sp|Q6XL73|DNJ39_ARATH ----> Chaperone protein dnaJ 39

Intron 1 GTATTAGCCG ... ATATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.48	17	14	18
A2	66.67	5	8	12
A3	63.64	6	5	16
A4	68	4	10	7
A5	50	1	1	1
A6	63.68	23	27.7	53
A7	59.22	42	53	69
A8	60.37	56	79	91.7
A9	63.23	41	59	82
A10	68.24	19	41	40.7

>TRINITY_DN117684_c4_g2_i1 from sample A1 / Example spliced isoform

GAGGGCTGAAGCAAGGAGGATTCTAAGAGGAATACACAGTATGAACATGTCTGCAAAGGTTTTATTTCAGGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAATC
GGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGC
TGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGGGAGAATAATTCATTGGCGG
ACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAGGG
TTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTACGCTTTTTTTCGCTG

>TRINITY_DN117684_c4_g2_i8 from sample A1 / Example unspliced isoform:

TCTTATAATTAATCTTTCACATTTGATGTTTGAACTTGGTGTAGGATGCAGATTCGAGGAGCGATCCATCAAAGGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATC
AATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAG
GGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGgtattagccgaggaga
aattcaaacgctgtggtgctgcatacaaatcattatgtgatgctttttctgacaagtaatattaccttgttgctttgaattattcctcatttaccaaaagtacacaccaagcaggattatcttcaaataaaattgacagcttggaatgtattatttattctttctggtagaagtttgttatcacaacacaatggttacaa
ggtcatattgatctcaagaacgagtggatgctaatccaaataaacaatcatatttatcttttcaattctagttcgtgcaacttactattgagtaagtgggtttgcttggtgactgctctacatcactggtgttcgcgaatcaggaatgaatttaagttttttcaggccttatcattgcagcatatttacagGGAGAATAA
TTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATA
GACTGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTACGCTTTTTTTCGCTG

Intron 2 GTAATATTAC ... ATATTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	48.15	14	8	18
A2	58.97	8	11	12
A3	56.1	9	7	16
A4	63.64	6	14	7
A5	71.43	1	4	1
A6	56.03	31	26	53
A7	58.73	39	42	69
A8	56.29	66	79	91
A9	65.25	41	72	82
A10	67.19	21	46	40

>TRINITY_DN107185_c0_g1_i3 from sample A3 / Example spliced isoform

AGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCTGAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGCA
TGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAGCAAAGTGGAAGAACAAATGGGGTTCAGATGCACATTCGACGAGCAATCCATCAAAGGATGCAGATTCGAGGAGCGATCCATCAAA
GGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATT
TCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGA
ATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAGGAGAATAATTCATTGGC
GGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAG

>TRINITY_DN107185_c0_g1_i2 from sample A3 / Example unspliced isoform:

AGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCTGAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGCA
TGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAGCAAAGTGGAAGAACAAATGGGGTTCAGATGCACATTCGACGAGCAATCCATCAAAGGATGCAGATTCGAGGAGCGATCCATCAAA
GGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATT
TCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGA
ATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAgtaatattaccttgttgc
tttcaattattcctcatttaccaaaagtatacaccaagcaggattatcttcaaataaaattgacagcttggaatgtattatttattctttctggtagaagtttgttatcacaacacaatggttacaaggtcatattgatctcaagaacgagtggatgctaatccaaataaacaatcatatttatcttttcaattctagtt
cgtgcaacttactattgagtaagtgggtttgcttggtgactgctctacatcactggtgttcgcgaatcaggaatgaatttaagtttttttcaggccttatcattgcagcatatttacagGGAGAATAATTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCA
TAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAG

Intron 3 GTAATATTAC ... ATATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	47.45	14	7.8	17.5
A2	58.19	8	10.8	11.6
A3	55.59	9	6.9	15.6
A4	62.75	6	13.6	6.6
A5	71.15	1	4	0.9
A6	55.27	31	24.8	51.9
A7	58.37	37.9	39.3	67.4
A8	55.86	64.9	75.6	89.2
A9	65.09	40.3	70.1	80.4
A10	66.55	21	44	39.8

>TRINITY_DN110779_c0_g2_i7 from sample A2 / Example spliced isoform

GAGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCTGAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGC
ATGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAGCAAAGTGGAAGAACAAATGGGGTTCAGATGCACATTCGACGAGCAATCCATCAAAGGATGCAGATTCGAGGAGCGATCCATCAA
AGCAATATGGAAAATATGCAAAACGTGTAAAGAGGGCTGAAGCAAGGAGGATTCTAAGAGGAATACACAGTATGAACATGTCTGCAAAGGTTTTATTTCAGGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAAT
CGAAGGATCAGAAAGAAGGCTAGCATCAATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGTTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTG
GCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAG
GTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAGGAGAATAATTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTT
ATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTACGCTTTTTTTCGCTGAAAAAA
AAAGTGGG

>TRINITY_DN110779_c0_g2_i1 from sample A2 / Example unspliced isoform:

GAGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCTGAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGC
ATGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAGCAAAGTGGAAGAACAAATGGGGTTCAGATGCAGATTCGAGGAGCGATCCATCAAAGCAATATGGAAAATATGCAAAACGTGTAA
AGAGGGCTGAAGCAAGGAGGATTCTAAGAGGAATACACAGTATGAACATGTCTGCAAAGGTTTTATTTCAGGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAAT
CGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGTTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGG
CTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAAT
TCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAgtaatattaccttgttgctttgaattattcctcatttaccaaaagtatacaccaagcaggattatcttcaaataaaattgacagcttggaatgtattatttattctttctggtagaagtttgttatcacaacacaatggttacaaggt
catattgatctcaataacgagtggattctaatccaaataaacaatcatatttatcttttcaattctagttcgtgcaacttactattgagtaagtgggtttgcttggtgactgctctacatcactggtgttcgcgaatcgggaatgaatttaagttttttgaggccttatcattgcagcatatttgcagGGAGAATAATTC
ATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGAC
TGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTACGCTTTTTTTCGCTGAAAAAAAAAGTGGG

Intron 4 GTAATATTAC ... ATCATTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52.37	9	7.8	12
A2	57.42	8	10.6	11
A3	62.5	6	7	13
A4	69.9	4	13.6	5
A5	71.43	1	4	1
A6	56.33	30	24.4	53
A7	57.33	39	39	66
A8	59.71	50	75.4	73
A9	67.11	35	69	74
A10	65.66	21	44.4	36

>TRINITY_DN45931_c0_g1_i8 from sample A10 / Example spliced isoform

GGGAGCCCGAGGTAATTAGTAAACTTTTGCTCATTTCCCCTCCTTATATATGCTTATGAACTTATTACTCCGAAATATCTGGTGGAGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCT
GAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGCATGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAG
CAAAGTGGAAGAACAAATGGGGTTCAGATGCAGATTCGAGGAGCGATCCATCAAAGCAATATGGAAAATATGCAAAACGTGTAAAGAGGGCTGAAGCAAGGAGGATTCTAAGAGGAATACACAGTATGAACATGTCTGCAAAGGTTTTATTTCAGGAGGGTGTTTCAAGTTGGGATGCTTGGAGAAAGAAGAATGGGAAA
ACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAAT
ATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATG
TTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCAGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAACATATTTGCAGGGAGAATAATTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAG
AAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGG
CAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTACGCTTTTTTTCGCTGAAAAAAAAAGTGGGA

>TRINITY_DN45931_c0_g1_i6 from sample A10 / Example unspliced isoform:

GGGAGCCCGAGGTAATTAGTAAACTTTTGCTCATTTCCCCTCCTTATATATGCTTATGAACTTATTACTCCGAAATATCTGGTGGAGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCT
GAGCGTCGTATATGCGATTACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGCATGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAG
CAAAGTGGAAGAACAAATGGGGTTCAGATGCACATTCGACGAGCAATCCATCAAAGGATGCAGATTCGAGGAGCGATCCATCAAAGCAATATGGAAAATATGCAAAACGTGTAAAGAGGGCTGAAGCAAGGAGGATTCTAAGAGGAATACACAGTATGAACATGTCTGCAAAGGTTTTATTTCAGGAGGGTGTTTCAAGT
TGGGATGCTTGGAGAAAGAAGAATGGGAAAACATTGTTCAATGAAAGTACTCCAAAAAATCACAATAATCAAGCCCATCCAAATCGAAGGATCAGAAAGAAGGCTAGCATCAATCGGTCATCACACACTACAGAGAGGGTAAAAGATTCCAGGAGGAGGATACGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGA
TGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAGCTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGG
CTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCAGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAgtaatattaccttgttgctttcaattattcctca
tttaccaaaagtatacaccaagcaggattatcttcaaataaaattgacagcttggaatgtattatttattctttctggtagaagtttgttatcacaatacaatggttacaaggtcatattgatctcaataacgagtggattctaatccaaataaacaatcatatttatcttttcaattctagttcgtgcaacttactatt
gagtaagtgggtttgcttggtgactgctctacatcactggtgttcgcgaatcgggaatgaatttaagttttttgaggccttatcattgcagCATATTTGCAGGGAGAATAATTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCATAGTTCTCAGCTGGAAT
CCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTTTGAATAGACTGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAACAATAGTAC
GCTTTTTTTCGCTGAAAAAAAAAGTGGGA

Intron 5 GTAAGTTCAA ... ATCTGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	14.29	7.3	1	1
A2	0	6.1	0	0
A3	0	12	0	0
A4	20.07	8.6	0	2
A5	11.11	8	0	1
A6	0	33	0	0
A7	17.87	74.7	0	16
A8	17.33	59.1	0	12
A9	12.55	64.4	0	9
A10	18.97	52.6	0	12

>TRINITY_DN43317_c0_g1_i9 from sample A6 / Example spliced isoform

GTAAACTTTTGCTCATTTCCCCTCCTTATATATGCTTATGAACTTATTACTCCGAAATATCTGGTGGAGCCTCTCCCTTTTTCCTCCACGGGACCATGTTCTTGCAGTTTCTGAAGTTGGAGGCAGTCAGATTCGACAGTCTGACCTGTTAATCGAAGAGTTATATTTTTAATTTCGAGTCTGAGCGTCGTATATGCGAT
TACCAAACCACAGACGCTTGCGATGCGAGGAGTACGAGAATAAGATGTTGAGAGTTGTTCGGTTGCATGTACCAGGAAGAAGAAGAAGATGCAAAGCTTAAATTCGAAGAGGAACGCCATTAATAATCCCATATTGAGTGGCCTCAGAGCTGCATTCATACACTCCACCGCACTTTCCCAAGCAAAGTGGAAGAACAAAT
GGGGTTCAGGAAAAGCAAAGGACCACATTTCCATTGGGATAGTGATGATCGAGAGGAGAGAATTTTTGAGTCAATATTTCAAGGAAGAAGCTTTTATTGGATGTCTGGTGATTTGAATGATTTGAAGTGGCGGACTTCATGGGGATTCAATAGGAGGGGCTGGAACAAATATTCTGAGACTTATGCTAGTGACAATGAAG
CTCCTTCTATAGGAGCAGTTTCTGATCGAATAGCTCTTGGTTTGGCTCCCAATGGCCCATTAACATTAGAGGATGTTAAACAAGCGTTTCGAATGTCTGCTTTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGG

>TRINITY_DN43317_c0_g1_i6 from sample A6 / Example unspliced isoform:

ATTAGAGGATGTTAAACAAGCgtaagttcaattttgtaggtcgtgttcattgaattagactaagtttacagttgggtaagttaaagttctcgtggtttctcttttccttctactagggaccattttaaggatagcaactgggttaatgaaactaggttatttgcctttgttggtatctgtgcagGTTTCGAATGTCTGCT
TTAAAATGGCATCCGGATCGGAATGAAGGTCCCTCTAAGGTATTAGCCGAGGAGAAATTCAAACGCTGTGGTGCTGCATACAAATCATTATGTGATGCTTTTTCTGACAAGGAGAATAATTCATTGGCGGACATACTTTCTAAACAGGCTTTGGATACAGAAGAAGGTTTATTAATATGGGAGGAATTCCGTAGTTCTCA
GCTGGAATCCAATGGAACTGTTCACTTTATGGATTGATGATGATATTTAGGATATGTTATTGTGGAAGATAACACATGAAGGACAATATGTTATTTTGACATTTTGTATATTATGAATAGACTGAAAGGGTTTTGGATTTAAGCCAGAACTGTGCTGTAATGGCAATATCATTGTACTATTTGATTTATTTATAAATAAC
AATAGTACGCTTTTTTTCGCTGAAAAAAAAAGTGGGTTTGCTTTTGCTGTTAGTGGATGGTGC