sp|Q42885|AROC2_SOLLC ----> Chorismate synthase 2, chloroplastic

Intron 1 GTAATGAAAA ... AACTTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	40.21	94	48.4	78
A2	28.44	80	30.6	33
A3	33.39	78.4	28.6	50
A4	32.39	48	21	25
A5	36.95	64	32	43
A6	31.37	35	0	32
A7	31	69	0	62
A8	29.55	31	0	26
A9	27.95	58	2	43
A10	31.18	52	0	47.1

>TRINITY_DN125752_c0_g1_i18 from sample A1 / Example spliced isoform

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAA
GCATCATGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGGA

>TRINITY_DN125752_c0_g1_i10 from sample A1 / Example unspliced isoform:

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGGTTCTTATCCCAGCCCGCTTATTATCCCAGCTTCGTTTTATTTAGCTTAACGGGAAAATATATTTTCTGCAAATAATTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCACT
GGGATCTCTTCTCCCAGTGAATTTCTGACTGGGATATATTTATGTTTCTGTATTTGCTTTGCAGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATCATgtaatgaaaatata
ttttctgcaaataatttttgtatttgccttgttcattctagtagaaattcattgggatctcttctcctaggaaattgtaaatgctctattgaatatcaatccccaatatcaaaaacagaatataataaactattggtctcgagaaggtagggcagtgctggggtaggttcgatagcaaggaggtgcttcggcagggtaga
tcacttgtagggatactctagtttggcaaggcagatagctcttattgggtgatcaggaaaggttcataaatatttgactcattgacctgttgtgtacctcaccatgacatatttgttaggcattggactctctctacatgagctattttgtttatatgctcgtgatttaaaagacatgagctattttgtttatatgctcg
tgatttaaaagaccacaattaggttacatttaccattttgaggatggcaaatttgatggacagtttgagtggcatcaactactccattaagatatattttcataatataacagaatataataaactattgaatatcagtgcataacataaaaaatacaggtaataatccacccgctgtaagttacatagaccagatcaat
atatgctagttttttctcttacaagatgcttcatattatcaccactagtgcctcttccaccagtaaccttgaaacttggtggagatgtgagatgaaacaggccctctccagcctggcccattcacattatataaatttcactatcacaaaaaaactaaggctgatgatcaggtgagcctgattctctttgtgggaaggca
gttctctgattagttcctctgctaggatgattgttatggataggagaagggcgagatggaggaacctgacctttggggagcatctgaaacacgttcataacatcacgggagtaccttctgctgtgcaatatgacattctagacatgattgatatcttgaaccctattgtttccagacccattttgctgttcttgtcttac
catgagattctggacatgatggatatcttgaaccctgttgtttccagacccaatttgctgatcttgtcttactgaggatcttgaagatacaagatcaacattagagacaagagaccttcgaccctctgcaatcaccatggctgggagaaccaaaatgaaaatcatctccaaccatagaacattgtaacaatggagcacca
ttgccataaatatcagtccagtgcaattatatgaaaaactggcttctgcaattgctttttcgttctataaattccttcctactgagaagaattctacagaagtgaagatatgagacgtagtagacaagcatattgatttgaaccaatgcaatgagcgcgtctgatatagatacatatatataatcattatactcccaata
aagaccagtacagttcattgtgtattttcaggacaagtgtgggttggttggttcccagaaaaacatgttttcttataacctgtaatctatttcgatgataccctaagaatcataatcacaggctcaaaacctaaaatagtttttgtatttgccttgttcattctagtagaaattcattgggaattccattttcaacatag
gtgactaattcatcccacaggtatccaaagtacttagtatgaattcatttatcatgtaaatataaactactcaggtccaagaagacaaagatttgtttcctatcttgtgctatgtggtactattagtttaatgcttattgtattatgatggaaacaaagactgaatattatcaattttgtgagtatgggaaggtgacaaa
gatgtacattatgtcctaggatttgagtgttccaaaagtggagaaattgatcatggtagcttgactttaggaacttgagaaattaagatctttattgttgttctttacctaaaaattgcccaaacttacttattgttgctggttgaggctaaatcaaggatgccactacaaggaagattcccacattatacctaggaccg
atcttactgctgtttggagggttgagacattgttaaaacatacccagaactatcagaatgcccaaaaacgctaggaaacaacctagcatggagtgctgctacaagaattaagctgcttgctttagggaggagtatctgtaagtctctaaggacttcggagccttgcatttttacttttcttgtgttgagggtgaagtcta
gtagaggggcaatcactaccaggcggagtagtgcaatgctactatctagtattaaatgtttagctgttgacacctataagccctatggtttggtccctaagtccaaacatgtatgctatccatgtatatctggacctgttaagtctaaccatcctgatttgtgttcctttatgtggttatggtaacgtgataagtacttg
gataactcataaaagctcttggagacaattcactctatgatgattatgtctactgacattgtgagtgcccggctacagagttgatactgtgaatagagaataggattatgtcatatatttaggcattgagttttacaaagtgattgacaattgtttaaagcattcaagcttttgaaagtccacatccactctttcttgat
tgcattttactgaacttgacagGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGG
AAAGTGTGACCTCTTCCAAGGAAAATGGGTGCATGACTCTCTTGGGCCG

Intron 2 GTAAATAGAT ... TGCTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.01	72	20.3	5.7
A2	33.36	56.3	28.2	12.3
A3	32.75	71.7	35	11.3
A4	26.14	26.3	9.3	10.7
A5	31.77	38	17.7	9.3
A6	33.33	1.7	0.8	0
A7	0	4	0	0
A8	-1	0	0	0
A9	0	1	0	0
A10	-1	0	0	0

>TRINITY_DN125752_c0_g1_i12 from sample A1 / Example spliced isoform

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGTTCAAGAAAAGATATAAAGAGAAGAAGGATGATCAGGGAGCG

>TRINITY_DN125752_c0_g1_i10 from sample A1 / Example unspliced isoform:

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGgtaaatagatctaaggcaagcaataatcagacgagcaagcgagaacaatccccggttcttatcccagcccgcttattatcccagcttcgttttatttagcttaacgggaaaatatattttctgcaaataatttttgtatttgccttgttcattctagtagaaattcact
gggatctcttctcccagtgaatttctgactgggatatatttatgtttctgtatttgctttgcagAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATCATGTAATGAAAATATA
TTTTCTGCAAATAATTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCATTGGGATCTCTTCTCCTAGGAAATTGTAAATGCTCTATTGAATATCAATCCCCAATATCAAAAACAGAATATAATAAACTATTGGTCTCGAGAAGGTAGGGCAGTGCTGGGGTAGGTTCGATAGCAAGGAGGTGCTTCGGCAGGGTAGA
TCACTTGTAGGGATACTCTAGTTTGGCAAGGCAGATAGCTCTTATTGGGTGATCAGGAAAGGTTCATAAATATTTGACTCATTGACCTGTTGTGTACCTCACCATGACATATTTGTTAGGCATTGGACTCTCTCTACATGAGCTATTTTGTTTATATGCTCGTGATTTAAAAGACATGAGCTATTTTGTTTATATGCTCG
TGATTTAAAAGACCACAATTAGGTTACATTTACCATTTTGAGGATGGCAAATTTGATGGACAGTTTGAGTGGCATCAACTACTCCATTAAGATATATTTTCATAATATAACAGAATATAATAAACTATTGAATATCAGTGCATAACATAAAAAATACAGGTAATAATCCACCCGCTGTAAGTTACATAGACCAGATCAAT
ATATGCTAGTTTTTTCTCTTACAAGATGCTTCATATTATCACCACTAGTGCCTCTTCCACCAGTAACCTTGAAACTTGGTGGAGATGTGAGATGAAACAGGCCCTCTCCAGCCTGGCCCATTCACATTATATAAATTTCACTATCACAAAAAAACTAAGGCTGATGATCAGGTGAGCCTGATTCTCTTTGTGGGAAGGCA
GTTCTCTGATTAGTTCCTCTGCTAGGATGATTGTTATGGATAGGAGAAGGGCGAGATGGAGGAACCTGACCTTTGGGGAGCATCTGAAACACGTTCATAACATCACGGGAGTACCTTCTGCTGTGCAATATGACATTCTAGACATGATTGATATCTTGAACCCTATTGTTTCCAGACCCATTTTGCTGTTCTTGTCTTAC
CATGAGATTCTGGACATGATGGATATCTTGAACCCTGTTGTTTCCAGACCCAATTTGCTGATCTTGTCTTACTGAGGATCTTGAAGATACAAGATCAACATTAGAGACAAGAGACCTTCGACCCTCTGCAATCACCATGGCTGGGAGAACCAAAATGAAAATCATCTCCAACCATAGAACATTGTAACAATGGAGCACCA
TTGCCATAAATATCAGTCCAGTGCAATTATATGAAAAACTGGCTTCTGCAATTGCTTTTTCGTTCTATAAATTCCTTCCTACTGAGAAGAATTCTACAGAAGTGAAGATATGAGACGTAGTAGACAAGCATATTGATTTGAACCAATGCAATGAGCGCGTCTGATATAGATACATATATATAATCATTATACTCCCAATA
AAGACCAGTACAGTTCATTGTGTATTTTCAGGACAAGTGTGGGTTGGTTGGTTCCCAGAAAAACATGTTTTCTTATAACCTGTAATCTATTTCGATGATACCCTAAGAATCATAATCACAGGCTCAAAACCTAAAATAGTTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCATTGGGAATTCCATTTTCAACATAG
GTGACTAATTCATCCCACAGGTATCCAAAGTACTTAGTATGAATTCATTTATCATGTAAATATAAACTACTCAGGTCCAAGAAGACAAAGATTTGTTTCCTATCTTGTGCTATGTGGTACTATTAGTTTAATGCTTATTGTATTATGATGGAAACAAAGACTGAATATTATCAATTTTGTGAGTATGGGAAGGTGACAAA
GATGTACATTATGTCCTAGGATTTGAGTGTTCCAAAAGTGGAGAAATTGATCATGGTAGCTTGACTTTAGGAACTTGAGAAATTAAGATCTTTATTGTTGTTCTTTACCTAAAAATTGCCCAAACTTACTTATTGTTGCTGGTTGAGGCTAAATCAAGGATGCCACTACAAGGAAGATTCCCACATTATACCTAGGACCG
ATCTTACTGCTGTTTGGAGGGTTGAGACATTGTTAAAACATACCCAGAACTATCAGAATGCCCAAAAACGCTAGGAAACAACCTAGCATGGAGTGCTGCTACAAGAATTAAGCTGCTTGCTTTAGGGAGGAGTATCTGTAAGTCTCTAAGGACTTCGGAGCCTTGCATTTTTACTTTTCTTGTGTTGAGGGTGAAGTCTA
GTAGAGGGGCAATCACTACCAGGCGGAGTAGTGCAATGCTACTATCTAGTATTAAATGTTTAGCTGTTGACACCTATAAGCCCTATGGTTTGGTCCCTAAGTCCAAACATGTATGCTATCCATGTATATCTGGACCTGTTAAGTCTAACCATCCTGATTTGTGTTCCTTTATGTGGTTATGGTAACGTGATAAGTACTTG
GATAACTCATAAAAGCTCTTGGAGACAATTCACTCTATGATGATTATGTCTACTGACATTGTGAGTGCCCGGCTACAGAGTTGATACTGTGAATAGAGAATAGGATTATGTCATATATTTAGGCATTGAGTTTTACAAAGTGATTGACAATTGTTTAAAGCATTCAAGCTTTTGAAAGTCCACATCCACTCTTTCTTGAT
TGCATTTTACTGAACTTGACAGGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGG
AAAGTGTGACCTCTTCCAAGGAAAATGGGTGCATGACTCTCTTGGGCCG

Intron 3 GTAATGAAAA ... AACTTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	40.18	95.3	50	78
A2	28.57	80	31	33
A3	33.43	78.7	29	50
A4	32.39	48	21	25
A5	36.95	64	32	43
A6	31.37	35	0	32
A7	31	69	0	62
A8	29.55	31	0	26
A9	27.95	58	2	43
A10	31.13	52	0	47

>TRINITY_DN113228_c3_g2_i1 from sample A3 / Example spliced isoform

GAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGGACGAACTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATTCCAAGTAGATCCAGCAGATCCAGGAGACGTGTCAGTCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAAGGGAGATAAGGTCAAG
AAAAGATATAAAGAGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATCATGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAA
TATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGGAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGGTACGGTCATACTATCTTAGATATTGTAATTTTCAGAAATATATTGAGGCCTATATACTTTTTCTTCCCTCATGATGAACTCGACA
TTTTTAAATACTGGAAACAGTATTCCACTGATACCATAAAGATCAATTCATTATCTTTAAATTTACAAAAAAAATATTGTACAGAGTAAC

>TRINITY_DN113228_c3_g2_i11 from sample A3 / Example unspliced isoform:

GAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGGACGAACTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATTCCAAGTAGATCCAGCAGATCCAGGAGACGTGTCAGTCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAAGGGAGATAAGGTCAAG
AAAAGATATAAAGAGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATCATgtaatgaaaatatattttctgcaaataatttttgtatttgccttgttcattctagtagaaatt
cactgggatctcttctcctaggaaattgtaaatgctctattgaatatcaatccccaatatcaaaaacagaatataataaactattggtctcgagaaggtagggcagtgctggggtaggttcgatagcaaggaggtgcttcggcagggtagatcacttgtagggatactctagtttggcaaggcagatagctcttattggg
tgatcaggaaaggttcataaatatttgactcattgacctgttgtgtacctcaccatgacatatttgttaggcattggactctctctacatgagctattttgtttatatgctcgtgatttaaaagacatgagctattttgtttatatgctcgtgatttaaaagaccacaattaggttacatttaccattttgaggatggca
aatttgatggacagtttgagtggcatcaactactccattaagatatattttcataatataacagaatataataaactattgaatatcagtgcataacataaaaaatacaggtaataatccacccgctgtaagttacatagaccagatcaatatatgctagttttttctcttacaagatgcttcatattatcaccactagt
gcctcttccaccagtaaccttgaaacttggtggagatgtgagatgaaacaggccctctccagcctggcccattcacattatataaatttcactatcacaaaaaaactaaggctgatgatcaggtgagcctgattctctttgtgggaaggcagttctctgattagttcctctgctaggatgattgttatggataggagaag
ggcgagatggaggaacctgacctttggggagcatctgaaacacgttcataacatcacgggagtaccttctcctatgcaatatgacattctagacatgatggatatcttgaaccctattgtttccagacccattttgctgttcttgtcttaccttctccagtgcaattatatgaaaaaatggcttctgcaattgctttttc
gttctataaattccttcctactgagaagaattctacagaagtgaagatatgagacgtagtagacaagcatattgatttgaaccaatgcaatgagcgcgtctgatatagatacatatatataatcattatactcccaataaagaccagtacagttcattgtgtattttcaggacaagtgtgggttggttggttcccagaaa
aacatgttttcttataacctgtaatctatttcgatgataccctaagaatcataatcacaggctcaaaacctaaaatagtttttgtatttgccttgttcattctagtagaaattcattgggaattccattttcaacataggtgactaattcatcccacaggtatccaaagtacttagtatgaattcatttatcatgtaaat
ataaactactcaggtccaagaagacaaagatttgtttcctatcttgtgctatgtggtactattagtttaatgcttattgtattatgatggaaacaaagactgaatattatcaattttgtgagtatgggaaggtgacaaagatgtacattatgtcctaggatttgagtgttccaaaagtggagaaattgatcatggtagct
tgactttaggaacttcagaaattaagatctttattgttgttctttacctaaaaattgcccaaacttacttattgttgctggttgaggctaaatcaaggatgccactacaaggaagattcccacattatacctaggaccgatcttactgctgtttggagggttgagacattgttaaaacatacccagaactatcagaatgc
ccaaaaacgctaggaaacaacctagcatggagtgctgctacaagaattaagctgcttgctttagggaggagtatctgtaagtctctaaggacttcgaagccttgcatttttacttttcttgtgttgagggtgaagtctagtagaggggcaatcactaccaggcggagtagtgcaatgctactatctagtattaaatgttt
agctgttgacacctataagccctatggtttggtccctaagtccaaacatgtatgctatccatgtatatctggacctgttaagtctaaccatcctgatttgtgttcctttatgtggttatggtaacgtgataagtacttggataactcataaaagctcttggagacaattcactctatgatgattatgtctactgacattg
tgagtgcccggctacagagttgatactgtgaatagagaataggattatgtcatatatttaggcattgagttttacaaagtgattgacaattgtttaaagcattcaagcttttgaaagtccacatccactctttcttgattgcattttactgaacttgacagGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCAT
GCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGGAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGGTACGGTCATACTATCTTAGATATTGTAATTTTCAGAAATATATTGAGGCCTATATACTTTT
TCTTCCCTCATGATGAACTCGACATTTTTAAATACTGGAAACAGTATTCCACTGATACCATAAAGATCAATTCATTATCTTTAAATTTACAAAAAAAATATTGTACAGAGTAAC

Intron 4 GTTTTTGTAT ... AACTTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.88	92	23	78
A2	29.2	80	29	33
A3	39.06	78	23	50
A4	34.25	48	16	25
A5	40.19	64	29	43
A6	47.76	35	0	32
A7	47.33	69	0	62
A8	45.61	31	0	26
A9	42.57	58	1	43
A10	47.47	52	0	47

>TRINITY_DN125752_c0_g1_i18 from sample A1 / Example spliced isoform

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAA
GCATCATGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGGA

>TRINITY_DN125752_c0_g1_i4 from sample A1 / Example unspliced isoform:

CATACCTTTCCTACTCCGCTGTGTTCGAGTTCTATCAATGGGTCCCCGTCCAACGATCCAGGAGATTCTTCTTACAATGAGTGTCGGCTTGTCCTATCAGTATCAATATTAGTTATCCATCGTTTTCAAAACGATTGTGCTGTCAGATTCGTCCAAGTCCTCACATCGCTCCAATCCCTAGTCGAATCGTCTATCCAAAT
TATCCAATGCTTCGTTTTCTGCTGATCTTCTTGATCGCCATAATGCTCAGAATGTAGTTGGCGAGTTCGAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGGACGAACTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATTCCAAGTAGATCCAGCAGATCCAGGAGACGTGTCA
GTCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAAGGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGGTTCTTATCCCAGCCCGCTTATTATCCCAGCTTCGTTTTATTTAGCTTAACGGGAAAATATATTTTCTGCAAATAA
TTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCACTGGGATCTCTTCTCCCAGTGAATTTCTGACTGGGATATATTTATGTTTCTGTATTTGCTTTGCAGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCC
TGTGGGACAAAAAGATAAGCATCATgtttttgtatttgccttgttcattctagtagaaattcattgggatctcttctcctaggaaattgtaaatgctctattgaatatcaatccccaatatcaaaaacagaatataataaactattggtctcgagaaggtagggcagtgctggggtaggttcgatagcaaggaggtgctt
cggcagggtagatcacttgtagggatactctagtttggcaaggcagatagctcttattgggtgatcaggaaaggttcataaatatttgactcattgacctgttgtgtacctcaccatgacatatttgttaggcattggactctctctacatgagctattttgtttatatgctcgtgatttaaaagacatgagctattttg
tttatatgctcgtgatttaaaagaccacaattaggttacatttaccattttgaggatggcaaatttgatggacagtttgagtggcatcaactactccattaagatatattttcataatataacagaatataataaactattgaatatcagtgcataacataaaaaatacaggtaataatccacccgctgtaagttacata
gaccagatcaatatatgctagttttttctcttacaagatgcttcatattatcaccactagtgcctcttccaccagtaaccttgaaacttggtggagatgtgagatgaaacaggccctctccagcctggcccattcacattatataaatttcactatcacaaaaaaactaaggctgatgatcaggtgagcctgattctctt
tgtgggaaggcagttctctgattagttcctctgctaggatgattgttatggataggagaagggcgagatggaggaacctgacctttggggagcatctgaaacacgttcataacatcacgggagtaccttctgctgtgcaatatgacattctagacatgattgatatcttgaaccctattgtttccagacccattttgctg
ttcttgtcttaccatgagattctggacatgatggatatcttgaaccctgttgtttccagacccaatttgctgatcttgtcttactgaggatcttgaagatacaagatcaacattagagacaagagaccttcgaccctctgcaatcaccatggctgggagaaccaaaatgaaaatcatctccaaccatagaacattgtaac
aatggagcaccattgccataaatatcagtccagtgcaattatatgaaaaactggcttctgcaattgctttttcgttctataaattccttcctactgagaagaattctacagaagtgaagatatgagacgtagtagacaagcatattgatttgaaccaatgcaatgagcgcgtctgatatagatacatatatataatcatt
atactcccaataaagaccagtacagttcattgtgtattttcaggacaagtgtgggttggttggttcccagaaaaacatgttttcttataacctgtaatctatttcgatgataccctaagaatcataatcacaggctcaaaacctaaaatagtttttgtatttgccttgttcattctagtagaaattcattgggaattcca
ttttcaacataggtgactaattcatcccacaggtatccaaagtacttagtatgaattcatttatcatgtaaatataaactactcaggtccaagaagacaaagatttgtttcctatcttgtgctatgtggtactattagtttaatgcttattgtattatgatggaaacaaagactgaatattatcaattttgtgagtatgg
gaaggtgacaaagatgtacattatgtcctaggatttgagtgttccaaaagtggagaaattgatcatggtagcttgactttaggaacttgagaaattaagatctttattgttgttctttacctaaaaattgcccaaacttacttattgttgctggttgaggctaaatcaaggatgccactacaaggaagattcccacatta
tacctaggaccgatcttactgctgtttggagggttgagacattgttaaaacatacccagaactatcagaatgcccaaaaacgctaggaaacaacctagcatggagtgctgctacaagaattaagctgcttgctttagggaggagtatctgtaagtctctaaggacttcggagccttgcatttttacttttcttgtgttga
gggtgaagtctagtagaggggcaatcactaccaggcggagtagtgcaatgctactatctagtattaaatgtttagctgttgacacctataagccctatggtttggtccctaagtccaaacatgtatgctatccatgtatatctggacctgttaagtctaaccatcctgatttgtgttcctttatgtggttatggtaacgt
gataagtacttggataactcataaaagctcttggagacaattcactctatgatgattatgtctactgacattgtgagtgcccggctacagagttgatactgtgaatagagaataggattatgtcatatatttaggcattgagttttacaaagtgattgacaattgtttaaagcattcaagcttttgaaagtccacatcca
ctctttcttgattgcattttactgaacttgacagGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAG
CTGGGACTGAGGAAAGTGTGACCTCTTCCAAGGAAAATGGGTGCATGACTCTCTTGGGCCG

Intron 5 GTTCTTATCC ... TGCTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.77	39	12	11
A2	29.84	47	21	19
A3	28.57	40	18	14
A4	33.33	23	7	16
A5	29.17	34	10	18
A6	0	1	0	0
A7	-1	0	0	0
A8	-1	0	0	0
A9	0	1	0	0
A10	-1	0	0	0

>TRINITY_DN125752_c0_g1_i18 from sample A1 / Example spliced isoform

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAA
GCATCATGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGGA

>TRINITY_DN125752_c0_g1_i10 from sample A1 / Example unspliced isoform:

GTCCATTTGATATGAATCTGGGCCTTTATCTCGGGGAAATTCAATAGTGAAAGGGAAAGCGAGCTTTATTCGGATAGAGCAAGCCTTTTTATTCTCAGGCTTCGGCTCTTCTTCCTTATTATTATAGATATCCTTTATGACAGTGGAGCTCATGTTGCTTTTCCAGGGGCGGCAGCAGCAAGATCAAAGGCAGGCAGCAA
GGGAGATAAGGTCAAGAAAAGATATAAAGAGGTAAATAGATCTAAGGCAAGCAATAATCAGACGAGCAAGCGAGAACAATCCCCGgttcttatcccagcccgcttattatcccagcttcgttttatttagcttaacgggaaaatatattttctgcaaataatttttgtatttgccttgttcattctagtagaaattcact
gggatctcttctcccagtgaatttctgactgggatatatttatgtttctgtatttgctttgcagAAGAAGGATGATCAGGGAGCGTTGCCCCTGGCCAGGAATCATACGCCTGGGTGACGAATATATCTGGCCCTCAGATCTCTCGATCAATCTCGACCCCTGTGGGACAAAAAGATAAGCATCATGTAATGAAAATATA
TTTTCTGCAAATAATTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCATTGGGATCTCTTCTCCTAGGAAATTGTAAATGCTCTATTGAATATCAATCCCCAATATCAAAAACAGAATATAATAAACTATTGGTCTCGAGAAGGTAGGGCAGTGCTGGGGTAGGTTCGATAGCAAGGAGGTGCTTCGGCAGGGTAGA
TCACTTGTAGGGATACTCTAGTTTGGCAAGGCAGATAGCTCTTATTGGGTGATCAGGAAAGGTTCATAAATATTTGACTCATTGACCTGTTGTGTACCTCACCATGACATATTTGTTAGGCATTGGACTCTCTCTACATGAGCTATTTTGTTTATATGCTCGTGATTTAAAAGACATGAGCTATTTTGTTTATATGCTCG
TGATTTAAAAGACCACAATTAGGTTACATTTACCATTTTGAGGATGGCAAATTTGATGGACAGTTTGAGTGGCATCAACTACTCCATTAAGATATATTTTCATAATATAACAGAATATAATAAACTATTGAATATCAGTGCATAACATAAAAAATACAGGTAATAATCCACCCGCTGTAAGTTACATAGACCAGATCAAT
ATATGCTAGTTTTTTCTCTTACAAGATGCTTCATATTATCACCACTAGTGCCTCTTCCACCAGTAACCTTGAAACTTGGTGGAGATGTGAGATGAAACAGGCCCTCTCCAGCCTGGCCCATTCACATTATATAAATTTCACTATCACAAAAAAACTAAGGCTGATGATCAGGTGAGCCTGATTCTCTTTGTGGGAAGGCA
GTTCTCTGATTAGTTCCTCTGCTAGGATGATTGTTATGGATAGGAGAAGGGCGAGATGGAGGAACCTGACCTTTGGGGAGCATCTGAAACACGTTCATAACATCACGGGAGTACCTTCTGCTGTGCAATATGACATTCTAGACATGATTGATATCTTGAACCCTATTGTTTCCAGACCCATTTTGCTGTTCTTGTCTTAC
CATGAGATTCTGGACATGATGGATATCTTGAACCCTGTTGTTTCCAGACCCAATTTGCTGATCTTGTCTTACTGAGGATCTTGAAGATACAAGATCAACATTAGAGACAAGAGACCTTCGACCCTCTGCAATCACCATGGCTGGGAGAACCAAAATGAAAATCATCTCCAACCATAGAACATTGTAACAATGGAGCACCA
TTGCCATAAATATCAGTCCAGTGCAATTATATGAAAAACTGGCTTCTGCAATTGCTTTTTCGTTCTATAAATTCCTTCCTACTGAGAAGAATTCTACAGAAGTGAAGATATGAGACGTAGTAGACAAGCATATTGATTTGAACCAATGCAATGAGCGCGTCTGATATAGATACATATATATAATCATTATACTCCCAATA
AAGACCAGTACAGTTCATTGTGTATTTTCAGGACAAGTGTGGGTTGGTTGGTTCCCAGAAAAACATGTTTTCTTATAACCTGTAATCTATTTCGATGATACCCTAAGAATCATAATCACAGGCTCAAAACCTAAAATAGTTTTTGTATTTGCCTTGTTCATTCTAGTAGAAATTCATTGGGAATTCCATTTTCAACATAG
GTGACTAATTCATCCCACAGGTATCCAAAGTACTTAGTATGAATTCATTTATCATGTAAATATAAACTACTCAGGTCCAAGAAGACAAAGATTTGTTTCCTATCTTGTGCTATGTGGTACTATTAGTTTAATGCTTATTGTATTATGATGGAAACAAAGACTGAATATTATCAATTTTGTGAGTATGGGAAGGTGACAAA
GATGTACATTATGTCCTAGGATTTGAGTGTTCCAAAAGTGGAGAAATTGATCATGGTAGCTTGACTTTAGGAACTTGAGAAATTAAGATCTTTATTGTTGTTCTTTACCTAAAAATTGCCCAAACTTACTTATTGTTGCTGGTTGAGGCTAAATCAAGGATGCCACTACAAGGAAGATTCCCACATTATACCTAGGACCG
ATCTTACTGCTGTTTGGAGGGTTGAGACATTGTTAAAACATACCCAGAACTATCAGAATGCCCAAAAACGCTAGGAAACAACCTAGCATGGAGTGCTGCTACAAGAATTAAGCTGCTTGCTTTAGGGAGGAGTATCTGTAAGTCTCTAAGGACTTCGGAGCCTTGCATTTTTACTTTTCTTGTGTTGAGGGTGAAGTCTA
GTAGAGGGGCAATCACTACCAGGCGGAGTAGTGCAATGCTACTATCTAGTATTAAATGTTTAGCTGTTGACACCTATAAGCCCTATGGTTTGGTCCCTAAGTCCAAACATGTATGCTATCCATGTATATCTGGACCTGTTAAGTCTAACCATCCTGATTTGTGTTCCTTTATGTGGTTATGGTAACGTGATAAGTACTTG
GATAACTCATAAAAGCTCTTGGAGACAATTCACTCTATGATGATTATGTCTACTGACATTGTGAGTGCCCGGCTACAGAGTTGATACTGTGAATAGAGAATAGGATTATGTCATATATTTAGGCATTGAGTTTTACAAAGTGATTGACAATTGTTTAAAGCATTCAAGCTTTTGAAAGTCCACATCCACTCTTTCTTGAT
TGCATTTTACTGAACTTGACAGGATTACAATGAAATTTCATTAGCGTATCGGCCCTCTCATGCGGATGCCACATATGACTTCAAATATGGTGTTCGCTTAGTGCAGGGAGGTGGCAGATCTTCAGCACACGAAACTATTGGAAGAGTAGCTGCTGGGGCTGTAGCAAAGAAGATGCTTCAGCTGAAAGCTGGGACTGAGG
AAAGTGTGACCTCTTCCAAGGAAAATGGGTGCATGACTCTCTTGGGCCG