCCTGCAAGCTATATATATTACTGCTGAGCCACCAGATTACATTGCTCTTTGCCTTTTCCTTGTCACAATCTCACAGTTGTCCCGATATGTATTGGACACACATCTGGGCACACTAACAAGCCGGACAAAGAAGGCAGTGCTTGATTTCTCCCCTCTGGTTATAGGCTTTGGTACATTCCTGAGGCAGTTCCATCC
TTCGCAATCGGCCCTTTATGTAGAGTACATGAGCCAGTATGTGCGAACACAAATTGTGAGCTTACCGGTCTCTCCAAATTTCAATGAGCTGCCTAAAAGGGGACCAGATGCAACATCAGAGGTCTCTAAAGCTGTGTTTTGGCTACTGTACTTCTGCAAGTATATGAAAATTTCTCATGATATTTTGGATTCATGCTTAC
CACCACTCATGTTCAACAATCCTACAGGATAAGATAAGCCTGATCACATAAAAATTTTCAGAAGTAGTCTTTGAATGTATTCAAGCCTTGTGTGTTATAGAGGGATTTAGATGAGGTGGGTTTTCATCATTTCATAGTAAATGAGAATAAAGAGCTTTATCTTCAAGAAGGTCATTGTATATGGAGGAGCTATTTTGTGT
CTATCTCCTCCACCGGCCTTCTCTTTCGACAATGCTTAGAACTAAATTTAAATTAAGCTATAGAAGCCCCCTGAAAGGTAACAGTAAGCAAACTTTTGTTTCCAGATAGGTTAAGTTTAATTACTTTTTGAGCTGGCAAAGATTATGACTCATGTTTATTTAGGACTCATGTTCTCTTCACGGCTTGAGAAATCTGCACC
AAGCTACTTAAAAATTTTCTGATAGTGTTCTAACTGGTTATCCTGTTAGTCCACGTCCTCAAGAGGATAATTCGATTGTTGTACTTGTCACAGCTGATCAGAGTCACTGGATTTTTTCTTAGAGTTTCTTAAAGTTGGTGATTTGTATTAAAAGTTTTTAGTTCATGCAATTAAACCATTTTGGCGAAAAATTAGTTGAT
GCTCTTTGATTAGACAAATTAGACCCTCTTCTATGGATCTATTTTCTTAAACTATAATGTTCGATTACTAGATAAACTCTACACTTGTATGTTACACTTGTACTTGTCACAGCTGATCAG

>TRINITY_DN46675_c0_g1_i8 from sample A10 / Example unspliced isoform:

CTCAATTCATTTACATTGCCAACACGAATAGGCATAAACCGCATGAATTTCTAAACAGTTCATGTTCAATGCCCGAGATGGGGTGTTTAGACGATTTCGATTTCGATTGCGGCTTAGGAGTAGACGCAATCTGATAAATTTCGTGAGCAAAACCGCATGAATTTCGAAACAACCCATGTTCAATGGCTGAGATGGGGTGT
TTAGACGATTTCGATTTCGATTGCGGCTTAGGAGGAGACGCAGACGGATCAATTTCACAACTATTAAAGCTGGTGAGCAGAGCTCAGGCGCTGATTGCAGAGCTGCTGAGATTATCTGATCGTGTTCCCTCTGCCTTCACTGACTCCCGCTACGCTCCCATTCTCTTCGATCTCAAATATTTCAAATCTCCAGAGGTTTT
TGAGGAGCTAGTTGAAGTGAACTCTGATTTGGTTGCTCTTGATGATGAATTTCGAGAAAGCTTTTCATTTATTTTGGAGAGGTTCTTTCTTCTATTTGATGGTATTGTTCGATACTATCAAGATCTGGTACATTATCTTGATGATTTGCAGGAAGGAGTGTATGTGCAAAGTACTATAGAGAGTGTTATGGAGAATGAGG
ATGGGCGACAACTATTAGTGGAAGCCTTAGTTCTTCTTGGAGTTCTGTTACTCTTGATGGAGCACCGTTTGAATGGTGGTGTGAGGGAGCGCCTGCTTGTTGCATTTTTTCGTACCAAGCGTTCTTCAGAAGTTTCAAATATTGATCTGTTATGCACGTTATGTCGTACATTTTCTCCTGTATCTGCCTCACCTTTATCA
TCTGTAACCACTTTTGTTCCTTTTCGTCAAGCTTCCCCATCACCAGTGACGCCTACTATGATTTTAGTTCAAAAACCAGAAGACTTGTTTGGTAGGTTCCCTATATGCAAACGGATTGTGGACGTTCTGATTAGTCACTTGCGCACAGATGATTTGTACAATCAAGTTCGCCACTATCCAAACCCTGATCAGTGGAGCAC
TGCATTATCGTCACAAGCTGGCTGTGTATTTATACTATTATGTTATTCTCCAGAACTTCTTACCAGTGGATATGTAATGAGGGAAATTGTGGAAAGATATTTTAAAGATGACTGGATCCTTCCAGTCTTCATGGCATTCACTGTGGATCTATCTTTTTCATGGGAAAGATACAAGGCTGCAAAGGCTGCATTGTCCTCTA
CTCTTGCACCAGCAACGATTCGTGATCTTTCTGACAAACACTACTCCAAGGTTAAGAATCTGTTAATGGATTTGAAGGGTCTTCTGTCAGATGGTGTTTTAACCCAAGATTACGTAATGAATAATACTCAATATCTGCTTTCTTTTATGAGGAACTGTAATGTCACTCTTCGCTGGCTTCTACTACATCGATCTACTGTG
AACAAAAAAATTCGAGACTCTATCATTGCTGTGGGAAATAGTCACAATGTGGGTGAAGATGAGTTGCTGTCATTGTTCTTAGAAACTGCAAGGCTAGAGTTTGAGTTAAAACGGGTGTATACTGAACTTCTGGAATACAAGGAAACTCACTGGCAACAGTGCAGGACTCGTGCTGCAGAGTGCATGCAGGAACTTTCTGA
TTTCTTCTCTGGATCTAAAATTTTGTCAAAGAAGATTAAAGACGAAAACTTACAGCAGTGGTTCAAGCAAATGTCCATACAGGTAGGTTCTCTTGACTACAAGACAACCAGAAATATAAGTCGAAAGGTTCAACATATGATCTCTGCATTAAAGGAAGCGGAGCAATTTCACCAGGTTGAAGCCAGTCTACAGACAAAGC
AATACTTGTCTGAGGCACGTATGAGTTTACAGGAGATGCTTCAAACCCTTAGTGTGCAAGAGAACACCCTTGCAACAATATCTGTGGTCAGTGATGCAGCATATGCTTGGGGTATAATGGGTCGGTTTACAGAGATGATACATAAAAGTATTGAAGAAGACCCTCTGACAGTATTAAAACTACAATGCTTGTTTCTTAAG
CTGCGATCTATGTTAGATATACCACTGCTACGGATATCACAAAGCAACAGCGCAGATCTGTTTTCTGTTTCTGAATATTACTCATCAGAACTTGTAACTTATGTGCGTACAGTACTGGAGATAATCCCTATCAATATTTTCAAAATCCTCAATGATATTGTTGCGAAGAAAACCAATAGGTTACATGACTTGCCGAGTCG
TATTGAAAAAGCCAGTTTTCGTGAGTTTGCTCAGTTGGATGAGCGATATACTTTAGCAAAGGCGACACACAAATTAGCTGTTTTCTCACAGGGAATACTGGCAATGTCAAAAACATTCATTGGGGTTATTGAGTTGGATCCTAGGCAACTGCTGGAGGATGGAATACGCAAGGAACTTGCAAGAGAAATTGAGAACACAT
TTAACAACTTCATTGTTTCCTCAGCTGTCCGAGCAGAAGAATTTGAAGAAAAGTTAGAGACTCTGTTGCTTTCAATACAATCACAACATCAATTAATGGAGTATTTTCAGGATTATGGTCATGTCCACGGTCATCAAATATGGCAAGAAGAGTCCATTCAAGTAGTCTCTCATCAGACGGAGCTGGAATGCAATGCATAT
CTCAAGAGGAAAACACAGGACTTGCGAAGTAGGTGCTTGAACATCAAGGATCTTTCAAGTGTGAGGACTTTTATTGGGCGATTGCTGCAGCAAATTCTCCATTTGACTGATCCATCCCAGTCAATGTATCTTGCTCCTATGAGTGGGTGGTTTGATGCAGGAGGCAAAGAGTTGCTTGGTTTACGGTCTTTCAGATTGCT
TGAATCCTGCTTAGGACCTGCAGGGATGACTGGCATTGATCGCCTCTTAAGTTTTATCATCACGAGAAGCCTTCAATGTGCACTAATTGATCTACACAACCAGCTGGGTAAAAGCTATCTGGAGCAACTAGGAAGTCTGGATGCTGCATTAGCTCCACCTGCTTCAATCCCTCATTTGGGCGTTTCTGTTTATAAAAAGA
TTGAAATCATAAATTCAACATGGGAACCATGGGTTGAATGTTTGGCCCATATTGGGCAGCTACAATTATTGCGATGCTTGCTTGCATCACAGTTAAGATCAGCATCTAAGGCAGAAGCAAGCACCATTTCATTTTCAGTAGAGGGGATTAATATTGCAGCAGTCCGTGAGATTAAGAGTTTTAACCAGAAAGGAAGCTCA
GGAGTAGCATTGGAAGAGAAGCAAGAAGAAGTTAGAAGATATCTTAGAGAACTAAGAAAACAAGTGCATTTGTGTGGCTTCTATTCGCCCCTGCAAGCTATATATATTACTGCTGAGCCACCAGATTACATTGCTCTTTGCCTTTTCCTTGTCACAATCTCACAGTTGTCCCGATATGTATTGGACACACATCTGGGCAC
ACTAACAAGCCGGACAAAGAAGGCAGTGCTTGATTTCTCCCCTCTGGTTATAGGCTTTGGTACATTCCTGAGGCAGTTCCATCCTTCGCAATCGGCCCTTTATGTAGAGTACATGAGCCAGTATGTGCGAACACAAATTGTGAGCTTACCGGTCTCTCCAAATTTCAATGAGCTGCCTAAAAGGGGACCAGATGCAACAT
CAGAGgtttatattatagcagtgacttcagtgtgattcatccctagtgttttctttaatagaatgttcatccatatgatacatttagattaactgcatgattaattatgttctctggtgttatatcatccattgcaatagtaattcatttgcattattttctttcagGTCTCTAAAGCTGTGTTTTGGCTACTGTACTTC
TGCAAGTATATGAAAATTTCTCATGATATTTTGGATTCATGCTTACCACCACTCATGTTCAACAATCCTACAGGATAAGATAAGCCTGATCACATAAAAATTTTCAGAAGTAGTCTTTGAATGTATTCAAGCCTTGTGTGTTATAGAGGGATTTAGATGAGGTGGGTTTTCATCATTTCATAGTAAATGAGAATAAAGAG
CTTTATCTTCAAGAAGGTCATTGTATATGGAGGAGCTATTTTGTGTCTATCTCCTCCACCGGCCTTCTCTTTCGACAATGCTTAGAACTAAATTTAAATTAAGCTATAGAAGCCCCCTGAAAGGTAACAGTAAGCAAACTTTTGTTTCCAGATAGGTTAAGTTTAATTACTTTTTGAGCTGGCAAAGATTATGACTCATG
TTTATTTAGGACTCATGTTCTCTTCACGGCTTGAGAAATCTGCACCAAGCTACTTAAAAATTTTCTGATAGTGTTCTAACTGGTTATCCTGTTAGTCCACGTCCTCAAGAGGATAATTCGATTGTTGTACTTGTCACAGCTGATCAGAGTCACTGGATTTTTTCTTAGAGTTTCTTAAAGTTGGTGATTTGTATTAAAAG
TTTTTAGTTCATGCAATTAAACCATTTTGGCGAAAAATTAGTTGATGCTCTTTGATTAGACAAATTAGACCCTCTTCTATGGATCTATTTTCTTAAACTATAATGTTCGATTACTAGATAAACTCTACACTTGTATGTTACACTTGTACTTGTCACAGCTGATCAG

Intron 2 GTTCATAATA ... TCATTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	34.43	20	7	14
A2	41.18	5	4	3
A3	27.78	13	4	6
A4	15.15	14	2	3
A5	77.78	1	0	7
A6	25.93	10	4	3
A7	0	21	0	0
A8	9.68	14	1	2
A9	20	18	3	6
A10	38.1	13	13	3

>TRINITY_DN41372_c0_g1_i5 from sample A7 / Example spliced isoform

CTCATTCACGCGACACGAAAACGGTTAAAGCTCGAAAACCGTCGGCGGCAGCTTTTCACACAGGACCGAACGACCTACCGCCCTTACAATTTCAATTCTTAGTGTAGCTGACCACAGGACCGAACGACGTACCGCCCTTATATCTTCCCTCCATTCACAATGTAGCTGACCACAAACGTTTCATGGAAAGGGAGCTAAAA
ATTCCACTGAAGGGGCCATGACAATACACCAACCTACCACATCGTCTGCATATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCC
AAGACATCGGCATTGCGAGTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGCCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACATTAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAA
GGAAATGCTGCAAGAGATAAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGCATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATG
ACATCCAGGAAAATATTCTACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATGCATTCCTGTCACAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGT
AAGATGAAAGAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCA
TCTTGACCAAGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAACTCTAAGCAGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGG
AGCAGTTAATTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAA
CCTAGGCTTGAGAGACTAAGTGCTGAACTTGGGATACTAAGTAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGATCT
GTTGCGAATATGGGAGAGTCATGGAAACATTTCTAGATTTTCTCGCATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTCAGACAACAAAAAAGGGTTCAACAGAATTATCCCGAGGGAAGTGTAATTTTGCCACTAGAACATCTGGATTATGATGTAAAATTTGAAAAAGCAATAAAGAGAGTCTTTGGAGGTT
ATGTTATTTCTGCATCAGATGAAGTTGCCAAGGATTTGATCCTTCAGCATGGTATTTGGAGTGTCACAATTGATGGCAAGGTAAGTCGTTTAGGCTCTGTAACAGGAGGATGGCGGGGCAATTCAAAAAGCAACTATGTTGAAGCTAAATTTGAGCACGACCATTTTGATGCCAAGTTGAATTCCGTAAACACTCTCCTT
ACAAGTTCAAGAAAGGAAATGGAAGAATTGGAAACATCGATGCTCAAATTTGAAGCTCTCAGTAAAGAGAAGGAAGAGTTTGTCCAAGAAATCAATAGTATAGAGTAGCAGGTGCTATTCTTAGTTTTGATGAGAACTTTGATGGTCAGTGACTTCAGATTCATAGCTAATGTGATTAATTTTGCATCTAGATCAAGGAC
CTGGGAAACAATCTAAATAGGCAGAAGATTAAGCTTGAAGAGAATCAAGATCTCTCTGCCTTTCTTAGAAAGGAGATGGAAACCAGAAGAAGACAATTGGATGCTGTGAAACTAACAAACCACTCCATTGAATCTGTTAAAGTTCTGGATCAGGCACTTCAAACGGCAAAGGATGAAGAATTAATTCTTCATGGTATTCT
AGATGACACGCTGTACAGGCAAGAGAAGATCAGGGCAGAGAAAAAGGAGTTGCAAGATGAAGTGTTAAAGATGGATGAAATGATCAAAACTGTTCATGTCTACGAGGATGAGATTCAACTTCTTGCAAAACAACTTGCAATAGTAGAAAATAAAATAGAAGATGCAAGGAAAGAAGAGGAAGAGAGATCTTCAGAATTTT
CTGCCCAGACAGAAGCCATGAATCACGACAAGCTTGTTATCTCTGAAATGCAAGGGAATATCCAATTGATAAGGAACTGCATATTAAAGCTAAGGTCAGATTGTGGAAAGGCTGAAAAGGAGCTGGAAACCTTACCACTAGCAGAGGTAGATTTCTCTTCTCTGTGCAAAGAGAAGATTCTAAATAAGAGCGATTATTAC
AAGAAGAAGAGAAAATTGAATAGTATGCTGGAAGATCTGAAGAAGCTAAAACTACAAGAGACACAGATTTCCCTTGATGAAAAAGTTGCTTTCAATGAGCAGATGGGGAAACTTGAACTCTTTAAAGAGAGATGGATATCTATAGCAGAGTCTATAGACATCTTGACAGAGGGCATTGAAAATACAAGAAGCAAGGTGCA
AATTGCTAATGAAACTACTTATAAGGAAATCCGGCATTCTTTTGTAGATTGCTGTAAGGTGTTTTTGCCAACAAAGAGAGTTGACCTGATCAAAACTGGACAGTTTGTGGAGGATGGAATTAAATTTTCTTTCTCTAATGATAAAGAAGGAGCTGAATGTGTTTCCGAGGAATGGAAGAACAACCTGGAAGAACTCTCAG
GTGGCCAGAAGACAGTTCTAAGCCTTGCCTTTATTCTAATGGTGGCAAAATGCAGCCAGTCCTCTGTTTATCTCATGGATGAAATCGATGCAGCGTTAGATGAACAGAATCAACAAAGTGTGGCAAAGTTGATAAAAAGTGTTATTGGTGAAGATAATCAGGTAATCTGTGTGAGTCACAATATTACCTTCCAGAGACAT
TGTGATAGGATTATTCAAGTGAGCAGAGTAGATGGATGCACGAAACATATTCAAAGCCACACTGTCAGCAAAAGCCAGCTTTCAAAGAAGACCAGGATACAGAACAATTAATTCATTCATGGCAACACCATGGAGCTGGCATTTTGTAATGCCTGTTGGAAACTGATACTACATTAGTGCTGGCAACAATGTAGAAATCA
TCTTCCTTAAATATAGCTCAACCTGGAAAGTTTCAGTTGTATTAAACCAGAACAAGGTCTCTCAAGGACAAGGACGCTAAAGGACATTCACACAAACCTAATGCTATATTTTGCTGGCAACATTGTAAAAGATCTTATTTTTAAATAGATATCCATTTTTTTTTTGCGACATGGGTATTCACAGAATAAATATGGAGGAC
ATACATATTCAATTGAAATCAGGTCAGTTCAAACTCCATATGGTATGAAGCAGCACTGTTAATTACAGGCTAGGATCTTAAGGAGGCCAGCCTTTCAATATCATTGTTAACTTTCTC

>TRINITY_DN41372_c0_g1_i2 from sample A7 / Example unspliced isoform:

AGCTAAAAATTCCACTGAAGGGGCCATGACAATACACCAACCTACCACATCGTCTGCATATATCAAATCTCTCAGgttcataatattatggttacctgaaagaatattttgtgctcgtggcatttttctgacataaattgcatgcaaatttcattaccagAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAG
TTCACGTTTACAAAAGGAATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCCAAGACATCGGCATTGCGAGTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGCCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACA
GGAGCGTCTTATAACATTAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAAGGAAATGCTGCAAGAGATAAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTAT
CTATCATCTCTGATGCATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGGAAAATATTCTACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATC
TCAAGTCAGCTGCATGCATTCCTGTCACAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCA
GCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAACTCTAAGC
AGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTA
CTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTAAGTGCTGAACTTGGGATACTAAGTAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCA
AGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGATCTGTTGCGAATATGGGAGAGTCATGGAAACATTTCCAGATTTTCTCGGATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTCAGACAACAAAAAAGGGTTCAAC
AGAATTATCCCGAGGGAAGTGTAATTTTGCCACTAGAACATCTGGATTATGATGTAAAATTTGAAAAAGCAATAAAGAGAGTCTTTGGAGGTTATGTTATTTCTGCATCAGATGAAGTTGCCAAGGATTTGATCCTTCAGCATGGTATTTGGAGTGTCACAATTGATGGCAAGGTAAGTCGTTTAGGCTCTGTAACAGGA
GGATGGCGGGGCAATTCAAAAAGCAACTATGTTGAAGCTAAATTTGAGCACGACCATTTTGATGCCAAGTTGAATTCCGTAAACACTCTCCTTACAAGTTCAAGAAAGGAAACATGGCATATTCCAATCTAAAGCTCTTTATTTGAGTGGGAAAAAATGAATGCAGAAAATGTAAGTAGGGTAGTTCAATTTGGAGATTA
AGGATATCTTCTCTAATGGGTTATCAAATGCCTTCTTGTGAGTTGGAGCCGTTTTCATAGTTGGCTAGCCCGATGAAATGCTTAGTGTAGGTGCTCTCTCTCCCTAAGTAGTAGTTAGCTATCCAGATTGAATGCCCAACATAGGTGCTCCCTTTCCATACGTAGCATTTGGGCTTACTCAATTTATTGTTAGAAATGAT
GGTTTTCTCCTCACATAAGATTGACCATGGTTCAATATATATGTCAAAAGCTTTCTGACAAGCCTTCATAGATATAGTCAAGGGTAACCCTCACTTTTAAATTTCTAGTTTCCATCCTCTTCTTCTTGTCTCTATTTTAAATGTGAAATTTTCGAAGATTTGATTTATAGGAATCTTATTAAAATGTGCATGAGTGCATA
GGGACACAAATTAGCAAAACAAATTGCATGATGACACCAAAAGTAAC

Intron 3 GTGCTATTCT ... TTGCATCTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	54.55	5	6	6
A2	38.89	11	6	8
A3	78.72	5	19	18
A4	100	0	7	5
A5	80	1	5	3
A6	60	1	3	0
A7	61.4	11	20	15
A8	77.78	1	5	2
A9	75	3	12	6
A10	75	2	7	5

>TRINITY_DN111031_c0_g1_i8 from sample A2 / Example spliced isoform

AAACGGTTCAAGCTCGAAAACCGTCGGCGGCAGCTTTTCACACAGGACCGAACGACCTACCGCCCTTACAATTTCAATTCTTAGTGTAGCTGACCACAGGACCGAACGACGTACCGCCCTTATATCTTCCCTCCATTCACAATGTAGCTGACCACAAACGTTTCATGGAAAGGGAGCTAAAAATTCCACTGAAGGGGCCA
TGACAATACACCAACCTACCACATCGTCTGCATATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCCAAGACATCGGCATTGCGA
GTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGGCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACATTAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAAGGAAATGCTGCAAGAGAT
AAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGCATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGGAAAATATTC
TACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATGCATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAG
CTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACA
AAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAATTCTAAGCAGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCA
ATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTA
AGTGCTGAACTTGGGATACTAAGTAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGATCTGTTGCGAATATGGGAGAG
TCATGGAAACATTTCCAGATTTTCTCGGATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTGAGACAACAAAAAAGGGTTCAACAGAATTATCCCGAGGGAAGTGTAATTTTGCCACTAGAACATCTGGATTATGATGTAAAATTTGAAAAAGCAATAAAGAGAGTCTTTGGAGGTTATGTTATTTCTGCATCAG
ATGAAGTTGCCAAGGATTTGATCCTTCAGCATGGTATTTGGAGTGTCACAATTGATGGCAAGGTAAGTCGTTTAGGCTCTGTAACAGGAGGATGGCGGGGCAATTCAAAAAGCAACTATGTTGAAGCTAAATTTGAGCACGACCATTTTGATGCCAAGTTGAATTCCGTAAACACTCTCCTTACAAGTTCAAGAAAGGAA
ATGGAAGAATTGGAAACATCGATGCTCAAATTTGAAGCTCTCAGTAAAGAGAAGGAAGAGTTTGTCCAAGAAATCAATAGTATAGAGGAGCAGATCAAGGACCTGGGAAACAATCTAAATAGGCAGAAGATTAAGCTTGAAGAGAATCAAGATCTCTCTGCCTTTCTTAGAAAGGAGATGGAAACCAGAAGAAGACAATT
GGATGCTGTGAAACTAACAAACCACTCCATTGAATCTGTTAAAGTTCTGGATCAGGCACTTCAAACGGCAAAGGATGAAGAATTAATTCTTCATGGTATTCTAGATGACACGCTGTACAGGCAAGAGAAGATCAGGGCAGAGAAAAAGGAGTTGCAAGATGAAGTGTTAAAGATGGATGAAATGATCAAAACTGTTCATG
TCTACGAGGATGAGATTCAACTTCTTGCAAAACAACTTGCAATAGTAGAAAATAAAATAGAAGATGCAAGGAAAGAAGAGGAAGAGAGATCTTCAGAATTTTCTGCCCAGACAGAAGCCATGAATCACGACAAGCTTGTTATCTCTGAAATGCAAGGGAATATCCAATTGATAAGGAACTGCATATTAAAGCTAAGGTCA
GATTGTGGAAAGGCTGAAAAGGAGCTGGAAACCTTACCACTAGCAGAGGTAGATTTCTCTTCTCTGTGCAAAGAGAAGATTCTAAATAAGAGCGATTATTACAAGAAGAAGAGAAAATTGAATAGTATGCTGGAAGATCTGAAGAAGCTAAAACTACAAGAGACACAGATTTCCCTTGATGAAAAAGTTGCTTTCAATGA
GCAGATGGGGAAACTTGAACTCTTTAAAGAGAGATGGATATCTATAGCAGAGTCTATAGACATCTTGACAGAGGGCATTGAAAATACAAGAAGCAAGGTGCAAATTGCTAATGAAACTACTTATAAGGAAATCCGGCATTCTTTTGTAGATTGCTGTAAGGTGTTTTTGCCAACAAAGAGAGTTGACCTGATCAAAACTG
GACAGTTTGTGGAGGATGGAATTAAATTTTCTTTCTCTAATGATAAAGAAGGAGCTGAATGTGTTTCCGAGGAATGGAAGAACAACCTGGAAGAACTCTCAGGTGGCCAGAAGACAGTTCTAAGCCTTGCCTTTATTCTAATGGTGGCAAAATGCAGCCAGTCCTCTGTTTATCTCATGGATGAAATCGATGCAGCGTTA
GATGAACAGAATCAACAAAGTGTGGCAAAGTTGATAAAAAGTGTTATTGGTGAAGATAATC

>TRINITY_DN111031_c0_g1_i10 from sample A2 / Example unspliced isoform:

AAACGGTTCAAGCTCGAAAACCGTCGGCGGCAGCTTTTCACACAGGACCGAACGACCTACCGCCCTTACAATTTCAATTCTTAGTGTAGCTGACCACAGGACCGAACGACGTACCGCCCTTATATCTTCCCTCCATTCACAATGTAGCTGACCACAAACGTTTCATGGAAAGGGAGCTAAAAATTCCACTGAAGGGGCCA
TGACAATACACCAACCTACCACATCGTCTGCATATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCCAAGACATCGGCATTGCGA
GTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGGCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACATTAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAAGGAAATGCTGCAAGAGAT
AAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGCATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGGAAAATATTC
TACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATGCATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAG
CTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACA
AAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAATTCTAAGCAGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCA
ATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTA
AGTGCTGAACTTGGGATACTAAGTAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGATCTGTTGCGAATATGGGAGAG
TCATGGAAACATTTCCAGATTTTCTCGGATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTGAGACAACAAAAAAGGGTTCAACAGAATTATCCCGAGGGAAGTGTAATTTTGCCACTAGAACATCTGGATTATGATGTAAAATTTGAAAAAGCAATAAAGAGAGTCTTTGGAGGTTATGTTATTTCTGCATCAG
ATGAAGTTGCCAAGGATTTGATCCTTCAGCATGGTATTTGGAGTGTCACAATTGATGGCAAGGTAAGTCGTTTAGGCTCTGTAACAGGAGGATGGCGGGGCAATTCAAAAAGCAACTATGTTGAAGCTAAATTTGAGCACGACCATTTTGATGCCAAGTTGAATTCCGTAAACACTCTCCTTACAAGTTCAAGAAAGGAA
ATGGAAGAATTGGAAACATCGATGCTCAAATTTGAAGCTCTCAGTAAAGAGAAGGAAGAGTTTGTCCAAGAAATCAATAGTATAGAGGAGCAGgtgctattcttagttttgatgagaactttgatggtcagtgacttcagattcatagctaatgtgattaattttgcatctagATCAAGGACCTGGGAAACAATCTAAAT
AGGCAGAAGATTAAGCTTGAAGAGAATCAAGATCTCTCTGCCTTTCTTAGAAAGGAGATGGAAACCAGAAGAAGACAATTGGATGCTGTGAAACTAACAAACCACTCCATTGAATCTGTTAAAGTTCTGGATCAGGCACTTCAAACGGCAAAGGATGAAGAATTAATTCTTCATGGTATTCTAGATGACACGCTGTACAG
GCAAGAGAAGATCAGGGCAGAGAAAAAGGAGTTGCAAGATGAAGTGTTAAAGATGGATGAAATGATCAAAACTGTTCATGTCTACGAGGATGAGATTCAACTTCTTGCAAAACAACTTGCAATAGTAGAAAATAAAATAGAAGATGCAAGGAAAGAAGAGGAAGAGAGATCTTCAGAATTTTCTGCCCAGACAGAAGCCA
TGAATCACGACAAGCTTGTTATCTCTGAAATGCAAGGGAATATCCAATTGATAAGGAACTGCATATTAAAGCTAAGGTCAGATTGTGGAAAGGCTGAAAAGGAGCTGGAAACCTTACCACTAGCAGAGGTAGATTTCTCTTCTCTGTGCAAAGAGAAGATTCTAAATAAGAGCGATTATTACAAGAAGAAGAGAAAATTG
AATAGTATGCTGGAAGATCTGAAGAAGCTAAAACTACAAGAGACACAGATTTCCCTTGATGAAAAAGTTGCTTTCAATGAGCAGATGGGGAAACTTGAACTCTTTAAAGAGAGATGGATATCTATAGCAGAGTCTATAGACATCTTGACAGAGGGCATTGAAAATACAAGAAGCAAGGTGCAAATTGCTAATGAAACTAC
TTATAAGGAAATCCGGCATTCTTTTGTAGATTGCTGTAAGGTGTTTTTGCCAACAAAGAGAGTTGACCTGATCAAAACTGGACAGTTTGTGGAGGATGGAATTAAATTTTCTTTCTCTAATGATAAAGAAGGAGCTGAATGTGTTTCCGAGGAATGGAAGAACAACCTGGAAGAACTCTCAGGTGGCCAGAAGACAGTTC
TAAGCCTTGCCTTTATTCTAATGGTGGCAAAATGCAGCCAGTCCTCTGTTTATCTCATGGATGAAATCGATGCAGCGTTAGATGAACAGAATCAACAAAGTGTGGCAAAGTTGATAAAAAGTGTTATTGGTGAAGATAATC

Intron 4 GTGTTGTTGA ... TGCTTAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	28.3	19	5	10
A2	33.33	8	2	6
A3	7.69	12	0	2
A4	17.65	14	3	3
A5	50	3	4	2
A6	0	4	0	0
A7	15.15	14	0	5
A8	44	7	7	4
A9	18.75	13	3	3
A10	28.89	16	4	9

>TRINITY_DN43980_c0_g1_i3 from sample A8 / Example spliced isoform

CTTCCCTCCATTCACAGTGCAGCTGACCACAACGTTTCAAGGAAAGGAAGCTAAAAATTCCACTGAAGGGGCCATGACAATACACCAACCTACCACATCATCTGCCTATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCCGCGAAGAACCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATTGTAGGCG
CCAACGGAAGCGGAAAATCAAATATATTAGATGCAATCTCCTTTCCCTTATGTGCCAAGACATCGGCATTGCGAGTCCGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGCCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACGTTAAGTGTTACAATAAATGCA
GATGATTCCCGACATTACAGAGTTGATGGCAAGGTCAAATCAATGAAAGACGTTAAGGTAATTTAAATATTTTCCTGTGAATTTTGTCCTTGTTGCGAGCTCTGGATCTCCAAAGAACAATCAATAAAGCTTTCTTTTAGTT

>TRINITY_DN43980_c0_g1_i11 from sample A8 / Example unspliced isoform:

CTTCCCTCCATTCACAGTGCAGCTGACCACAACGTTTCAAGGAAAGGAAGCTAAAAATTCCACTGAAGGGGCCATGACAATACACCAACCTACCACATCATCTGCCTATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCCGCGAAGAACCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATTGTAGGCG
CCAACGGAAGCGGAAAATCAAATATATTAGgtgttgttgatttaaaaatccgtgagcaattgatttctttgttttcgtagggattgaatgcatcttttacgttaaatgcaggtaaattcttagatatttttgcatgcttaacagATGCAATCTCCTTTCCCTTATGTGCCAAGACATCGGCATTGCGAGTCCGTTATAAT
GCCGAGCTGCAGTCGACGGATACTAAAGAGGCCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACGTTAAGTGTTACAATAAATGCAGATGATTCCCGACATTACAGAGTTGATGGCAAGGTCAAATCAATGAAAGACGTTAAGGTAATTTAAATATTTTCCTGTGAATTTTG
TCCTTGTTGCGAGCTCTGGATCTCCAAAGAACAATCAATAAAGCTTTCTTTTAGTT

Intron 5 GTAATGATTA ... TGTGATTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25	9	4	2
A2	33.33	9	6	3
A3	75	1	1	5
A4	47.17	14	8	17
A5	46.67	4	3	4
A6	36.84	6	5	2
A7	29.41	6	3	2
A8	27.27	8	4	2
A9	29.73	13	10	1
A10	20	10	3	2

>TRINITY_DN96018_c0_g1_i3 from sample A4 / Example spliced isoform

TGTGGGATGACGAATCAAACTTTCGGTGGGCTGGGGGTTAACTTCTGCAGATGCTAGTGGCATTGCTTCTTCTTCGAGGAAATGCTGCAAGAGATAAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGC
ATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGGAAAATATTCTACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATG
CATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTT
GCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAACTCTAAGCAGTTAAATGCTACCGT
GCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATA
CAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTAAGTGCTGAACTTGGGATACTAAGCAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATAC
TTTCTTGCTATAAATATAATTTCTGGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGATCTGTTGCGAATATGGGAGAGTCATGGAAACATTTCCAGATTTTCTCGGATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTGAGACAACAAAAAAGGGTTCAACA

>TRINITY_DN96018_c0_g1_i2 from sample A4 / Example unspliced isoform:

CTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATGCATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGG
GAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTA
GGTTTGAGGGACACAACTCTAAGCAGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAAT
AAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTAAGTGCTGAACTTGGGATACTAAGCAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATG
TTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGgtaatgattaatccatctctcttggtataatgagtgtcctttcagaaaaattcttgaacctcagcttttgtatcttgtgattcagGATCCTTAAAGAAGATATGTGTCACTGAGACAACAGACGCAGCAGCAGAT
CTGTTGCGAATATGGGAGAGTCATGGAAACATTTCCAGATTTTCTCGGATCTGGCCTCTTGATCGACTTAGGGTTGTTGATAGATTGAGACAACAAAAAAGGGTTCAACA

Intron 6 GTTCATAATA ... TCATTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	35.93	18.3	7.9	12.6
A2	48.38	4.1	4.6	3
A3	30.88	11.4	4.9	5.3
A4	14.33	13.6	2.3	2.3
A5	77.78	1	0	7
A6	26.98	9.9	4.3	3
A7	3.25	21	0	1.4
A8	17.52	14	2.6	3.4
A9	23.1	17.1	3.6	6.7
A10	38.1	13	13	3

>TRINITY_DN121797_c2_g1_i1 from sample A3 / Example spliced isoform

GCGACACGAAAACGGTTAAAGCTCGAAAACCGTCGGCGGCAGCTTTTCACACAGGACCGAACGACCTACCGCCCTTACAATTTCAATTCTTAGTGTAGCTGACCACAGGACCGAACGACGTACCGCCCTTATATCTTCCCTCCATTCACAATGTAGCTGACCACAAACGTTTCATGGAAAGGGAGCTAAAAATTCCACTG
AAGGGGCCATGACAATACACCAACCTACCACATCGTCTGCATATATCAAATCTCTCAGAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAGTTCACGTTTACAAAAGGAATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCCAAGACATCG
GCATTGCGAGTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGGCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACATTAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAAGGAAATGCT
GCAAGAGATAAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGCATCTGGTGCAGGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGG
AAAATATTCTACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCTCAAGTCAGCTGCATGCATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAA
GAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAGCTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCA
AGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAACTCTAAGCAGTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAA
TTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTACTTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTT
GAGAGACTAAGTGCTGAACTTGGGATACTAAGCAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAAGATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGTAATGATTAATCCATCTCTCTTGGTATAATGAGTGTC

>TRINITY_DN121797_c2_g1_i5 from sample A3 / Example unspliced isoform:

GCGACACGAAAACGGTTAAAGCTCGAAAACCGTCGGCGGCAGCTTTTCACACAGGACCGAACGACCTACCGCCCTTACAATTTCAATTCTTAGTGTAGCTGACCACAGGACCGAACGACGTACCGCCCTTATATCTTCCCTCCATTCACAATGTAGCTGACCACAAACGTTTCATGGAAAGGGAGCTAAAAATTCCACTG
AAGGGGCCATGACAATACACCAACCTACCACATCATCTGCCTATATCAAATCTCTCAGgttcataatattatggttacttaaaagaatattttgtgatcgtcgcatttttctgacatacattgcatgcaaatttcattaccagAGTGCGCGGTTTCAAATCCTTCGGCGAAGAAGCGCAGAAGTTCACGTTTACAAAAGG
AATTAACCTCATCGTAGGCGCCAACGGAAGCGGCAAATCTAATATATTAGATGCAGTCTCCTTTGCCTTATGCGCCAAGACATCGGCATTGCGAGTACGTTATAATGCCGAGCTGCAGTCGACGGATACTAAAGAGGGCTGCGAAGTGGTTCTTGAATTGGCAGTCACGGGAAATAATGGACAGGAGCGTCTTATAACAT
TAGGTGTTACAATAAATGCAGATGATTCCCGGCATTACAGAGTTGATGGCAAGGTCAAATCAGTGAAAGACGTTAAGGAAATGCTGCAAGAGATAAGGCTCTATCTTGAAGGATCAGGTGCAGTAGTTCACCAATCTCGGGTCACTGAGTTAGCTGACAGCAACTCGTCGAAGTTACTTGTATCTATCATCTCTGATGCA
TCTGGTGCAGGTATATATCACAGACAAAATGAAGTAATGACATGTTTATCAGACATAAAATGCAAATCAGCTGTACGGTCTACTCTGTCACTTTTTTCCATTGTGCTCTTCCCCACTTCTGGCTAAGGGCACTCTGTTGATCAAAGATGCCCAATCTTGGGATCCCACAGGGTATTCTGAAATTACTTCAGCATGTGTTG
CTCTGAGGAGGTTTTGATGTCCATTTGAAGGTGGAATGAAGAAGTAGAAAGAGCTCAACAAGAATTGAAAAAGACACGGAAAGGCTTGGATGACATCCAGGAAAATATTCTACTGCTGGAAAAGATAATTGAAAAGGATCAAGCATGCTTGAAGGTCTTGTCTAGTATAAAGCAGCTTGAGTCAGAAGTGTCATTTATCT
CAAGTCAGCTGCATGCATTCCTGTCAGAGGAACTACTATGCTTGAGAAAGGAGATTGATGCACAACGTCATCTGTTAAACTCTGAAGATTGTAAGATGAAAGAACAAGAGCTTATTTTACATAGGAGAAAAGAAAAAGTTGAGGAATTGAAAAAGCAATTGAAATTACCGACTGGGAATCTTGAAAGTGAAAGGCTTCAG
CTTCTTGATTCTGTTGCTACGAAGGAGGAGCAGAAATCTACATATGAGAGAAAACTCCACGCTGCACAAGATGCAAATTTGAGATTGGGCCATCTTGACCAAGTAATACAAAGTCTTGCAGAAAAAGTTTCCTGCATAAATTTGCAAATTGAACAGAAGCAAGAATTTGTCAGTAGGTTTGAGGGACACAACTCTAAGCA
GTTAAATGCTACCGTGCCAATGCATTTCTACTTAGAAGAACTGAAAGATGCTATCATTGCTTCAGAGGAAAAACTGCAAGAGCTTCACACGGAGCAGTTAATTGTAGCCAATTCTCTTAACTTCCTTTCTGCCAAGAAAGAATCAAAAGAGAGACAGCTCATAGAAGTGAAAAATAAGTTGTCTTTTTTGTCTGATTTAC
TTCATTCTTTAAATACAAATGGCAGTGACAGTAGGATAAAAGAATTATCTCATCAGATATCACAACTTGAGAAGCAAAAAGAAGATTTAAAACCTAGGCTTGAGAGACTAAGTGCTGAACTTGGGATACTAAGCAATTCAGAATCTTCTTTACCAGCATGGCCATTGCACTCATGTTTCACCTTTAAGAACAGGCTTCAA
GATGCTTCTAGATACTTTCTTGCTATAAATATAATTTCTGGTAATGATTAATCCATCTCTCTTGGTATAATGAGTGTC