sp|Q94AF7|PFD1_ARATH ----> Prefoldin subunit 1

Intron 1 GTGAGTCTCG ... ATTTCTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	19.88	137	15	34
A2	19.25	130	5	31
A3	19.2	139	3	33
A4	16.17	98.5	5	19
A5	30.77	63	0	28
A6	18.07	1061	39	234
A7	18.76	866	34	200
A8	19.98	957	46	239
A9	20	940	45	235
A10	19.84	719	30	178

>TRINITY_DN39785_c2_g1_i12 from sample A9 / Example spliced isoform

GGGATATGTAAATAGTGAAATAAAACGACATTAAACCAAAGTAGATTTGCGATTTGAACTTTGAAACCGGGGATATTGAAACTCCATTTTGACTGTCAAAAGAGGTTTTGATCAGGCGAATTTCAAGCATCCTCCGTCTGACAGAGCATACTTGTAAAGTCTGTATTCCAAGGAGGCTGTTAAAATGGCAGGAGAAATCA
ATAGAGAGGCATTTGTTGAACTTCAAGGTCGGATGATTGAAACATCAAGCAAACTTAAGCAGGTGCAAATGCAAATTCGCAATAAAGAAGCCGAAAAAAAGCGATCCTTTCTTACGTTGGAAGAGTTACAACAGTTGCCCGATGAAACAAATACATATAAATCTGTTGGCAAATCATTCATTTTGGAGCCCAAGTCAGTG
TTAATTACGGAGCAGAAGGAGAAAATAAAAGAATGTGATAGTTCTGTTGCTTCCTTACAGACCTCAAAGGAATACCTGGAAAGGCAGATGACGGAGGTTGAAAGCAATTTTAAAGAGTTACTGCAGCAAGACCCAGGACTTGCTCGACAAATTATGTCAATGTCAATGTCATAATGGTCCTGAATATTCAAGTTATTTGT
ATTGAATATGTGCTGGTTTACATGCACACTTTTATTATCAGGTTTTCAGATTTAACCATAACTATCATCATGTCAAGTATTGTATTTAGATAAATAGGGTATAAATGCAACCATTTGAAATCTGGAAGCAAGATTGCTTTAGGTTTATGAGTAAAATTTTAATCCTCTTTGATTTTGAAGTTTTGTTTTCTCTTCTGTGG
AAGATCCAGGTTTCTAAAACGGGCCCTCATCTAGCTGTAAGTAGCTGAACTAAAATTTCTTGAATAATTTACAAGTTAGGTGTTGGAAATATGTGGGCAGCTAGTTAATTTTATCTAGGCAAAGTTACATCCATGTACAAAGCATTGGCTCCAATGTGATAGGTAACATTTATGGTGGTATGCATAACATAATTGGGGGC
CATGCTCTTTTTCTCATAATGTACCCAGTTGTTTACTTTTCAGTCCGAGATTCTCTAACCCGTACGGGGTAGGCCCGCGGTGTAGATACCATGCACAAATAAAGCCTTGATATTAAGGGTCTCCAAAATCTTAGATATAATATCCATAAACATTCA

>TRINITY_DN39785_c2_g1_i3 from sample A9 / Example unspliced isoform:

GATGAAAGAAGCATTGCGGGGCTTTGAAAAGACTGATAGATGTCAAAGTTGGTTGAGAATTATGCAGAATTATGTTTTGGCTTTCCCATGAACTGTTGGGCTAATCCCAAAACAGTACATCTGAAGTCTGAAGACTTTCGAAAATCAGAGCAGAGAAGCTTTCTTTCTGAAACAGTTTAGACAAGTCCGAAGCTGGTTTG
TAGATAGCCACAGGCTTGAATTCGGTTGAACGTAAGAAGGCCGATGATGATCTGAAGCCTGAAAAGTCCGAAATTCACTTAAAGTTGACTGGTACAGATCCTAGGCTTGAAAGCCCTAACTCAGAGCAGACCTAAAGTTCCAGTGAAACGTCTTAGTCATATATATATCAAGCAGTTAGAAGTTGTTGCTGGTCTCAAGA
CCTCAAAATATGAGGGTATTTCAAGTTCTAATATGTTAAAAACGGTGCAATATGGAAGGATGGCCTACAGCACACACGTTTAAAGCATGAGCAAATCCACACGTCAAGCCCTCATGGAGGATAAGCAGCCTCAGCAGATCTTCATGAAACTTGGAAGAAAAGGGTATCAAACCCGTGATTTATGGAACAATATAATTCCC
ATGAAATTATAAGGGTCCCGAGTCCTTGAATTAAGGAACTTTAAGTCAAGCACCTGATTGAGTGAGTCTATTATGCACTATAAAAATAAAAGCTCAGGTCGGCTCTATAATTAAAAATTGAAGGGACTTGTGGAGCATAAATACACAAGTCGAGGAGTAGTTTTTGTTTGCTGATTTGCTGAGGGAAGTGGCGGTGGTTT
CTGAAGAGAAAGGAGGGCGAGGGAGCTGAGGAGAAAGGAAGGCGAGGGTGCTAAGGAGAGGACTTGTAAGAGGAAGCCACAGAAGTCTGAGATCCGATCTAGGAGAACAAAGTGTTTAGAACTGATCTAGAAATTCACGGTGTAGTAGGTGAAGTGTCTAGAAATTCTTCTTCAGCAGGGAAACCGTCTCCGCTTGTGAC
CTGTGAGTTGATTGGCCAAATCTGAGGTATGTACAAACAGATGTTTGAGGACTGAACACAATCACAGGACAGTCCTAAAGTTGCAGACAAATATCAAGCTTTCCTTTGTATTCATCTTCAAGAGGGTGGTAGGGTGGTGGAAGGACAGGATACATGTTCTCAACAGGTTGAAGCCTGTACTTAAGTGTAGAAGCACTGAA
CACAATCACAGGACAGTCCTAAAGTTGCAGACAAATATCAAGCTTTCCTTTGTATTCATCTTCAAGAGGGTGGTAGGGTGGTGGAAGGACAGGATACATGTTCTCAACAGGTTGAAGCCTGTACTTAAGTGTAGAAGCACTGAACACAATCACAGGACAGTCCTAAAGTTGCAGACAAATATCAAGCTTTCCTTTGTATT
CATCTTCAAGAGGGTGGTAGGGTGGTGGAAGGACAGGATACATGTTCTCAACAGGTTGAAGCCTGTACTTAAGTGTAGAAGCACTCTATCAGTTGCAGCTGATTTTCTTTAGAGGTTGTTGCCTCACTCCAGTTGAGCTGGAGCATTACAAGGTGCAAATGCAAATTCGCAATAAAGAAGCCGAAAAAAAGCGATCCTTT
CTTACGTTGGAAGAGTTACAACAGTTGCCCGATGAAACAAATACATATAAATCTGTTGGCAAATCgtgagtctcgctttatgtgatctaggaggcatttcttattgcttggaattggttccaccatcccatttaaaatgtgttagaaattagaatttcatatgttgcatttgtatgcacacatacaaacaatgttaaaat
tagtgattggtgaaatccagtcaaaggctacagaaatgaggaaactgtgtacagctcctctatgccaagtttcttctgttggttacttttccaatcatatatgtgatagtacaaatgactggtgttttaattgcatttctacagATTCATTTTGGAGCCCAAGTCAGTGTTAATTACGGAGCAGAAGGAGAAAATAAAAG
AATGTGATAGTTCTGTTGCTTCCTTACAGACCTCAAAGGAATACCTGGAAAGGCAGATGACGGAGGTTGAAAGCAATTTTAAAGAGTTACTGCAGCAAGACCCAGGACTTGCTCGACAAATTATGTCAATGTCAATGTCATAATGGTCCTGAATATTCAAGTTATTTGTATTGAATATGTGCTGGTTTACATGCACACTT
TTATTATCAGGTTTTCAGATTTAACCATAACTATCATCATGTCAAGTATTGTATTTAGATAAATAGGGTATAAATGCAACCATTTGAAATCTGGAAGCAAGATTGCTTTAGGTTTATGAGTAAAATTTTAATCCTCTTTGATTTTGAAGTTTTGTTTTCTCTTCTGTGGAAGATCCAGGTTTCTAAAACGGGCCCTCATC
TAGCTGTAAGTAGCTGAACTAAAATTTCTTGAATAATTTACAAGTTAGGTGTTGGAAATATGTGGGCAGCTAGTTAATTTTATCTAGGCAAAGTTACATCCATGTACAAAGCATTGGCTCCAATGTGATAGGTAACATTTATGGTGGTATGCATAACATAATTGGGGGCCATGCTCTTTTTCTCATAATGTACCCAGTTG
TTTACTTTTCAGTCCGAGATTCTCTAACCCGTACGGGGTAGGCCCGCGGTGTAGATACCATGCACAAATAAAGCCTTGATATTAAGGGTCTCCAAAATCTTAGATATAATATCCATAAACATTCA

Intron 2 GTATGTGTCA ... GCATTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.42	58.5	31	10
A2	22.64	43	17	8
A3	26.96	39.5	18	11
A4	33.77	25.5	16	10
A5	37.56	7.5	6	3
A6	20.12	110.5	34	21
A7	19.16	190.5	55	34
A8	22.62	165	49	47
A9	25.07	191	78.5	48
A10	27.6	144	69.5	39

>TRINITY_DN124154_c1_g1_i5 from sample A1 / Example spliced isoform

CTCTCTATAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAAGAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAA
AAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGA
GAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCT
TTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCTCAGATAAACATGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGTTCAGGGGTTTGATGTCAACCTGAAGATTGCGAAGA
ATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATCAATTTTTGTGTTAATGGAATCAACCTGGTTATGTTGTTTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCA
ACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGATTAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGT
TATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTACTGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGT
ATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTATGAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

>TRINITY_DN124154_c1_g1_i7 from sample A1 / Example unspliced isoform:

CTCTCTATAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAAGAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAA
AAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGA
GAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCT
TTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCTCAGATAAACATGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGgtatgtgtcatttttctcttcctttatacaggcact
ggatcttagtaacatatgccattttattataactggaaccatgcattgacagTTCAGGGGTTTGATGTCAACCTGAAGATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATCAATTTTTGTGTTAATGGAATCAACCTGGTTATGTTGT
TTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGAT
TAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTAC
TGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTAT
GAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

Intron 3 GTATGTGTCA ... GACAGTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.67	75	27.8	12
A2	24.42	51	16.5	10.3
A3	26.06	48	17	11.9
A4	35.17	27	14.8	10.1
A5	39.17	9	5.8	3.7
A6	19.96	132	32.9	22.3
A7	18.28	229	51.4	35.6
A8	18.96	188	44.4	47.2
A9	24.85	226	74.9	48.5
A10	26.59	178	64.8	39.4

>TRINITY_DN124154_c1_g1_i6 from sample A1 / Example spliced isoform

ATTTTTTTTTTTGGGTATTAAAACCACAGGCTTATGCATCATTCTTAAGGGACCTCATAACATTTCCTAGGCAACATTCTGGCGTGATTTTGAAGTGTGTATATGAGCAAATTCTACAAAATATGAAGCAGAAAGTTGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAA
TCCATTGCTAAGAAGAGGCAACGGAGAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGC
TCATCCGGTATTTGTTTCAAATCCTTTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCTCAGATAAACATGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGGGGTTTGATGT
CAACCTGAAGATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATCAATTTTTGTGTTAATGGAATCAACCTGGTTATGTTGTTTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCC
CTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGATTAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCA
TTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTACTGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTT
CTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTATGAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

>TRINITY_DN124154_c1_g1_i7 from sample A1 / Example unspliced isoform:

CTCTCTATAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAAGAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAA
AAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGA
GAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCT
TTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCTCAGATAAACATGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGgtatgtgtcatttttctcttcctttatacaggcact
ggatcttagtaacatatgccattttattataactggaaccatgcattgacagttcagGGGTTTGATGTCAACCTGAAGATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATCAATTTTTGTGTTAATGGAATCAACCTGGTTATGTTGT
TTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGAT
TAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTAC
TGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTAT
GAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

Intron 4 GTATGTGTCA ... CAACCTGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.09	84	26.3	25.5
A2	21.87	55	16.3	14.9
A3	24.61	54	16.5	19.1
A4	30.03	29	14.3	11
A5	36.13	11	6	6.5
A6	20.99	158	32.5	52.3
A7	19.24	267	49.8	79.3
A8	22.76	212	42.3	85.5
A9	23.21	250	73.4	79.3
A10	25.8	199.2	62.9	77.5

>TRINITY_DN124154_c1_g1_i3 from sample A1 / Example spliced isoform

CTCTCTATAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAAGAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAA
AAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGA
GAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCT
TTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCACAGATAAACAGGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGA
TGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATGAATTTTTGTGGTAATGGAATCAACCTGGTTATGTTGTTTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTT
TGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGATTAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCA
CAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTACTGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTT
TCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTATGAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

>TRINITY_DN124154_c1_g1_i7 from sample A1 / Example unspliced isoform:

CTCTCTATAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAAGAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAA
AAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGATTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGA
GAAAGAGAAATATATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCT
TTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCTCAGATAAACATGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGgtatgtgtcatttttctcttcctttatacaggcact
ggatcttagtaacatatgccattttattataactggaaccatgcattgacagttcaggggtttgatgtcaacctgaagATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATCAATTTTTGTGTTAATGGAATCAACCTGGTTATGTTGT
TTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGAT
TAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACTTGGAATTTACTAGACTTAC
TGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGAAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTAT
GAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTG

Intron 5 GTAAGTTGGA ... TTCTGAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20	72	16	20
A2	21.74	90	29	21
A3	21.36	81	21	23
A4	24.71	64	19	23
A5	24	19	11	1
A6	20.43	111	35	22
A7	18.75	208	39	57
A8	21.51	166	47	44
A9	20.59	216	69	43
A10	19.57	189	57	35

>TRINITY_DN101309_c0_g1_i2 from sample A4 / Example spliced isoform

TAGGGATATGTAAATAGTGAAATAAAACGACATTAAACCAAAGTAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAA
GAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAAAAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGA
TTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGAGAAAGAGAAATACATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTAGCAAAGGAAACAAAACAGCTGGCA
GCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCTTTCTCTGCTGTTCAACAACACCTTGAAAACACACTTGGTCCACAGATAAACAGGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCG
ATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAAAAGCTTGATATGAATTTTTGTGGTAATGGAATCAACCTGGTTATGTTGTTTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTG
GGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGATCATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGATTAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGA
ATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGTTCGTAAGATACATGTGAGAGGGCTTGCACCTGGAATTTACTAGACTTACTGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTT
TTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTTTATTAATGTGATCAGGAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTATGAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTGTTTGACAATTCTAAAGTAAA
AATTACCTTATTCTTTTTCCAAAAGAAATATTGGAGTATCAACAG

>TRINITY_DN101309_c0_g1_i1 from sample A4 / Example unspliced isoform:

TAGGGATATGTAAATAGTGAAATAAAACGACATTAAACCAAAGTAGATTTGCGATTTGAACTTTGAAACCGGGGACATTGAAACTCCATTTTCACTGTGAAAAGAGGTTTTGATCAGGCCAATTTCAAGCATCCTCCGTCTGACAGGGGTTCGTTGTTTGTTTGAAGCATTTTCCAACAACTCTTAACAATGGTAAAGAA
GAGGACAACCCGTCAAAAGGTGAAAGACAAAGCCAAAAAGGTGTCTTCTGATATAAAGCAAGAAAATGGATCTACACCTGCGGAAGAAAGTGTAACTGATACAGGAAGTTTGCATGAACAAATTCCACAAAATATGAAGCGGAAAATGGCCAAGCAAATGCGCTTCTATGCTAAGTTGCAAGAGACTCAACAAGCTTTGA
TTGCTACAAAATCCATTGCTAAGAAGAGGCAACGGAGAAAGAGAAATACATCAGGTCAAACATTGAAGGATTTGTCATCTCTCTCTGAATCCCTTCCAATGTTTAGTGATAAAAAATCTGTTTCCCAAGTATATGACAGTGCCAAGGTGAACTGCAAATCCCGTCAAAAGCTTGTgtaagttggattctatgaaagtaat
ttactttgctaagaataaatggtaaactttaccatttttatgctgtgtagactaataattgatacactagaattaacttctctgtgaccttattctgaacagAGCAAAGGAAACAAAACAGCTGGCAGCTGTGCTGGCTCATCCGGTATTTGTTTCAAATCCTTTCTCTGCTGTTCAACAACACCTTGAAAACACACTTG
GTCCACAGATAAACAGGGAGTCCAAGCCTAAACATGGCAACAAGGAAAAATCCTCTAAAGGGTCAAAGAAGAAAAAGGGGTTAAAGGCATCTCCATCTAGCACAGTACAAGCAATGGAGCTATAGCGATTGCGAAGAATTCTGTGAATGAAGTTATGAACAGATGAGAAAATGATTTGCTATTCTATTTCAGTTAGCAAA
AAGCTTGATATGAATTTTTGTGGTAATGGAATCAACCTGGTTATGTTGTTTGAACATAATTGTTCACTTGTTTCATCTGTATGAAGCGACAACTTCCACAGAAAGTACTGGATAGCCCTCTGTGCTGGGTTCAAGCAACAACGTCTCAATCTCTTTGGGAGTTTGACTTTTCATGGTTCTTTTAGGTTACAATCGAGGAT
CATATAAGATGCATAGTTCGGTTGCATGAATGACTAATGAAATAGTGATTAGACAAGAAAATTTGTAACAAATGACAATCCTTTTCATGTGAGATGATGGAGGATTGGAATCGTGCATTTTGCAAGAATAACACAGTTATATTCTGTAGGATATCAATTAGCACAAATGGAAATGAACCTGATATTGAGAGTTAGACGGT
TCGTAAGATACATGTGAGAGGGCTTGCACCTGGAATTTACTAGACTTACTGTTAGATGCAACAGTTGTGGAACAGAGGCTTGTCTATCAATGTACTTGGGGTTATATATCTGGTTTTCTTCATGTTTTTGACCTTGTATTAGTTGCCTCTGGTTACATTTCTTTCTCTCCTTTGAGGTATCTGATTTGTTAAGTTGACTT
TATTAATGTGATCAGGAGTGTTCCTCCCGAGGAAAGAGTATGTTGTTATGAGAGGCATTATTTTCTCTGGAAGGCTTGATCAGTTCATCTGGGTTTTGCCTAACTTGTTTGACAATTCTAAAGTAAAAATTACCTTATTCTTTTTCCAAAAGAAATATTGGAGTATCAACAG