sp|O64527|NB_ARATH ----> Peroxynitrite isomerase Rv2717c

Intron 1 GTGAAGAAAA ... ATGAGTTAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	58.06	13	28	8
A2	60	10	21	9
A3	42.11	11	9	7
A4	64.71	6	14	8
A5	64.71	3	5	6
A6	64.2	58	132	76
A7	65.96	64	157	91
A8	66.6	85	211	128
A9	63.14	75	164	93
A10	60.36	44	92	42

>TRINITY_DN35551_c0_g1_i6 from sample A9 / Example spliced isoform

ATTATCCAAGGCAATAATTCAAATGAAAAATTAATTGAACTATTTGATTCGCCCAAAGCATCTACAACTATACCTGTATGAACACGACATAAGCGGAAGTGGCGGTTCAGAAATCGATTGAATGGAAGGAGGCGCAATTCATCCAGGCATAGCTCCCATTTCATTCTTGCTGGGCACATGGCGAGGGGAGGGCGAGGGAG
GATTCCCTACAATCCAATCCTTTAAGTATGGAGAAGAAATTAAGTTCTGGCACTCTGGCAAGCCGGTGATTGCCTATACTCAGAAGACATGGAAATTAGCTTCTGGTGAACCAATGCATGCGGAGAGTGGCTACTGGAGGCCCAAAATGGATGGATCTATAGAAGTCATTATTGCTCAAAGCACTGGACTAGCAGAGGTT
CAGAAAGGGATCTATGATGCTGAGAAGAAAATTGTGAAGCTTCAAAGTGAGCTTGTTGGAAATGCATCCAAGGTGTGCAGTGTTTGTGTTTTTGAGGAAGATGGATAAAGAAAAGGTAAAGGTATTGGTCCCTTTGAGTTTGCAGCATGATAGTCTTGGATAGGTACAGCACTTCCGGAGTTTCCAGTGATGACACATGG
ACAAGTGTCTGTTGGTGAGGGTGTCTTAGCTACACCTTGATGATGTACAAGTGATAGAGCAAATGATACCATGGGTTTATTGATGCAGTGGTTGTGATTGGATATACATGTGTGGTTAGAAGTTGCTTTATGATTGCTCATCATGTATTCCCTAGATCATAGCATGGATTTGGTTATATGATGATGTCGGAGACCCTTCA
GCTAGAGCATTTTATTTGATTGGGGGCATATTTCATGTCCCTGTATGATGTATCACATTATTGAGGGGAGCACTGTAACATATATAATAATGATAATAACAAATAATAGTTAACTAAGGGATAATATTAATAAATAATAGTTAACTAAGG

>TRINITY_DN35551_c0_g1_i1 from sample A9 / Example unspliced isoform:

ATTATCCAAGGCAATAATTCAAATGAAAAATTAATTGAACTATTTGATTCGCCCAAAGCATCTACAACTATACCTGTATGAACACGACATAAGCGGAAGTGGCGGTTCAGAAATCGATTGAATGGAAGGAGGCGCAATTCATCCAGGCATAGCTCCCATTTCATTCTTGCTGGGCACATGGCGAGGGGAGGGCGAGGGAG
GATTCCCTACAATCCAATCCTTTAAGTATGGAGAAGAAATTAAGTTCTGGCACTCTGGCAAGCCGGTGATTGCCTATACTCAGAAGACATGGAAATTAGCTTCTGGTGAACCAATGCATGCGGAGAGTGGCTACTGGAGGCCCAAAATGGATGGATCTATAGAAGTCATTATTGCTCAAAGCACTGGACTAGCAGAGGTT
CAGAAAGGGATCTATGATGCTGAGAAGAAAATTGTGAAGCTTCAAAGTGAGCTTGTTGGAAATGCATCCAAGgtgaagaaaataacacgagtttttgagctaaatggcaatgagttaagGTGTGCAGTGTTTGTGTTTTTGAGGAAGATGGATAAAGAAAAGGTAAAGGTATTGGTCCCTTTGAGTTTGCAGCATGATAG
TCTTGGATAGGTACAGCACTTCCGGAGTTTCCAGTGATGACACATGGACAAGTGTCTGTTGGTGAGGGTGTCTTAGCTACACCTTGATGATGTACAAGTGATAGAGCAAATGATACCATGGGTTTATTGATGCAGTGGTTGTGATTGGATATACATGTGTGGTTAGAAGTTGCTTTATGATTGCTCATCATGTATTCCCT
AGATCATAGCATGGATTTGGTTATATGATGATGTCGGAGACCCTTCAGCTAGAGCATTTTATTTGATTGGGGGCATATTTCATGTCCCTGTATGATGTATCACATTATTGAGGGGAGCACTGTAACATATATAATAATGATAATAACAAATAATAGTTAACTAAGGGATAATATTAATAAATAATAGTTAACTAAGG

Intron 2 GTATGACTGG ... TCGCGCCAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25.64	29	0	10
A2	8	23	0	2
A3	15.15	56	0	10
A4	29.63	19	0	8
A5	18.75	13	0	3
A6	20.97	196	0	52
A7	16.1	224	1	43
A8	20.18	265	2	67
A9	21.97	270	0	76
A10	17.71	223	0	48

>TRINITY_DN35344_c0_g1_i5 from sample A8 / Example spliced isoform

ATTTGATTCGCCCAAAGCATCTACAACTATACCTGTATGAACACGACATAAGCGGAAGTGGCGGTTCAGAAATCGATTGAATGGAAGGAGGCGCAATTCATCCAGGCATAGCTCCCATTTCATTCTTGCTGGGCACATGGCGAGGGGAGGGCGAGGGAGGATTCCCTACAATCCAATCCTTTAAGTATGGAGAAGAAATT
AAGTTCTGGCACTCTGGCAAGCCGGTGATTGCCTATACTCAGAAGACATGGAAATTAGCTTCTGGTGAACCAATGCATGCGGAGAGTGGCTACTGGAGGCCCAAAATGGATGGATCTATAGAAGTCATTATTGCTCAAAGCACTGGACTAGCAGAGGTTCAGAAAGGGATCTATGATGCTGAGAAGAAAATTGTGAAGCT
TCAAAGTGAGCTTGTTGGAAATGCATCCAAGGTGAAGAAAATAACACGAGTTTTTGAGCTAAATGGCAATGAGTTAAGGTATGTGATTGAGATGGCTACAACAACAAATGATTTACAACCCCATCTTCAAGCATTGCTTAAGAAGATATAACTCTGAACTTAAACACATGATTATAAGAAGCATGATGTTTGTACACGAA
CCTTGTTTTCAGATTACTTTTTAATATTGCTACCCTAAGATGTCTCGTTCCTTTATTTTCTAAAATTAGATGTGTCAATACTGGGTGTATGGTTCTCTTTGATCGTTATAAAAATTAGATGATCATCCATGAAATTCTTAAATTATTTAAAAGTGTTAGAGGAACACCATGACCTAGTGAGATTAACACGACAATATATT
CTTGGGAGATTGAATTGGGGTCTAAGTGAAGAAAGCTCACTTGATACTTTTGAGTCACAACCCACTTGATAATTTCCACATAAA

>TRINITY_DN35344_c0_g1_i1 from sample A8 / Example unspliced isoform:

TTAAGTTCTGGCACTCTGGCAAgtatgactggcaaggacaatagacaaggaataattcaacgccattggaggaagattttttgtgattggatttgaaagcagttacctcgcgccaagGCCGGTGATTGCCTATACTCAGAAGACATGGAAATTAGCTTCTGGTGAACCAATGCATGCGGAGAGTGGCTACTGGAGGCCCA
AAATGGATGGATCTATAGAAGTCATTATTGCTCAAAGCACTGGACTAGCAGAGGTTCAGAAAGGGATCTATGATGCTGAGAAGAAAATTGTGAAGCTTCAAAGTGAGCTTGTTGGAAATGCATCCAAGGTGAAGAAAATAACACGAGTTTTTGAGCTAAATGGCAATGAGTTAAGGTATGTGATTGAGATGGCTACAACA
ACAAATGATTTACAACCCCATCTTCAAGCATTGCTTAAGAAGATATAACTCTGAACTTAAACACATGATTATAAGAAGCATGATGTTTGTACACGAACCTTGTTTTCAGATTACTTTTTAATATTGCTACCCTAAGATGTCTCGTTCCTTTATTTTCTAAAATTAGATGTGTCAATACTGGGTGTATGGTTCTCTTTGAT
CGTTATAAAAATTAGATGATCATCCATGAAATTCTTAAATTATTTAAAAGTGTTAGAGGAACACCATGACCTAGTGAGATTAACACGACAATATATTCTTGGGAGATTGAATTGGGGTCTAAGTGAAGAAAGCTCACTTGATACTTTTGAGTCACAACCCACTTGATAATTTCCACATAAA