sp|Q43298|CH62_MAIZE ----> Chaperonin CPN60-2, mitochondrial

Intron 1 GTGTGCGTTC ... CTGAAAGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	84.62	1	5	6
A2	60	5	9	6
A3	77.78	1	5	2
A4	86.67	1	6	7
A5	100	0	1	1
A6	68.89	7	17	14
A7	62.16	7	13	10
A8	67.74	5	11	10
A9	66.67	8	18	14
A10	71.43	6	16	14

>TRINITY_DN41146_c0_g1_i14 from sample A8 / Example spliced isoform

AACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGGAACCCAC
AGCTATGGACTACTGAAAAGCATATGGTGACAACCGACAATGATCAATACACAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTCGTAATGGGAGGGATATTATATCAATGGCGGTTTGTGGCATTTCAACTAAGGCCAATGTGCTATTGAACTTTGAAGTTTTATTTTCTTATGTTAGACT
TGAGCGAACATGTTGCTTGCCCTGCTGTTGGACCAGGCAAATGTCATGTTGACACGGTCAAGGTGGGGATCATTGATCCCCTGAAAGTAATAAGAACTGCATTGATTGGTGCTGCACAGTAAGAATTTAACTTTATGTTGTCATTTGTGTTTAGCATCTTGACTATCCAGTATATATATTTTGTTTCTGTG

>TRINITY_DN41146_c0_g1_i13 from sample A8 / Example unspliced isoform:

CTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATGAGATAAGCCGATAAAGGT
CGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCTACTACAGTCAAGTCTATCTCTCTCATACAGGCAAACAGATTCTCAGGTCAGAGGGG
TTAATTATGGACGAGCCCTTTGCACATTATTAATAAAGTTGATCCATTTATTCTATCGAAATTTTCTGCAATGACAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGA
TTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGgtgtgcgttctacatggtgtcctgttctgaaagcagGTGACAACCGACAATGATCAATACACAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCA
AAGTTGCCTTCACAGTTCGTAATGGGAGGGATATTATATCAATGGCGGTTTGTGGCATTTCAACTAAGGCCAATGTGCTATTGAACTTTGAAGTTTTATTTTCTTATGTTAGACTTGAGCGAACATGTTGCTTGCCCTGCTGTTGGACCAGGCAAATGTCATGTTGACACGGTCAAGGTGGGGATCATTGATCCCCTGAA
AGTAATAAGAACTGCATTGATTGGTGCTGCACAGTAAGAATTTAACTTTATGTTGTCATTTGTGTTTAGCATCTTGACTATCCAGTATATATATTTTGTTTCTGTG

Intron 2 GTCAGAGGGG ... GCAATGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	43.59	18	15.8	12
A2	42.57	12.5	13.5	5
A3	22.36	14	5.1	3
A4	53.85	6	8	6
A5	32.63	5	2.9	2
A6	39.61	10.5	8.8	5
A7	27.14	18.5	9.8	4
A8	42.86	8	5	7
A9	21.3	17.5	5.5	4
A10	25.13	15	3.1	7

>TRINITY_DN96966_c0_g1_i1 from sample A4 / Example spliced isoform

TATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATG
AGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAA
ACAGATTCTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGAT
GAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTTGACA
CGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCC
TGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATAGAACATTACAGTTCCCCTTATTGGGCATTTGATTGTGTATTCAAGCCAACTTAAAGGAAATATGTCTATTGAAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAA
ATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCAAATGGGAAAAGAAGACACTTCATGGTTTGTGTC

>TRINITY_DN96966_c0_g1_i4 from sample A4 / Example unspliced isoform:

TATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATG
AGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAA
ACAGATTCTCAGgtcagaggggttaattatggacgagccctttgcacattattaataaagttgatccatttattctatcgaaattttctgcaatgacagGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAG
TGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGA
GGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTTTCCC
AAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATAGAACATTACAGTTCCCCTTATTGGGCATTTGATTGTGTATTCAAGCCAACTTAAAGGAAATATGTCTATT
GAAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCAAATGGGAAAAGAAGACACTT
CATGGTTTGTGTC

Intron 3 GTAGTTTTCA ... ATTGGACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	4	4.5
A2	58.34	1	2	1
A3	100	0	2	4
A4	87.3	1	10	4
A5	65.72	1	1	3
A6	100	0	10	6
A7	100	0	3	9
A8	93.22	1	14	13.5
A9	75.96	3	16	3
A10	70.33	4	13	6

>TRINITY_DN41602_c0_g5_i3 from sample A10 / Example spliced isoform

AAGAGGGTGGTCTCAACACGTAACAAGATTCGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATGAGATAAG
CCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAAACAGATT
CTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGG
AACCCACAGCTATGGACTACTGAAAAGCATATGGTGTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGAGGGCATTGGCAAATGTCATGTTGACACGGT

>TRINITY_DN41602_c0_g5_i2 from sample A10 / Example unspliced isoform:

AAGAGGGTGGTCTCAACACGTAACAAGATTCGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATGAGATAAG
CCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAAACAGATT
CTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGG
AACCCACAGCTATGGACTACTGAAAAGCATATGGTGTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACACAGTTCCTGGGAGGGCATTGgtagttttcactcaaagttgccttcacagtttgtaatgggagggatattatatcaatggcggtttgtggcatttcaactaaggcca
atgtgctattgaactttgaagttttattttcttatgttagacttgagcgaacatgttgcttgccctgctattggaccagGCAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGC
TGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATAGAACATTACATTTCCCCTTATTGGGCATTTGATTGTGTATTCAAGCCAACTTAAAGGAAA
TATGTCTATTGAAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCAAATGGGAAAA
GAAGACACTTTATGGTTTGTGTCACGTGAGATCATTGTGACTTGACTTACTTCGAGGTTCAATATGACTGGAGCTCTCTTCCAGCAAAATACATAGATTTCTGCCTTCCCATTGTCTATCGTTCATTTTCGGGAGATTGTTCGAAGATGTGAAGATTGCCTACTCATCTGCTCCTCCCATCAGCCCATCAATGGGGAATC
CAGATGGATCGACGGAGGCTGTCATCTTCTCCTACACCCCCCTAATAATCATCCTTGCAGTTTTCCTGGTGTTCTTGCTCCTCATTGCGCTGGGGTTATGTGTCCGTACCGTACATATGACACTGGCACTGTGCGCCCGTGCCGGACAATGCTGTAGAGGGTGTTGCCGCAGACGATGGCGGGTGGTCGTCTGGCCAGTT
GTTGAGACTACCTAAAGAAGGTGAGAATCAGAGAATAACTAAAATCATCACTAATCATGATGGAGAGAATTAGGGTTACTCCAATCAAAATTAAAAAGTTTTGCAGAGTTGCATCAGTGAGCACAAGTGTTGACAGTGGATATGTGGTTAGAAGCCCAAAGAAGTGTCTCTCTCTTGAATCTTCTTTGCACGACTGTAAA
TATGAACTTCCAGTCAACTCCGTTATATGTTTTGCTTGTATCTATTTTGACAGTTGTAGTTTGTCTCGCTGAATTGGCTGCAAGTTTGTTTTTTGTAAATGTAGTTTAGAAGTCTGTGAACATTTATAAAAGCATTCTGCTTTTCTATGATTATTCCTTTTAGATTTTCTTTTAGTTTTCAGGCACTAGGGGAGGGATGC
TAGTAAGTGAGCGTTTTTTTTACCGGTAGTGGTGCAGCTTAATTCTCCATGTTCCCGAGCTTGTTTTTCCTCCAAAATTTTTATGACATATACTTTGTCATGTTCTTTATCTAACCATATTGGTCTTGAG

Intron 4 GTTTGTGGCA ... ATTGGACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	84.34	1.2	6.2	4.2
A2	16.92	4	0.8	1.2
A3	17.2	8.8	1.8	4.6
A4	42.59	13.8	10.3	4.5
A5	-1	0.2	0.2	1.2
A6	60.13	4.7	7	4.5
A7	24.99	14	4.7	8.6
A8	72.5	7.2	18.8	9.8
A9	51.09	8.5	8.8	2.5
A10	70.7	4	9.7	6.2

>TRINITY_DN39466_c0_g2_i4 from sample A6 / Example spliced isoform

GCAGTATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATATACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGG
GATGAGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAG
GCAAACAGATTCTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTG
GGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTT
GACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATAAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGT
GTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATGGCATTTAGTTTGACCTTGTTACTGTCTAGACTC

>TRINITY_DN39466_c0_g2_i3 from sample A6 / Example unspliced isoform:

GCAGTATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATATACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGG
GATGAGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAG
GCAAACAGATTCTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTG
GGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGgtttgtggcatttc
aactaaggccaatgtgctattgaactttgaagttttattttcttatgttagacttgagcgaacatgttgcttgccctgctgttggaccagGCAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATAAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAG
TATATCATTGCTGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATGGCATTTAGTTTGACCTTGTTACTGTCTAGACTC

Intron 5 GTAAGAATTT ... CTGCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	14.29	3	0	1
A2	7.69	6	0	1
A3	0	10	0	0
A4	5.61	8.5	1	0
A5	90	0.3	1.5	0
A6	33.33	1.3	1.3	0
A7	20.36	10.3	2.3	3
A8	26.56	14.5	4.5	6
A9	8	13.3	0.3	2
A10	40	3	2	2

>TRINITY_DN46194_c1_g2_i6 from sample A7 / Example spliced isoform

GCAGTATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATATACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGG
GATGAGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAG
GCAAACAGATTCTCAGGTCAGAGGGGTTAATTATGGACGAGCCCTTTGCACATTATTAATAAAGTTGATCCATTTATTCTATCGAAATTTTCTGCAATGACAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCG
AAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTGTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACACAGTTCCT
GGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTT
TCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATAGAACATTACATTTCCCCTTATTGGGCATTTGATTGTGTATTCAAGCCAACTTAAAGGAAATATGTC
TATTGAAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCAAATGGGAAAAGAAGAC
ACTTTATGGTTTGTGTCACGTGAGATCATTGTGACTTGACTTACTTCGAGGTTCAATATGACTGGAGCTCTCTTCCAGCAAAATACATAGATTTCTGCCTTCCCATTGTCTATCGTTCATTTTCGGGAGATTGTTCGAAGATGTGAAGATTGCCTACTCATCTGCTCCTCCCATCAGCCCCTCAATGGGGAATCCAGATA
GATCGACGGAGGCTGTCATCTTCTCCTACACCCCCCTAATAATCATCCTTGCAGTTTTCCTGGTGTTCTTGCTCCTCATTGCGCTGGGGTTATGTGTCCGTACCGTACATATGACACTGGCACTGTGCGCCCGTGCCGGACAATGCTGTAGAGGGTGTTGCCGCAGACGATGGCGGGTGGTCGTCTGGCCAGTTGTTGAG
ACTGCCTAAAGAAGGTGAGAATCAGAGAATAACTAAAATCATCACTAATCATGATGGAGAGGATTAGGGTTACTCCAATCAAAATTAAAAAGTTTTGCAGAGTTGCATCAGTGAGCACAAGTGTTGACAGTGGATATGTGGTTAGAAGCCCAAAGAAGTGTCTCTCTCTTGAATCTTCTTTGCACGACTGTAAATATGAA
TTTCCAGTCAACTCCGTTATATGTTTTGCTTGTATCTATTTTGACAGTTGTAGTTTGTCTCGCTGAATTGGCTGCAAGTTTGTTTTTTGTAAATGTAGTTTAGAAGTCTGTGAACATTTATAAAAGCATTCTGCTTTTCTATGATTATTCCTTTTAGATTTTCTTTTAGTTTTCAGGCACTAGGGGAGGGATGCTAGTAA
GTGAGCGTTTTTTTTACCGGTAGTGGTGCAGCTTAATTCTCCATGTTCCCGAGCTTGTTTTTCCTC

>TRINITY_DN46194_c1_g2_i8 from sample A7 / Example unspliced isoform:

CAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACAgtaagaatttaactttatgttgtcatttgtgtttagcatcttgactatccagtatatatattttgtttctgtgcttgtctctgcttgcagTATGTGTTCAATGAGAACCACAACAGAGT
ATATCATTGCTGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGGTTATTTAGTTTGATAGAACATTACATTTCCCCTTATTGGGCATTTGATTGTGTATTCAAGCCAAC
TTAAAGGAAATATGTCTATTGAAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCA
AATGGGAAAAGAAGACACTTTATGGTTTGTGTCACGTGAGATCATTGTGACTTGACTTACTTCGAGGTTCAATATGACTGGAGCTCTCTTCCAGCAAAATACATAGATTTCTGCCTTCCCATTGTCTATCGTTCATTTTCGGGAGATTGTTCGAAGATGTGAAGATTGCCTACTCATCTGCTCCTCCCATCAGCCCCTCA
ATGGGGAATCCAGATAGATCGACGGAGGCTGTCATCTTCTCCTACACCCCCCTAATAATCATCCTTGCAGTTTTCCTGGTGTTCTTGCTCCTCATTGCGCTGGGGTTATGTGTCCGTACCGTACATATGACACTGGCACTGTGCGCCCGTGCCGGACAATGCTGTAGAGGGTGTTGCCGCAGACGATGGCGGGTGGTCGT
CTGGCCAGTTGTTGAGACTGCCTAAAGAAGGTGAGAATCAGAGAATAACTAAAATCATCACTAATCATGATGGAGAGGATTAGGGTTACTCCAATCAAAATTAAAAAGTTTTGCAGAGTTGCATCAGTGAGCACAAGTGTTGACAGTGGATATGTGGTTAGAAGCCCAAAGAAGTGTCTCTCTCTTGAATCTTCTTTGCA
CGACTGTAAATATGAATTTCCAGTCAACTCCGTTATATGTTTTGCTTGTATCTATTTTGACAGTTGTAGTTTGTCTCGCTGAATTGGCTGCAAGTTTGTTTTTTGTAAATGTAGTTTAGAAGTCTGTGAACATTTATAAAAGCATTCTGCTTTTCTATGATTATTCCTTTTAGATTTTCTTTTAGTTTTCAGGCACTA

Intron 6 GTTATTTAGT ... TCTATTGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52.38	10	14	8
A2	-1	0	0	0
A3	100	0	3	3
A4	70.37	4	9	10
A5	33.33	6	4	2
A6	80	1	4	4
A7	87.5	2	14	14
A8	74.19	4	15	8
A9	66.67	4	8	8
A10	52.38	5	8	3

>TRINITY_DN96966_c0_g1_i3 from sample A4 / Example spliced isoform

TATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATG
AGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAA
ACAGATTCTCAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAGTGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGAT
GAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGAGGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTTGACA
CGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTTTCCCAAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCC
TGTTCTGAAAGCAGGTTTAAACTTCAGTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAA
CCAAATGGGAAAAGAAGACACTTCATGGTTTGTGTC

>TRINITY_DN96966_c0_g1_i4 from sample A4 / Example unspliced isoform:

TATAAAGAAGAGGGTGGTCTCAACACGTAACAAGATTTGGCAATTTCAGGATCGACAAGATGGGAAACGATAAACGTAACCTGTTTCAATAAAATTTAACTTCAGTGAAAGAAAAACTATGTGGGTTTGGCTTGTAGGCTGAAAGGATTCAACACTCAGATTTCTGGGAAAGATGGCAGTAATGGCACAGCACGGGGATG
AGATAAGCCGATAAAGGTCGTGCTGGAATCGGTCGTGGTTATCAGGGGAGGATGAGTTTGATCAGAAATAAATAAATTGGCCACTTTGCTTCTCTGTTTTTCTTTCTATTTCTATCTGTCTTTTTTTTAATCTCTTTGGTGTTACCAAAATTATTATCAGCCAGCCACTACAGTCAAGTCTATCTCTCTCATACAGGCAA
ACAGATTCTCAGGTCAGAGGGGTTAATTATGGACGAGCCCTTTGCACATTATTAATAAAGTTGATCCATTTATTCTATCGAAATTTTCTGCAATGACAGGTAACATCCGGTGATGATCGATACACAGTGCATGGGAGGCCATTCTCAGACTTCACTCAAACTTGGCATAGTAAAGGCAGGGATCATTGATTCCCCGAAAG
TGATCAGAACTGCATTGATTGATTTCTGCAGGTGTGTCTTCACTGTTAACCACAACAGAGTGTGTCATTGTTGAGCTTCCCTGGGATGAGAAGGAACCCACAGCTATGGACTACTGAAAAGCATATGGTTTGCGTTCTACATGGTGTCCTGTTCTGAAAGCAGGTGACAACCGACAATGATCAATACGCAGTTCCTGGGA
GGGCATTGGTAGTTTTCACTCAAAGTTGCCTTCACAGTTTGTAATGGGAGGGATATTATATCAATGGCGGCAAATGTCATGTTGACACGGTGAAGGTGGGGATCATTGATCCCCTGAAAGTAATCAGAACTGCATTGATTGGTGCTGCACATATGTGTTCAATGAGAACCACAACAGAGTATATCATTGCTGAGTTTCCC
AAGAATGGGAAGGAAACCTCAGCTATGGGTGGCGGTATGGACTACTGAAAAGCACATCTAGACTGTTGTGCTTTCTACAAGGTGTCCTGTTCTGAAAGCAGGTTTAAACTTCAGgttatttagtttgatagaacattacagttccccttattgggcatttgattgtgtattcaagccaacttaaaggaaatatgtctatt
gaagTGCCCTGCAGTTACTTCAACCTAGCAACCTAGCTTTTCCTGGAGAGAAAAACTGTAATCAAAGGGATTTCAGGAAAGAAGAAAATAAAAAATTCACCTTCTGGAGATAAAAGGTGCTTGATATACACCCATCCACAGACATCAAGAACGAGCCCCTGCTACTTTCAGTGACAACCAAATGGGAAAAGAAGACACTT
CATGGTTTGTGTC