sp|Q8W4F1|PAP10_ARATH ----> Probable plastid-lipid-associated protein 10, chloroplastic

Intron 1 GCATTGCATT ... ATTGGATTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	76.74	10	7	33
A2	72.09	12	6	31
A3	52.27	21	8	23
A4	50	9	3	9
A5	76.92	6	3	20
A6	60.92	34	8	53
A7	56.67	52	16	68
A8	55.96	48	12	61
A9	61.03	53	11	83
A10	79.52	17	6	66

>TRINITY_DN37359_c0_g1_i6 from sample A6 / Example spliced isoform

AACCCACACCAAGTGAGCGCTCAAATGTGTAAAACAACATTACCGATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATT
TGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTTGCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGGTAAGCGTGGAGC
AATATGATGCTGGTATACCAATCAATCTGAACCAGCTAGACGGAACGTGGCTTCTGCAATACACATCAGCATCGGATGTCCTTGTTTTATTTCAAGCTGCCAGCCTTCCCCTTTTTCAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTT
CCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACG
CAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTT
TTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAA
ATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGATATTCATTTTTAAAGTTCAGGGGTGGAAGTCCTTCTGTTTGTGGA

>TRINITY_DN37359_c0_g1_i3 from sample A6 / Example unspliced isoform:

AACCCACACCAAGTGAGCGCTCAAATGTGTAAAACAACATTACCGATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATT
TGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTTGCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGGTAAGCGTGGAGC
AATATGATGCTGGTATACCAATCAATCTGAACCAGCTAGACGGAACGTGGCTTCTGCAATACACATCAGCATCGGATGTCCTTGTTTTATTTCAAGCTGCCAGCCTTCCCCTTTTTCAGgcattgcatttaagggaatgctcgaagggaatgttgggagagagatcagataagagtgttatgcatagtgagggggttgga
aaaatgatttttctaaattttgcagtgtggggggtcacaaaggttccaacaaatggctgcaacattggattagGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTG
CAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAA
GCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATC
CAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGAT
ATTCATTTTTAAAGTTCAGGGGTGGAAGTCCTTCTGTTTGTGGA

Intron 2 GTACCTTTAT ... TTATTTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	12.79	32	2	5.5
A2	13.18	19.6	0	3.5
A3	12.5	15	0	2.5
A4	10	16	1	2
A5	16.66	6	1	1.5
A6	10.52	79	10	10
A7	10.72	88	5	12
A8	10.23	113	4	14
A9	7.02	98	4	8
A10	8.65	86	6	9

>TRINITY_DN37359_c0_g1_i1 from sample A6 / Example spliced isoform

AGTTCTGTATCTGACTTGAAGGCCTTGATTTATTTCAAGTTATTGGTATTGTAACCGGCTAAGGTTATGGCGATGTTGTATTTTTTTCAATTCATCATTTTCTGTCCTATCATGCATGGACTTTCATTTTCTTGTATCTTTGTGGTTGTCACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGT
TATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGG
CCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCA
TGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGATATTCATTTTTAAAGT
TCAGGGGTGGAAGTCCTTCTGTTTGTGGA

>TRINITY_DN37359_c0_g1_i5 from sample A6 / Example unspliced isoform:

TTTTTACTAACTTATTGTATCTGGTTAATTCTCTCAGTTTATTACAGATAATCATTATTTTGAACCGTGGTTTGAGTCCCAAATATCAGAATCTATAGACCGCTGTTTCTTTTTTTTTCCCAAATTTTTATAATGGCACAGATGATTGTGTATTTTCAGTAATACATCACATTTTTACAAAAATGACTTTTAAATGGCCA
GGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGGGACAAGAATGTACCACATCAGGAGACATTCCCATGATGGATGACAATAGCTTGAATTAGTCTCTTTTGGATTGAAGTATTAAAGGAGCTGCCTGATTAGGACATTGGAACT
CTTGCAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGgtacctttatgttatatctatagatacaacaaatttgcttgcatgatagtatttggtcatcaactcaagtgtattcatgtctgaagaagtggtgtcccttatttcttgcccatgct
ttgattaggttttacttataaatttgtttatttgtagGCCTTCACCTGGTGGACT

Intron 3 GCAAGTTTTC ... GTTGTCACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	28.68	46.2	20	17
A2	28.46	45.9	26	10
A3	16.7	45.1	7	11
A4	27.96	19.4	9	6
A5	35.13	17.8	16	3
A6	19.96	88.5	19	25
A7	23.66	129.4	44	36
A8	25.28	115.8	38	40
A9	23.15	123.3	45	29
A10	25.68	106.9	46	27

>TRINITY_DN120162_c2_g1_i12 from sample A1 / Example spliced isoform

GCTTTTCCCATCAATTCTGCTCAGTTGAGTATCTCCCATTGGTTCCTCCTTTAGTCAGTTCTTTGACCAGTCAATTTCTTCAATCAAATTAGCCTTAGTCAATTACTCATTTTGTTGACCATCCAACTACATAGCCAATGTGTTGCCCCAAACACTGTACACTTTCTGGATTCAACTTATCGTCAATATCCGGATCTGAT
TTTGGATTAGGATTCCTTTCATTATAAGATATATTTCAGCTTTTCGTGTTGAGATGGATGCATATTAGCATCTTTGAAACAAACTAGGTTCATTTACTAGCAAATATCCAACAGAAGGACTGTAGACAGAAATACATATAGGACAGTAATATAAATAATAAAGTATGAATGAATAGAAAAGAGATATGATTACAATGCTA
TGGTACTGTGTACATATATGCATTGACTGGTCACCATGGTTGATAGGTCATGTCTTTTAATTAGGATGTGTCTTTTCATTTATTATATTAAGTTATTAACCATTATTTATTATCGTTATCATTATTTAATAATTTATTGATGCATATATATTTATGATCACTACAATCTTGGTTACCTTCCTTTCCAAAACAAGTTTAAT
GCCTTTTTATCCATCATTCTGAGACATACAAGAAGAACTGTTACTATGGATTCTACTTTGGAACCCAACAGTAACATCCTTTCTTAGTTCCATATTAATGATAAGACTTAAACTTAACTCTTAACTTTTTTGCTTATAAGGCATTGCATTTAAGGGAATGCTCGAAGGGAATGTTGGGAGAGAGATCAGATAAGAGTGTT
ATGCATAGTGAGGGGGTTGGAAAAATGATTTTTCTAAATTTTGCAGTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGGAAAATGAAG
GTGCAACATTATTAGTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTT
CTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCC
TTTGTAATGGTTGATTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCA

>TRINITY_DN120162_c2_g1_i19 from sample A1 / Example unspliced isoform:

GCTTTTCCCATCAATTCTGCTCAGTTGAGTATCTCCCATTGGTTCCTCCTTTAGTCAGTTCTTTGACCAGTCAATTTCTTCAATCAAATTAGCCTTAGTCAATTACTCATTTTGTTGACCATCCAACTACATAGCCAATGTGTTGCCCCAAACACTGTACACTTTCTGGATTCAACTTATCGTCAATATCCGGATCTGAT
TTTGGATTAGGATTCCTTTCATTATAAGATATATTTCAGCTTTTCGTGTTGAGATGGATGCATATTAGCATCTTTGAAACAAACTAGGTTCATTTACTAGCAAATATCCAACAGAAGGACTGTAGACAGAAATACATATAGGACAGTAATATAAATAATAAAGTATGAATGAATAGAAAAGAGATATGATTACAATGCTA
TGGTACTGTGTACATATATGCATTGACTGGTCACCATGGTTGATAGGTCATGTCTTTTAATTAGGATGTGTCTTTTCATTTATTATATTAAGTTATTAACCATTATTTATTATCGTTATCATTATTTAATAATTTATTGATGCATATATATTTATGATCACTACAATCTTGGTTACCTTCCTTTCCAAAACAAGTTTAAT
GCCTTTTTATCCATCATTCTGAGACATACAAGAAGAACTGTTACTATGGATTCTACTTTGGAACCCAACAGTAACATCCTTTCTTAGTTCCATATTAATGATAAGACTTAAACTTAACTCTTAACTTTTTTGCTTATAAGGCATTGCATTTAAGGGAATGCTCGAAGGGAATGTTGGGAGAGAGATCAGATAAGAGTGTT
ATGCATAGTGAGGGGGTTGGAAAAATGATTTTTCTAAATTTTGCAGTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGgcaagttttc
aacttcatatagatgaagatagagttctgtatctgacttgaaggccttgatttatttcaagttattggtattgtaaccggctaaggttatggcgatgttgtatttttttcaattcatcattttctgtcctatcatgcatggactttcattttcttgtatctttgtggttgtcacagGAAAATGAAGGTGCAACATTATTA
GTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGA
TGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGA
TTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCA

Intron 4 GTAAGCGTGG ... CCTTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	64.18	12	30	13
A2	71.88	9	34	12
A3	72.6	10	32	21
A4	76.19	5	17	15
A5	73.91	3	9	8
A6	69.33	23	67	37
A7	74.86	22	72	59
A8	71.43	21	66	39
A9	69.15	29	78	52
A10	57.82	31	40	45

>TRINITY_DN40070_c0_g1_i6 from sample A7 / Example spliced isoform

GATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATTTGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTT
GCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAA
ATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACA
ATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTG
GTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAG
GCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCG

>TRINITY_DN40070_c0_g1_i2 from sample A7 / Example unspliced isoform:

GATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATTTGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTT
GCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGgtaagcgtggagcaatatgatgctggtataccaatcaatctgaaccagctagacgga
acgtggcttctgcaatacacatcagcatcggatgtccttgttttatttcaagctgccagccttcccctttttcagTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAG
CGTTCCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTT
TACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTG
TTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTA
TGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCG

Intron 5 GCATTGCATT ... AATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48	13	7	17
A2	41.46	12	6	11
A3	33.33	21	8	13
A4	18.92	15	3	4
A5	46.67	8	3	11
A6	31.48	37	8	26
A7	25.32	59	16	24
A8	28.44	39	12	19
A9	27.27	52	11	28
A10	27.42	45	6	28

>TRINITY_DN37359_c0_g1_i4 from sample A6 / Example spliced isoform

AACCCACACCAAGTGAGCGCTCAAATGTGTAAAACAACATTACCGATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATT
TGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTTGCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGGTAAGCGTGGAGC
AATATGATGCTGGTATACCAATCAATCTGAACCAGCTAGACGGAACGTGGCTTCTGCAATACACATCAGCATCGGATGTCCTTGTTTTATTTCAAGCTGCCAGCCTTCCCCTTTTTCAGTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAA
GGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGC
ATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCA
GTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCA
TAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGATATTCATTTTTAAAGTTCAGGGGTGGAAGTCCTTCTGTTTGTGGA

>TRINITY_DN37359_c0_g1_i3 from sample A6 / Example unspliced isoform:

AACCCACACCAAGTGAGCGCTCAAATGTGTAAAACAACATTACCGATGGATATGGTTGTGTTTGGTGGTTGTTCAATACCATCCAATTTTCATGGAAGAGCACTGCAGAAGACCAGAATGGCAGCACTACTGCAGAACAGCAAACCCAAAATGCAACCATCTGCTTTGCAATTATTCATGACTTATACACCTTTACCATT
TGGGATTTTAACGAAAGATCGCAGGGGTGCAACTAGATTCGCTTGCAGAGCATACACAGAGTCTTCTGAGTCACAGGCCGCGAGAGAATTGCAGAAGCGCAAGATAGAGTTGCTCAGAGCTGCCCAAAATACTCAGCGTGGATTCCAGGCTTCTCATGATCAGCGCGCTGCTATTGAAGAAGCTATGGTAAGCGTGGAGC
AATATGATGCTGGTATACCAATCAATCTGAACCAGCTAGACGGAACGTGGCTTCTGCAATACACATCAGCATCGGATGTCCTTGTTTTATTTCAAGCTGCCAGCCTTCCCCTTTTTCAGgcattgcatttaagggaatgctcgaagggaatgttgggagagagatcagataagagtgttatgcatagtgagggggttgga
aaaatgatttttctaaattttgcagTGTGGGGGGTCACAAAGGTTCCAACAAATGGCTGCAACATTGGATTAGGTTGGACAAATTTATCAAAAGTTTGAATGTAAAGGATGTGATGATGGAGGAATTGTTCGCAACATAGTTCGTTGGAGCGTTCCAAGTATTTTACAGGAAAATGAAGGTGCAACATTATTAGTCACTG
CAAAATTTTCACTGTTATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAA
GCTGAGAGGAGGAGGCCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATC
CAGTACTTCCATTCATGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGAT
ATTCATTTTTAAAGTTCAGGGGTGGAAGTCCTTCTGTTTGTGGA

Intron 6 GTATGAACAA ... ACTCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	18.49	38	9.4	2
A2	3.62	16	0.6	2
A3	27.12	24	9.5	0
A4	11.4	22	3.1	5
A5	9.46	11	1.2	0
A6	11.95	74	10.6	9
A7	13.04	92	14.5	3
A8	11.96	103	14.9	5
A9	6.84	88	6.8	5
A10	7.66	90	7.8	4

>TRINITY_DN37359_c0_g1_i1 from sample A6 / Example spliced isoform

AGTTCTGTATCTGACTTGAAGGCCTTGATTTATTTCAAGTTATTGGTATTGTAACCGGCTAAGGTTATGGCGATGTTGTATTTTTTTCAATTCATCATTTTCTGTCCTATCATGCATGGACTTTCATTTTCTTGTATCTTTGTGGTTGTCACAGGAAAATGAAGGTGCAACATTATTAGTCACTGCAAAATTTTCACTGT
TATCTCAGCGCAATATATATTTGCAGTTTGAAGAGGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGG
CCTTCACCTGGTGGACTGTATTACCTTTCGTATTTGGATCGCGATATGCTTTTGGGGCGTGCACTTGGTGGTGGTGGAATTTTCGTTTTCAGTCGGACACAACCCTTTCAAGTTTAACTGTCTGCAGAACCTCTGTTTTTTATAATTTCCAGCTGATTGGCTCCTTTGTAATGGTTGATTTTATCCAGTACTTCCATTCA
TGATAAGAAAACACATTTGGCTGTATTGGATTTTATTGTGCATTGGTGCCTTTGTTATGAACAAAAGGCTACTTTCTGCCTTAAGTACCCATAAACCCAACCAGGAAGGAAATAGCTTTATTCTTTGTCATTTTATGAAATAGTGTTTTTGATGGCTTTGCAATCTATATATGCATTTTTAAGATATTCATTTTTAAAGT
TCAGGGGTGGAAGTCCTTCTGTTTGTGGA

>TRINITY_DN37359_c0_g1_i2 from sample A6 / Example unspliced isoform:

TTTTTACTAACTTATTGTATCTGGTTAATTCTCTCAGTTTATTACAGATAATCATTATTTTGAACCGTGGTTTGAGTCCCAAATATCAGAATCTATAGACCGCTGTTTCTTTTTTTTTCCCAAATTTTTATAATGGCACAGATGATTGTGTATTTTCAGTAATACATCACATTTTTACAAAAATGACTTTTAAATGGCCA
GGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGgtatgaacaatatttgtttgagcatgctgcgtgctttatgttttagtctgcacctgtctcttagattgtagctttatatattaacttgtatgtttttatcatttcacttgat
caaaccggagaagcactccaagccatcttgcatgatattgaagttgaactcatcaattatgaaactgtacaactttgggaatggattctagggacaagaatgtaccacatcaggagacattcccatgatggatgacaatagcttgaattagtctcttttggattgaagtattaaaggagctgcctgattaggacattgga
actcttgcagATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGTACCTTTATGTTATATCTATAGATACAACAAATTTGCTTGCATGATAGTATTTGGTCATCAACTCAAGTGTATTCATGTCTGAAGAAGTGGTGTCCCTTATTTCTTGCCCAT
GCTTTGATTAGGTTTTACTTATAAATTTGTTTATTTGTAGGCCTTCACCTGGTGGACT

Intron 7 GTATGAACAA ... TGGATTCTAG

Found issues: Low number of reads

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.43	1	2	3
A2	-1	0	0	0
A3	80	1	4	4
A4	23.08	5	0	3
A5	-1	0	0	0
A6	38.46	4	2	3
A7	45.45	3	4	1
A8	75	1	2	4
A9	50	1	0	2
A10	50	2	1	3

>TRINITY_DN37359_c0_g1_i5 from sample A6 / Example spliced isoform

TTTTTACTAACTTATTGTATCTGGTTAATTCTCTCAGTTTATTACAGATAATCATTATTTTGAACCGTGGTTTGAGTCCCAAATATCAGAATCTATAGACCGCTGTTTCTTTTTTTTTCCCAAATTTTTATAATGGCACAGATGATTGTGTATTTTCAGTAATACATCACATTTTTACAAAAATGACTTTTAAATGGCCA
GGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGGGACAAGAATGTACCACATCAGGAGACATTCCCATGATGGATGACAATAGCTTGAATTAGTCTCTTTTGGATTGAAGTATTAAAGGAGCTGCCTGATTAGGACATTGGAACT
CTTGCAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGTACCTTTATGTTATATCTATAGATACAACAAATTTGCTTGCATGATAGTATTTGGTCATCAACTCAAGTGTATTCATGTCTGAAGAAGTGGTGTCCCTTATTTCTTGCCCATGCT
TTGATTAGGTTTTACTTATAAATTTGTTTATTTGTAGGCCTTCACCTGGTGGACT

>TRINITY_DN37359_c0_g1_i2 from sample A6 / Example unspliced isoform:

TTTTTACTAACTTATTGTATCTGGTTAATTCTCTCAGTTTATTACAGATAATCATTATTTTGAACCGTGGTTTGAGTCCCAAATATCAGAATCTATAGACCGCTGTTTCTTTTTTTTTCCCAAATTTTTATAATGGCACAGATGATTGTGTATTTTCAGTAATACATCACATTTTTACAAAAATGACTTTTAAATGGCCA
GGTTGCAGTTGGGAACTTGAGGATCAATGAACAATTACAGGCACTAATAGCTCCAGCATTTTTGCCACGAACATCTTTGAGTCTGGAGgtatgaacaatatttgtttgagcatgctgcgtgctttatgttttagtctgcacctgtctcttagattgtagctttatatattaacttgtatgtttttatcatttcacttgat
caaaccggagaagcactccaagccatcttgcatgatattgaagttgaactcatcaattatgaaactgtacaactttgggaatggattctagGGACAAGAATGTACCACATCAGGAGACATTCCCATGATGGATGACAATAGCTTGAATTAGTCTCTTTTGGATTGAAGTATTAAAGGAGCTGCCTGATTAGGACATTGGA
ACTCTTGCAGATTTTGCAATTTTTACGCAGTTTTGAAACAAAGATCCCACTTCTTGGGAATAGTGATGATCAAGCTGAGAGGAGGAGGTACCTTTATGTTATATCTATAGATACAACAAATTTGCTTGCATGATAGTATTTGGTCATCAACTCAAGTGTATTCATGTCTGAAGAAGTGGTGTCCCTTATTTCTTGCCCAT
GCTTTGATTAGGTTTTACTTATAAATTTGTTTATTTGTAGGCCTTCACCTGGTGGACT