sp|Q9FMJ0|P4KB1_ARATH ----> Phosphatidylinositol 4-kinase beta 1

Intron 1 GTACTCTTCA ... ATTTCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	5.47	121	1	7
A2	1.92	51	0	1
A3	0	100	0	0
A4	0	70	0	0
A5	5.13	37	0	2
A6	0	25	0	0
A7	0	75	0	0
A8	0	28	0	0
A9	0	50	0	0
A10	0	62	0	0

>TRINITY_DN126983_c2_g3_i4 from sample A1 / Example spliced isoform

GTCGGAGTGCGAAAGAGGAATTATTATTATCATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAACAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGAT
CAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTT
TCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGCAGTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATT
GAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTA
AAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATC
CTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTT
GTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGG
CAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCAT
AAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAA
GGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTT
TCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGT
CCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTT
TGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAA
ATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAAT
AGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAAC
GACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAAC
ACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGA
AAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGGTAATCATACTTTATTTCACTTACATGATCAAATTGAGGCTGCGAAGGTTTTGGTTAGACAAAAGGTTGGAAGACTTATTTTATA
GTTAAAGATTGAGCATTGCATTGACATCATCAATTAAATTACAAAATCTAGCATTTAAATTGGGAAACCAGCTGCATGATTTAGCAGTGCTCCGTGATTTACAGTTCTTTGCATATTTGTTTTCATTCGTAAATATTTCTGGCTGTGTTGCATATATCTGGATGTAGCAGAGAGTATTCCAGCAAGCACAGCTGCTTCTG
CCTTGGCAGCTGGGGGTTCTTTGGCAACTGCTATTTTGGCTCATGTTCTACTCTTTTACTGATCCAATTATTAGCCTTTAGGGTTAATTACTCTTCCATTTGCATTTCACACTTTATCAGCTACATTTCTGCATGTTCACAAGGTGACTCTGGAAAAAGAACACACCTTTAAAATCTTGGAGGAGTGGCTCTTCGGGCCA
AAAGTGGAATTCTATTAATGGTTTAACATAGGAAATACCTTTCTCCTTTTGCATCGAAAGGGAAAATTGCACTTTTTTCATTCTATGGCATGGCTGGCACTCATTAT

>TRINITY_DN126983_c2_g3_i13 from sample A1 / Example unspliced isoform:

ATCGTAAAAATGCCTTGCGGGAGgtactcttcagatattgttcccttggcttgataattttatcatcttggtattaaggttctgcagcattattatagcatgtgatgtatttagatgtttaattttatgttagtttatgaatattattttttgaaaggaaaattagctggtacagaaagatacgtattttacttttacaa
tttatttctgcagTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGTATTCTCTAAATTAACTCACTTAGATTTCTTTTGAAGATTCTGCTGTATCTCTTCTGTATGCCAATACCATGCAATATTTCTGTTCTTATGAGGACGTAACTGCTTGTATATTTAAGTATGTTTTGACATGCTGGGT
TTCTTTTTCCCAATCATATATTATTATTTCTGACATTAATTGAACTATCTTTTTTAACCAGAATGGGTAAATATTTTTGTGTTAAAGGGGCTGAAGAATAACAGCAGCCAAAATGATACAGTCCAAAGTCAGTCCTCAAAAGGCTCTATCTTCTGTAGAGCAACGCCACAAAATTTTATCCTTAGCATACACTATACAGT
GTACACATATTGCACTGTATTTACTGCATTCACAAAGTATTTATAGCTATACTATCAAATAAACTGGTCTAACAAAACATTGCAATTGAAATACATAAAGACATAAGAAGCTAAGAGAATACATGGCCACTATGACCTTCTTCCATCTGCATGGCCACTATGACCTTCTTCCATCTGCATGG

Intron 2 GTAACTACCA ... TGTTGAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	6.02	78	5	0
A2	10.53	51	6	1
A3	7.58	61	5	2
A4	1.89	52	1	0
A5	14.29	48	8	0
A6	0	72	0	0
A7	1.87	105	2	0
A8	2.35	83	2	0
A9	1.27	78	1	0
A10	2.9	67	2	0

>TRINITY_DN115907_c0_g1_i6 from sample A3 / Example spliced isoform

ATGATAATGATGCTAATTCGCAATTTAATTAGTTTTTAATTCCGCTGGAGTGCGAAAGAGGAATTATTATTATAATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAATAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCC
TTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGG
TAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGTAGTTAGCGGGGATTGAGTCTTTCCTGG
CAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGG
AATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGG
GGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCT
TTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACT
AAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATT
TTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTG
ACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAA
TCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTC
GACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCA
CATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTG
TATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCC
ATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTG
CAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAAT
ATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCC
ATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTT
ATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTA
TGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTT
TGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCA
TCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTT
GATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGTAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGACGAGGCTTCTGC
ATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTC
TAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGGTTGGGAACTGGATTTTTCTGAC
ATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGC

>TRINITY_DN115907_c0_g1_i5 from sample A3 / Example unspliced isoform:

TGAGTGTTTAATTTTCATAAGATTTTATACAAGGGATCTTGTTGACTCGTATCTGATGTGGGATTGGTCTGGATGTAATATGATTAGGTTTGGGGATCCTCTTTGATTAGTATGAACATTTTCTATTATTCATGTTTATCTATACGCCATGTTGAAGCTGCAAATGCCATCTTTCCGGTTAAAAGTTATTACTTGATTGT
GCACCTCATAGATTCATATTGCCAAGGCCAATAGAAATGAAAAACATTGTCGTGGTGGCCATATTGTTGTTCTACAGCTATTCAAATGCTACTGTTTGTATACCAACCTATAATCATCTCAATTATGTATCTATCAAGTGCCAAGACGGATCAAATCTTTGGAGGTGCAAACCTTTTTATGGTGCAAAAACTTAAGGAAT
GATTTGCACCTGAGGGATTTCATGATTCATCCTTCTCGGTGCTTGATAGATCTGATTTCATGATTTCATGATTTATTATTATTTTGTAAATTTGAAAAGCTGACATTGTGTCAGCAATACACTCACAAGTAACACTTCTAATCGGTACTAGGCTGTAGAATGTGCATTTCAGTACAATTATTTTGGATATACTTTTACTA
TGCAGCAATTTGACTTTTTAGATGTCTAATCTGATTGGAGCTATTCTTTCATTGTAGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGgtaactaccattgttggcatctatgacttttctcccatttggcat
cttgcaattgtttctttggctcttaaattagcatttgttgagcagGCATCGGTAC

Intron 3 GTGATGGCAA ... CACTGTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	15.53	87	6	16
A2	18.56	79	3	18
A3	19.67	98	3	24
A4	23.36	82	6	25
A5	25.64	29	0	10
A6	16.81	99	0	20
A7	18.46	159	0	36
A8	11.72	113	0	15
A9	12.12	145	2	20
A10	13.91	130	0	21

>TRINITY_DN115907_c0_g1_i3 from sample A3 / Example spliced isoform

ATGATAATGATGCTAATTCGCAATTTAATTAGTTTTTAATTCCGCTGGAGTGCGAAAGAGGAATTATTATTATAATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAATAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCC
TTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGG
TAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGTAGTTAGCGGGGATTGAGTCTTTCCTGG
CAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGG
AATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGG
GGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCT
TTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACT
AAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATT
TTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTG
ACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAA
TCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTC
GACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCA
CATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTG
TATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCC
ATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTG
CAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAAT
ATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGCAGGGTAATGATGGTGGCCAACCAAAGGCAACAGA
TCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTGTAAGTTCAAAATATACTTTTTAGATACATACATATGAATTCTACCTTCCAGTGATATTAATGAGATAGTATTGTTACTGCATTTCCTGTCACACATGGTTAACAAGAT
AAATGAGAAAGACAAACCATTACTATTTAGGATAGTTTCCAAGTGCTCGAGATTGGAGAATGCAATCCCTTATTTTCTGATAACTACTGAATAGGTTTTTGAGTTGGAAGCCTTGATCAGCAA

>TRINITY_DN115907_c0_g1_i7 from sample A3 / Example unspliced isoform:

ATAAGATCACATCCTGAGAGGCACTCTTTGTTCCTTCTAATTTACTACAAATGACTAAAGAGTTTGTTTTCATGTTTCTCTCTTTAAATATACTTGTGAATGAATATGTCTGCCGGTTCTTGTGTTTAGTTTTTTGTCATTATGTGCTAGACAGAAGGATTTCCTTAATTTGATGATTGAAATCTCCTTTGCAGTTAGCA
ACTAAGGGGTTTTCCATGGAGTTTATAATCTGGTAGTTTTGTTTTTTCAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGgtgatggcaaaggccaagggctgtgatttgtgtcattggtttgcccctttttttcttgatttttgactt
taattacctattgatgtgacccaatattattcttgttggttttgctattcataattcctttttttctttggttttctgataacattcatttgattgcactgtttagCAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCT
ATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGGTAATCATACTTTATTTCACTTACATGATCAAATTGAG

Intron 4 GTGATGGCAA ... TGTTTAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	15.53	87	6	16
A2	20.95	83	3	22
A3	22.14	102	3	29
A4	25.22	86	6	29
A5	27.91	31	0	12
A6	17.74	102	0	22
A7	18.36	169	0	38
A8	12.88	115	0	17
A9	13.37	149	2	23
A10	15.72	134	0	25

>TRINITY_DN115907_c0_g1_i6 from sample A3 / Example spliced isoform

ATGATAATGATGCTAATTCGCAATTTAATTAGTTTTTAATTCCGCTGGAGTGCGAAAGAGGAATTATTATTATAATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAATAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCC
TTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGG
TAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGTAGTTAGCGGGGATTGAGTCTTTCCTGG
CAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGG
AATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGG
GGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCT
TTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACT
AAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATT
TTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTG
ACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAA
TCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTC
GACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCA
CATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTG
TATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCC
ATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTG
CAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAAT
ATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCC
ATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTT
ATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTA
TGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTT
TGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCA
TCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTT
GATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGTAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGACGAGGCTTCTGC
ATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTC
TAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGGTTGGGAACTGGATTTTTCTGAC
ATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGC

>TRINITY_DN115907_c0_g1_i7 from sample A3 / Example unspliced isoform:

ATAAGATCACATCCTGAGAGGCACTCTTTGTTCCTTCTAATTTACTACAAATGACTAAAGAGTTTGTTTTCATGTTTCTCTCTTTAAATATACTTGTGAATGAATATGTCTGCCGGTTCTTGTGTTTAGTTTTTTGTCATTATGTGCTAGACAGAAGGATTTCCTTAATTTGATGATTGAAATCTCCTTTGCAGTTAGCA
ACTAAGGGGTTTTCCATGGAGTTTATAATCTGGTAGTTTTGTTTTTTCAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGgtgatggcaaaggccaagggctgtgatttgtgtcattggtttgcccctttttttcttgatttttgactt
taattacctattgatgtgacccaatattattcttgttggttttgctattcataattcctttttttctttggttttctgataacattcatttgattgcactgtttagcagGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCT
ATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGGTAATCATACTTTATTTCACTTACATGATCAAATTGAG

Intron 5 GTTAGTGCTT ... TTTCATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	66.89	50	108	94
A2	70.64	38	99	83.8
A3	57.1	74	95	102
A4	67.13	38	79	76.2
A5	64.03	35	60	64.6
A6	40	3	1	3
A7	68.18	7	15	15
A8	71.43	1	2	3
A9	71.43	4	9	11
A10	56.86	22	29	29

>TRINITY_DN126983_c2_g3_i8 from sample A1 / Example spliced isoform

GTCGGAGTGCGAAAGAGGAATTATTATTATCATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAACAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGAT
CAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTT
TCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCT
CAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGAT
TTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGA
ATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACC
TCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAG
TGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGA
GTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAAC
TGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGAT
GAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCG
GCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCAT
TGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGAT
TCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGT
GCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATC
AGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTA
AAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGTGATGGCAAAGGCCAAGGGCTGTGATTTGTGTCATTGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCT
ATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCC
GAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTA
TGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAG
GACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTT
CGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAG
TCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGCAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGA
GAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCT
CTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAA
TTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCG

>TRINITY_DN126983_c2_g3_i9 from sample A1 / Example unspliced isoform:

GTCGGAGTGCGAAAGAGGAATTATTATTATCATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAACAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGAT
CAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTT
TCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGgttagtgctttcttccgcgcatgttcttgcagatttggtcctgtcgtcaaatttgtccgaaacaaggatattttttcatgcagTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATT
GAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTA
AAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATC
CTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTT
GTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGG
CAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCAT
AAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAA
GGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTT
TCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGT
CCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTT
TGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAA
ATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAAT
AGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAAC
GACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAAC
ACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGA
AAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAAC
AATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGT
TGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGT
AGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTA
CTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAG
TAGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGCAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAG
GCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGACTC
CATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAAC
CCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCG

Intron 6 GTTGGCATAC ... TTGCAAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	18.52	132	29	31
A2	21.47	64	23	12
A3	16.67	85	17	17
A4	10.78	91	11	11
A5	21.31	24	4	9
A6	17.7	200	29	57
A7	18.7	163	29	46
A8	16.52	240	47	48
A9	16.82	136	23	32
A10	15.79	104	15	24

>TRINITY_DN126983_c2_g3_i1 from sample A1 / Example spliced isoform

GAGTTTGAAATGAACTGGAAGTATCTCATTGTGTCTGCTATTTCATTTTAGGAATGTTAAGTTTTTAGTGTAGTCTTTTTCACAAACAACTAAAGACTGCACCTTAATCGAGGAGTCTTATTGTGTGGCTTAATCTTCCTTAAGTTACAAACCTAAAGCGAAACTCTGTAGCAGCCATCTAGAAGCTGTTCTCTGAATGG
AGGAATCTTGTTTGACATTGTGTAAATTTGTCAAAGTTATAAACCAAAAATAAAAGTTTGTATGGTTATAATTGTTGTTGAAATTCCTGTAGCTGTAATCTCTATCAATCTCGTTTATATGTTAGGAAAGAAGCAGGAGCAATTTGTATTTATTGTTAGCTCAGTTTACCATATAACTTGACTGATCTTGCTTAATTTAT
AGTAAAGGGGCAGAAACTATGTATTTGTATTGGCCTATAAGCCCCAAATGTGTATATCAACTATTGGATGCAACACACTGTAGAACATCATGGTTATTGGTAAATTACGGGCAGCTTATGTCATTTACATGATTTGACTGACAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGAT
GAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGGTATTTAGTGCTGTAGTGGGGCTGGAACTTATGAATTTGAGAATCTGCTATTGATTTTTTTGGAATGTTTAGAATTTAGCTATTATGATTTTTAAAGGTCCATATGTAACATGGATTCTAATA
AGTAAAGGTGAGTCAAGAATGTATTTTGTAGAATCATATGAATTTTTTTTTGCAAATTGTATTGGACCTTATAATATTGTTTCTGTGGTTTGCAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATT
TCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGG
TGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGAT
TTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGG
GGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTC
TTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTA
CTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTT
CAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCA
GCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTG
CCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGCAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTC
TGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTG
CAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGT
CTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCG

>TRINITY_DN126983_c2_g3_i14 from sample A1 / Example unspliced isoform:

GTCGGAGTGCGAAAGAGGAATTATTATTATCATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAACAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGAT
CAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTT
TCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGCAGTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATT
GAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTA
AAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATC
CTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTT
GTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGG
CAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCAT
AAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAA
GGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTT
TCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGT
CCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTT
TGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAA
ATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAAT
AGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAAC
GACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAAC
ACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGA
AAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAAC
AATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGT
TGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGT
AGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGgttggcatactcattcataattgtatcttagtaatcttttcaggatatacatgtctttgtttaagcctgac
atcatgccagctttgttattggtttacttacgaaatacttacgaaatttccggccgttcatattatgtttgcaaacagCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGC
ATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAG

Intron 7 GTATGTACTT ... CATTTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	6.57	78.8	5.5	8.9
A2	6.29	83.8	5.8	2.5
A3	6.98	68.6	5.1	6.5
A4	9.03	89.2	8.8	8.5
A5	7.92	32.4	2.9	0.7
A6	7.24	130.2	10.5	4.5
A7	6.56	194.6	14	7.7
A8	8.24	156.3	14.2	10
A9	4.66	179.1	8.8	8
A10	3.39	131.8	4.7	4.7

>TRINITY_DN126983_c2_g3_i1 from sample A1 / Example spliced isoform

GAGTTTGAAATGAACTGGAAGTATCTCATTGTGTCTGCTATTTCATTTTAGGAATGTTAAGTTTTTAGTGTAGTCTTTTTCACAAACAACTAAAGACTGCACCTTAATCGAGGAGTCTTATTGTGTGGCTTAATCTTCCTTAAGTTACAAACCTAAAGCGAAACTCTGTAGCAGCCATCTAGAAGCTGTTCTCTGAATGG
AGGAATCTTGTTTGACATTGTGTAAATTTGTCAAAGTTATAAACCAAAAATAAAAGTTTGTATGGTTATAATTGTTGTTGAAATTCCTGTAGCTGTAATCTCTATCAATCTCGTTTATATGTTAGGAAAGAAGCAGGAGCAATTTGTATTTATTGTTAGCTCAGTTTACCATATAACTTGACTGATCTTGCTTAATTTAT
AGTAAAGGGGCAGAAACTATGTATTTGTATTGGCCTATAAGCCCCAAATGTGTATATCAACTATTGGATGCAACACACTGTAGAACATCATGGTTATTGGTAAATTACGGGCAGCTTATGTCATTTACATGATTTGACTGACAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGAT
GAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGGTATTTAGTGCTGTAGTGGGGCTGGAACTTATGAATTTGAGAATCTGCTATTGATTTTTTTGGAATGTTTAGAATTTAGCTATTATGATTTTTAAAGGTCCATATGTAACATGGATTCTAATA
AGTAAAGGTGAGTCAAGAATGTATTTTGTAGAATCATATGAATTTTTTTTTGCAAATTGTATTGGACCTTATAATATTGTTTCTGTGGTTTGCAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATT
TCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGG
TGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGAT
TTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGG
GGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTC
TTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTA
CTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTT
CAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCA
GCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTG
CCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGCAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTC
TGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTG
CAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGT
CTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCG

>TRINITY_DN126983_c2_g3_i11 from sample A1 / Example unspliced isoform:

TCTTTGACTATTTCAAAgtatgtacttcgaattgttttacatgttactgttttctatgtagtgtttggaaagttattttaatatttttatgaatcattttacagGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGTGAATTTTATGTTGGGACTT
TGATAAGATGTTTTAACTTTTATCTTTTAATTATTGTTTTGTAACTTCTGAAAGATTTGACATTATGAGGAATATGAGTGCAAGACAGCTGGAGGTTGCAACTAATATTGAATAGCCTCGGAGGAAAATTGTTTGTAGATTAGTGTTGTACATTGTTATAATAATTTGCTTCCTTTAAAAGTAATGTTTGAGAATGGTCT
TATGATTATCACTATACATTTATGTTCTTTTCCTCTTAAGTTGCAAGAAAGAGGGAAAAGAGTAGGGGTTGCAAAACGTAATTTTTCAAAATCATAGGAATGGTGTTACTTCTTTTGAAAGATTTGATATTATTTCGAGGAATATAACTTATAAGTCCAAGACACCTGGAGGTTGCAACTAATATTTAATATCCTTGGAG
GAAAAGTGCTCCAAGTTCTTTCTAGATTAGTGTTGTAACTTGTACATTCCTG

Intron 8 GTATTTAGTG ... TGGTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.93	89	16	40
A2	26.13	41	11	18
A3	23.4	72	7	37
A4	21.83	77	17	26
A5	24.14	33	8	13
A6	21.74	18	5	5
A7	21.02	62	14	19
A8	23.36	41	9	16
A9	24.8	47	9	22
A10	20.3	53	10	17

>TRINITY_DN126983_c2_g3_i4 from sample A1 / Example spliced isoform

GTCGGAGTGCGAAAGAGGAATTATTATTATCATTTTTAAGATTAATAACGAAATTCATGCTTGTGAAGAGAGAGGAACGTAATTTTATGAAATGGAACAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGAT
CAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGTGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTT
TCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGCGCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGCAGTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATT
GAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTA
AAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATC
CTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTT
GTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGG
CAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCAT
AAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAA
GGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTT
TCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGT
CCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTT
TGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAA
ATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAAT
AGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAAC
GACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAAC
ACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGA
AAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGGTAATCATACTTTATTTCACTTACATGATCAAATTGAGGCTGCGAAGGTTTTGGTTAGACAAAAGGTTGGAAGACTTATTTTATA
GTTAAAGATTGAGCATTGCATTGACATCATCAATTAAATTACAAAATCTAGCATTTAAATTGGGAAACCAGCTGCATGATTTAGCAGTGCTCCGTGATTTACAGTTCTTTGCATATTTGTTTTCATTCGTAAATATTTCTGGCTGTGTTGCATATATCTGGATGTAGCAGAGAGTATTCCAGCAAGCACAGCTGCTTCTG
CCTTGGCAGCTGGGGGTTCTTTGGCAACTGCTATTTTGGCTCATGTTCTACTCTTTTACTGATCCAATTATTAGCCTTTAGGGTTAATTACTCTTCCATTTGCATTTCACACTTTATCAGCTACATTTCTGCATGTTCACAAGGTGACTCTGGAAAAAGAACACACCTTTAAAATCTTGGAGGAGTGGCTCTTCGGGCCA
AAAGTGGAATTCTATTAATGGTTTAACATAGGAAATACCTTTCTCCTTTTGCATCGAAAGGGAAAATTGCACTTTTTTCATTCTATGGCATGGCTGGCACTCATTAT

>TRINITY_DN126983_c2_g3_i1 from sample A1 / Example unspliced isoform:

GAGTTTGAAATGAACTGGAAGTATCTCATTGTGTCTGCTATTTCATTTTAGGAATGTTAAGTTTTTAGTGTAGTCTTTTTCACAAACAACTAAAGACTGCACCTTAATCGAGGAGTCTTATTGTGTGGCTTAATCTTCCTTAAGTTACAAACCTAAAGCGAAACTCTGTAGCAGCCATCTAGAAGCTGTTCTCTGAATGG
AGGAATCTTGTTTGACATTGTGTAAATTTGTCAAAGTTATAAACCAAAAATAAAAGTTTGTATGGTTATAATTGTTGTTGAAATTCCTGTAGCTGTAATCTCTATCAATCTCGTTTATATGTTAGGAAAGAAGCAGGAGCAATTTGTATTTATTGTTAGCTCAGTTTACCATATAACTTGACTGATCTTGCTTAATTTAT
AGTAAAGGGGCAGAAACTATGTATTTGTATTGGCCTATAAGCCCCAAATGTGTATATCAACTATTGGATGCAACACACTGTAGAACATCATGGTTATTGGTAAATTACGGGCAGCTTATGTCATTTACATGATTTGACTGACAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGAT
GAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGgtatttagtgctgtagtggggctggaacttatgaatttgagaatctgctattgatttttttggaatgtttagaatttagctattatgatttttaaaggtccatatgtaacatggattctaata
agtaaaggtgagtcaagaatgtattttgtagaatcatatgaatttttttttgcaaattgtattggaccttataatattgtttctgtggtttgcagCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATT
TCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGG
TGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGAT
TTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGG
GGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCTATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTC
TTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGACACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTA
CTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTT
CAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCA
GCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTG
CCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGCAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTC
TGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTG
CAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGT
CTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCG

Intron 9 GCCGCCGCAG ... CCTACTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.19	52	83	81
A2	55.64	61	71	82
A3	57.61	39	73	33
A4	55.12	68	79	88
A5	67.74	15	23	40
A6	55.56	76	82	108
A7	64.73	73	148	120
A8	60.11	72	85	132
A9	66.48	60	134	104
A10	59.51	83	140	104

>TRINITY_DN107461_c0_g1_i6 from sample A5 / Example spliced isoform

GGGGGAGGAACGTAATTTTATGAAATGGAATAAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTT
TGACAAATTTGGGGCAGATACAGATGCAGATGCAGGCTCTCTCTGACAAATTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGTTAGTGCTTTCTTCCGC
GCATGTTCTTGCAGATTTGGTCCTGTCGTCAAATTTGTCCGAAACAAGGATATTTTTTCATGTAGTTAGCGGGGATTGAGTCTTTCCTGGCAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGT
TGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGTCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTG
ACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACAAAATAGTTCTATCATGGTGCGGCTTCTCG
GATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTCTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCC
GGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGC
CACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCG
TTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTA
GTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGG
CAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGATATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAAT
TATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAAT
GCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAA
TTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAG
CCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGAT
GCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGTGAAAGATCGACATAATGGGAATTT
GTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCT
GTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGAT
TACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAA
AGTAGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGTAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAA
AGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGAC
TCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGA
ACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCTCAACCATGGCATATTTTGTCCCCACAAAGCATTTTCGATATAAATTCGTATTGCACAATTAACCTATAGTGATTAAAA
CCATTTTGATTGGC

>TRINITY_DN107461_c0_g1_i5 from sample A5 / Example unspliced isoform:

GGTGAGTCAAGAATGTATTTTGTAGAATCATATGAATTTTTTTTTGCAAATTGTATTGGACCTTATAATATTGTTTCTGTGGTTTGCAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACT
TTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATA
ATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAA
GACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGgccgccgcagccaaaggagaggccccaataggacttcctgtaaaaaaagttagtcatggttcatcaaatacaaattccgagggtaatgatggtggccaaccaaaggcaacagatccattagcaggggagct
atgggaggtgaaaaaggaaaggatcagaaaggcttctatctatgggaaattgcctggttgggatctccgttctattattgtgaaaagtggcgatgattgcaggcaggagcatcttgctgtgcagcttatttctcatttctatgatattttccaagaggcagggctaccactttggttgcgtccttatgaagttcttgtta
cttcttcatatactgctttgattgaaacaattccagacacggcatcggtacatgctattaaaagcaggcatccgaacatcgcaagcttgcgggagttcttttcagacaaatacaaggaaaactcacctgctttcaagcttgcgcagagaaactttgttgagagtatggctggatattccatactatgctacctacttcag


GTGAAAGATCGACATAATGGGAATTTGTTGATGGATGAGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGT
CCTATGCATTCAAGGATTTTTGACCTGTAGAAAACATGCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAG
ATGCCTGGCGGACAAGGCAGTATGATTACTACCAACGTGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGC
AGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTTACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGTAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTCTGTAAG
GAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGTAATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTGCAACAC
AAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCTCTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGTCTGCAG
AGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTATCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCTCAACCATGGCATATTTTGTCCCCACAAAGCATTTTCGATATAAATTCGTAT
TGCACAATTAACCTATAGTGATTAAAACCATTTTGATTGGC

Intron 10 GTTAGTGCTT ... TTCCTGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.73	62	108	92
A2	64.57	45	99	65
A3	57.31	73	95	101
A4	57.14	57	79	73
A5	58.42	42	60	58
A6	60	2	1	5
A7	59.32	12	15	20
A8	50	4	2	6
A9	48.57	18	9	25
A10	52.05	35	29	47

>TRINITY_DN107176_c0_g1_i3 from sample A4 / Example spliced isoform

AAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGGGCAGATACAGATGCAGAT
GCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTAT
GTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGATTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGT
GTCAACGAATTTGGCTCGAATGCCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAGGAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCA
AAGAGGCTTGAAAGGGGGAGGAGAGAACGAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCCCCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTTTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACA
TGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTTACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCG
AGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTCAGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAG
CCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGTTTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGA
CCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAGGATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGA
AGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCTGATTTCTTGTCGTTTCGGAGGTTATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACT
GAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACGGCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATC
ACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATTCCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAG
AAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAACTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGAT
CAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTCTGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAA
CAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGGATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCG
TTCCAAGTACAATAGCAATGGCTGAAGTAAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGGTAATGATGGTGGCCAACCAAAGGCAACAGATCCATTAGCAGGGGAGCTATGGGAGGTGAAAAAGGAAAGGATCAGAAAGGCTTCT
ATCTATGGGAAATTGCCTGGTTGGGATCTCCGTTCTATTATTGTGAAAAGTGGCGATGATTGCAGGCAGGAGCATCTTGCTGTGCAGCTTATTTCTCATTTCTATGATATTTTCCAAGAGGCAGGGCTACCACTTTGGTTGCGTCCTTATGAAGTTCTTGTTACTTCTTCATATACTGCTTTGATTGAAACAATTCCAGA
CACGGCATCGGTACATGCTATTAAAAGCAGGCATCCGAACATCGCAAGCTTGCGGGAGTTCTTTTCAGACAAATACAAGGAAAACTCACCTGCTTTCAAGCTTGCGCAGAGAAACTTTGTTGAGAGTATGGCTGGATATTCCATACTATGCTACCTACTTCAGGTGAAAGATCGACATAATGGGAATTTGTTGATGGATG
AGGAAGGACATATCATACACATCGATTTTGGTTTTATGCTATCCAATTCTCCTGGAGGTGTGAATTTTGAAAGTGCTCCCTTCAAGTTGACCCGAGAACTTCTAGAGGTAATGGATTCTGATGCAGAGGGAAGTCCGAGCGAGTTCTTTGACTATTTCAAAGTCCTATGCATTCAAGGATTTTTGACCTGTAGAAAACAT
GCAGAACGGATCATATTGCTGGTTGAAATGTTGCAGGACTCCGGTTTCCCCTGTTTTAAAGGTGGACCAAAAACGATACAAACTTTGCGAAAGCGCTTTCATTTAAGTTTGACTGAAGAGCAATGTGTTTCGTTGGTTCTCTCTCTCATCAGCAGCAGCTTAGATGCCTGGCGGACAAGGCAGTATGATTACTACCAACG
TGTGTTGAATGGTATCTTGTGAGAATTCATATTGTTCGAAGCATTTCATTCTCAGGTTTCTGTGTTTCGTTGGCCATCTTTGTTGAGGAGCTTTTGCTTCACCTTCAGGGAAAGGGATTTGTATCATATGCTTCAAGTTGAGCAATTTGATACCTTGCCTGGCAGCATTGTATAAGTAAAAAATTGAAAAGTAGGAACTT
ACATCCTTGATTTTATACGTTTAGCTCGCATTGAAGTCAATGTAGTAGTCAGAGTTTCTGGAAGATTGAAATTCGAGTAATTCATGTGTATCTCTAATATCTTGCTTATTGTTTTTCCTATTTTAATAGAATGCAGATGAGGCTTCTGCATTGCTTCTGTAAGGAATAACATTTTTTGGGGGTTGTTAAAAGGCCATCGT
AATGAGTTTTCAATGATGTTTAGAGTTTCCCCTTGAGAGATATAAAACTGCACACGTTTTATATCTACACCCAGAGACTGCGATTGTTGACTGTTCATGTATATATAAAGCTGGATTGTGCTTTACTGCATAATGTAGATCTCAGACTCTAAATGTGCAACACAAAAAGATACTGTAAATGGTCCAAGACTCCATTCTCT
CTTCGGACATGCATTGTAGCAAGGCCTCTATTGTCTCTTCGAACATGTATTGTAGCAAGGGAAGGCACTGAAGCAACAATGACGATTCTTTACATAAACCGTCTTACTGCGTGGGCAATTCACCTGTTTGGGAACTGGATTTTTCTGACATCAGAGTCTGCAGAGTCTGGTGGTAGCGTTCGTAGTTTGAACCCCATGTA
TCTCAATAGAGTTCTATAGGAGAATTAAGTTCATAATTTGGAATATTATGTTCATAACAGAGTATTCTGAAGTCAAACGTAATTCAAGATATAAAGTCTCTTTTTCTTGCCTCG

>TRINITY_DN107176_c0_g1_i9 from sample A4 / Example unspliced isoform:

AAAAGTGAAAAATTAGAACGAGCTCGGTTTGTGGAGGGGGGACGACAAACCCTGCTCCCTTGTTCTCATCCTTGATTGGCGTGGCGATTATTTGTTTGTGATCAATCTTTGAACGGCTTGTCACCTTCGGCATTCCATGCGATTCGAAACTTCAGATCACCGCACCTTTTGACAAATTTGGGGCAGATACAGATGCAGAT
GCAGGCTCTCTCTGACAAACTTGGCGGAGATTGAATCCATCACTTACGCACGAATTTGGTAGGTGTTCATTCTCTTTCGATGTCGCCGATTTAGTCAGTTTTTCGGAGGAATTTGGTGAACATGCGCTGTTCTTCGACGAATTTGGCAAAGgttagtgctttcttccgcgcatgttcttgcagatttggtcctgtcgtca
aatttgtccgaaacaaggatattttttcatgcagttagcggggattgagtctttcctggcagGATTTGGCCTAGTCTACTGTAGAAGAATTCTATCGGCATTGAGTCGTATGTAGGTGACGTCTCCGGAGAAATTGGCCCGGATTAAGGCCTTGCTTTATATGATTTGTTGTACACAGTATATCTCAAAATTGGCGTAGA
TTAGAGGAAAATGGTGGTTAAATCAGACGATTCGAGGAAGAAGATTTAAGAAATCGAGGAATCACCAGATCAGTCAGCGTTTCGTCTTAAGTCCAATTACTAAAATCGTGTGTCAACGAATTTGGCTCGAATGCCCAGGGTTTGAATCTAGGGTTAGACAGTTAGCTTGACGCGATGCCGAAGATTTTACAGGGAATCAG
GAAAATTTCAGAGTAGGGTTGCTGTATAGATGGACATGGTGGGAGTGGATAGAGAAGGGGGCAGCATTACCGTTGTCCAAGAAGCCGCCGCTCATTTGGATCCTTTCGTCAAAGAGGCTTGAAAGGGGGAGGAGAGAACGAAATAGTTCTATCATGGTGCGGCTTCTCGGATTAGCGAGGGCAGAATCAGATGATTTTCC
CCGCGACATTACACGGAATGCGAACGGGACAGGAGATAACGGCTGGCTCATCCGGTTTTTTGATTCGGCATTTTTCTGCGAGTGGATTGCAGTTAGCTATTTGTACAAACATGAACATCCAGGAGTCAGAGACTATCTTTGCAACAGAATGTATACTTTGCCGCACTCCGGGATCGAGAGCTACCTCTTTCAGATTTGTT
ACATGCTCGTGCACAAGCCCAGCCCTTCGCTCGACAAGTTTGTTATCGACATGTGCACTAAGTCTCTTAGGATTGCACTTAAAGTACACTGGTTTCTTATGGCAGAGGCCGAGGATTCAGAGGATAATGAGGGGGTCAGCAGAATCCAGGAAAAGTGTCAGATGGCTGCCACTTTGATGGGGGAGTGGCCACCCTTGGTC
AGGCCTCAGAATAATCTGCCTAGTCCTGGGAGCCGGAATCGTGTATTGAATAAGCTATTTTCTTCGAAGCAACGGCTTCTGTCTCTTACTTCGCCACCTCATAAATCTCAGCCACTCGCATCTCCTATTGCTGCTACAAATAGTAACACTCAGGAGGAAAACAAAATCGTTGCAGATGAATCCGAGTCATCCTTGAAAGT
TTTCAAGAAACTCATGCCTGGACCAAAGGTGAGAGATGCACTGTTCAAAAAATTCATTGACAAGGAGGATGAAGAACTGGACAAAACAAAAGAATCATCAAAGGAGGCTGACCAGGAAAGCTTTTTTCGGAGGCTACTAAGGGACAACAAAGAAGAGGATGAAAAAGTAGTTCGCGGCGAAGAACTGGCAAATTCTGAAG
GATTCTTCAGGCGATTGTTTCGGGACAGAGGTGATGCAGAAGAAAAGGGTGGGGCCAAATCAGGGGAAGAAGATGAAAAAGATGGATTTTTCCGCAGGCTTTTCAGGGAGAAGAGCGAGGACCGTGAAAAGAGAGATGGGCAGGATAAAACCGAGGATGATGACAAGGGCAATGGCAGCTGTGATGAGGATGAGGGTTCT
GATTTCTTGTCGTTTCGGAGGTTATTCAGGATTCACCCCGAAGATGAGAAGACCTTGTCGACTTCCATGGAGAATTGTTCCTTAAGTACTCCTGAAAGCAGTCCTGGCACTGAGAATTTTTTCAAGAGATTATTTAGGGATCGTGATCGATCTGTTGAAGATTCTGAATTATTTAGTCTAAAGCGGCAGAGGGAGAAACG
GCCAGGATCTCCAAGGCAGCGGAGTGATAGGTCATCTGCTAAACCACCTTTGCCAATCACATCTCAAATTCGAAAAGGGACTTACCATGTGTCTTTGGATTTTGTTCAATCACTATGTGATACATCATATGGTTTGGTGGATGTGTACCCAATGGAAGATCGTAAAAATGCCTTGCGGGAGTCATTGGCTGAGCTCAATT
CCAATCTGGCATCTTCCCAAAGTAGTGGAGGCATCTGCTTTCCAATGGGAAAAGGCTTGTATCGTGTGGTACATATACCAGAAGATGAAGCTGTTCTCTTAAATTCTAGAGAAAAGGCACCTTATCTGATTTGTGTTGAGGTTCTAAAAGGAGAGAACCAAAGCTTAAATTCACAAAACAAGGATTCTTCGTCTCATAAA
CTTTCGAGAGGAGGAATTCCATTAGCAAATGGAGATGTGCAGTTGCAACGCCCACCTCCATGGGCATTTCCACTTTGGAATCAGCATGATGTGCAGCGGAATAGCACTGATCAGATGTTAAGATCTGCTTCCCAAGCCATTGATCAAGCGATGGCACATTTATGGGAAGCCAAAGTAAAATTTGTGCATGTGAGCCTTTC
TGTTGACCGTCGAAGTGTTGAGAGTTCTTCAGAAAATAATGAACCAGGAGTCATATCTGCAAAGATGGTGAATAATGATCTTCAGCAAGACAGTGAACAAACGACTTCTAACAGTTTATGGGTCAATGATGTGAAGACTGAAACAGAAGTTGGAGACAGATTGGGGGATGCAGGCAGTACTCATCAGGCTGGTAATAGGG
ATCAGCTCACTGATGGAGAATGGATAAGTGTGACTTTGACTGCAGTTCCTGGTGTCAATATGGAAGATTTAGAAGACCAAGAACCCGCAAAAAGAAAAGAACACCGCCGCGTTCCAAGTACAATAGCAATGGCTGAAGTAAAGGTGGGCCTGTTTTCCAAACCAAATTGTTGGTGACTATGATTTCATATCTTACAGTAT
TGAAATTGATGCAGTAAGGCAAGGCCGCCGCAGCCAAAGGAGAGGCCCCAATAGGACTTCCTGTAAAAAAAGTTAGTCATGGTTCATCAAATACAAATTCCGAGGTGATGGCAAAGGCCAAGGGCTGTGATTTGTGTCATTGGTTTGCCCCTTTTTTTCTTGATTTTTGACTTTAATTACCTATTGATGTG