sp|Q84W56|RNJ_ARATH ----> Ribonuclease J

Intron 1 GTAAAACCCA ... ACGTTATAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25	9	3	3
A2	40	6	3	5
A3	55.56	2	1	4
A4	43.48	13	12	8
A5	39.13	7	3	6
A6	33.33	1	1	0
A7	-1	0	0	0
A8	33.33	2	1	1
A9	33.33	2	1	1
A10	-1	0	0	0

>TRINITY_DN96712_c0_g1_i22 from sample A4 / Example spliced isoform

TTGTAGCCTTCCAACGCCTCCAACTTATATCACCTCAGCTGAAGCTTCATAGCGTCCTTGTTACAGAAGTTCATCATTTGGACAACAGCGAAATAATCAGTCGAACACCCTGCCATCTGCATTCAACAAACTCCTTTACTCTTCATTTCTCTGGACGGACTGTATATTCACTTCAGCACCACTCAATGAATTCAAATCTC
CATAACCATTTGTAGTTCAGTTTATCCCACCTGGGTGCTTGTATTTTCAAGTCCCCACACTGTTTTAACACCGTCTTTGACTTACAGGTGGGAAGTCGATTGTTATCTAGTTGGGTTTCTTCAGGATAGAGCTGGGTACCATGGCTGTGATTAATGGGCTTCCATACAGTCCAGAGGTCATGGCTACGGGTATTTTGGAT
TACAGAAACAGAGCTGGGTGGTCACATTGGAGCAGAAAATGTAACAGAACAGCTATCATTTTCCCGAATAATTTATCAGGTCTGCCCTTCAGCAGTTACAACGAGAGAGTTCCTAGATTTGTTATTGCAGAAAGCAAGGGAAATCCCACAGAATCCATGAGATTGAAGCCAGGTAATAACTTAGTCATTCCTGTCTGTCT
GTAATATTTTAAGGGCAATAAATAGCTAAGCAGCCTGAGTAAGTGTATTATCTTTGAAACCACAATCAAAACACACAACCTAGAGATTTTGCATCTGCTATGTCCAAACTCAGCAGATCATGTGTAACGTACCTCTATTCCCGATATCAAAGTAGGGTCTGCTCGTCTAAATTTTCATTATTGGCAGTAGTATGTAAATC
AAAATACAACACATTAAGTCCATTTACAACTTAGAAACTCTTCTTCTTGATTACTGTGACAGAGTTTGGATTTATATTAGTCTACATGATTCAAATTTACGATTTCTAAATGCAAAGTCTAGCTAAGAATCTCTTTAGACAATGAAATCAAACGAGATCTTACTTCAGTTAGGATTAGCATTTCACAATTTGCTGCATAG
CACCTTTCCAAGATGGTGACTATCAAGCATAAATGACATATTCAAATCTTCGCAAACATAAACCTTTGCTTCATACACAACTCTACTTCAGAAATTCGTCATTTAACTCCACTCAACAATATCCTAGATTCTCTCACATGGAGGACTTGTTCTCTTCTCCAAGAAGGTGAATCCCCGGGTTTAGGGTTATTGTCTTTAAA
CTCATGCTTGAAATATATTACACAATGATTAGAATTGTGATTCAATATTCATCAAAGTCATTATAAACATAGGGGAATGAATCAAAAATACACATGTTTCTTGCCTTATCATTCAC

>TRINITY_DN96712_c0_g1_i2 from sample A4 / Example unspliced isoform:

TTGTAGCCTTCCAACGCCTCCAACTTATATCACCTCAGCTGAAGCTTCATAGCGTCCTTGTTACAGAAGTTCATCATTTGGACAACAGCGAAATAATCAGTCGAACACCCTGCCATCTGCATTCAACAAACTCCTTTACTCTTCATTTCTCTGGACGGACTGTATATTCACTTCAGCACCACTCAATGAATTCAAATCTC
CATAACCATTTGTAGTTCAGTTTATCCCACCTGGGTGCTTGTATTTTCAAGTCCCCACACTGTTTTAACACCGTCTTTGACTTACAGgtaaaacccacatcagttccttcacataccatcttattacatttattgccctttgcattctcaatgattttcaagtaattttctcatgtatcctgattgattttccgttaaaa
atcacgttataagGTGGGAAGTCGATTGTTATCTAGTTGGGTTTCTTCAGGATAGAGCTGGGTACCATGGCTGTGATTAATGGGCTTCCATACAGTCCAGAGGTCATGGCTACGGGTATTTTGGATTACAGAAACAGAGCTGGGTGGTCACATTGGAGCAGAAAATGTAACAGAACAGCTATCATTTTCCCGAATAATTT
ATCAGGTCTGCCCTTCAGCAGTTACAACGAGAGAGTTCCTAGATTTGTTATTGCAGAAAGCAAGGGAAATCCCACAGAATCCATGAGATTGAAGCCAGGTTCTTCAACTTTCAATAAATCTAGAAGAGGCTCAAGTAGTGCTGAAGGGCCTAGAAAAAGCATGGATGATGGGGTCCAGAGGAAATTGGAGCTGTTTCATG
AAGGGGTTGAAGGACCACCACTGCGTGTCCTGCCATTAGGAGGTTTGGGGGAAATAGGGATGAACTGTATGCTCATAGGTCATTATGATCGATACATCTTGGTTGATGCTGGTCTCATGTTTCCAGACTATGACGAACTTGGGGTACAGAAAGTTTTACCTGATACAACTGTTATTCAACGATGGAGGAATAAGATTGAA
GCAGTTGTTATTACACATGGGCATGAGGATCACATTGGAGCATTGCCTTGGGTAGTTCCCGCATTGGATCCTCATACTAAAATTTTCTCAACATCATTTACCATGGAGCTCATTAAAAGACGATTAAAGGAATTCGATATTCATGCTGAGGCTAGACTTAACATCATTACTATAAGCGAGAGGTTTCAGGCTGGACCATT
TGAGATAGAAGCTATTCGAGTTACACATTCCATTCCAGATTGTTGTGGGTTGGTACTTCGCTGTAAAGATGGGACAATTTTACATACAGGAGACTGGAAGATTGACGAATCTCCTGTGGATGGAAAGACCTTTGATCGATCAACATTAGAAGAACTTGGAAAGGAAGGCATTACATTGATGATGAGCGACTCTACCAACA
TTCTTTCACCGGGAAGAACTACCAGTGAAACTGATGTAGCAGAAGCTTTGTTGCGAAATATTGCTGCTGCAAAGGGAAGAGTTATCACCACTCAATTTGCATCAAATGTTCATCGTCTCGGCAGTGTGAAAGCTGCAGCTGAGTTGACTAGTAGGAAGCTGGCTTTTGTTGGGATGTCATTAAGGACTTACTTGGATGCT
GCTACCAAAGCTGGACAAGCACCTTTTGATCCATCAACTTTGGTTAAAGCTGAGGATATGGATGCATATGCTCCTAGGGATTTGCTAATTGTAACAACAGGATCACAGGCAGGCAGAACCTCGTGCAGCTCTCAACCTGGCATCATTTGGAAGCAGTCATTCCCTCAAGCTAAACAAAGATGACTTGATTTTATACTCAG
CAAAGGTTATACCTGGAAATGACATTCGTGTGATGAAGATGATGAATCGGATAGCAGGGATTGGTTCTACAATAATGATGGGAAGAGGAGATAATTTGCATACATCTGGTCATGCTTACCGTGGAGAATTGGAGGAAGTCCTCAGGCTGGTAAAGCCTCAGCATTTCCTACCTGTTCATGGAGAATTTGCTTTTCTGAAA
GAGCATGAGTTACTTGCAAAATCTACTGGTATACGACACACTACTGTAAGTTGATTTTTCAAATTCATAATATTTTACATATTTCTTGTAATATCAAAAGAACTATCAATAGGAACACAAAGTTCAAAAAATACTCTGATCATGGTAGCTTGCAGTAGAGGATTTGTATTTTAACATTCTGGTCTTTTCCCAAAC

Intron 2 GTAGGTTTGG ... ACGGTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	10	13
A2	100	0	7	11
A3	100	0	5	11
A4	100	0	0	2
A5	57.89	4	3	8
A6	-1	0	0	0
A7	100	0	0	4
A8	-1	0	0	0
A9	100	0	0	1
A10	77.78	1	1	6

>TRINITY_DN107503_c1_g1_i10 from sample A5 / Example spliced isoform

GCAAAAGATAAGATTGCTCTTGTTTTGGCTCAAGTGTTTGTATTTTCTTTCTTCCATTTTGAATTGCACTCCAACAAATAGCCGATACGATTCCACTCTTTTCTGGTACATTCTCAGCTTCATTGCAGCTCCACATTTGATATTTTCAAATGAATGCGTTGAGGTGCGAGGGGATGCTCTTCCCAACAAAGGACTACCAT
GGCTGGTGGCCGACTATCCTTACCCCGAACAGATATTCAGGGTTCCGGCTTGGCATCATCACTAGAAGAAAAAATGTGTGCAGATTTGCCAAGGCAGATTCACAACATTATAATAAATCTCGAAATAGTTCTAGGAGCCTGGAAGGGCCTGGAAGGAGCATTGAGGATGGAGTACATCGTAAATTGAAGCAGTTCCATGA
AGGATCTGAAGGACCACCTTTACGCATCCTGCCATTAGGAGGTCTGGGGGAAATAGGGATGAACTGTATGCTTGTAGGTCATTATGATCGGTATATTATTGTGGATGCTGGCCTCATGTTTCCAGACTATGATGAACTTGGCATCCAGAAAGTATTACCTGACACAACTTTCATTCGACGCTGGAGTCATAAGATAGAAG
CAGTTGTTATAACACATGGCCATGAGGATCACATTGGAGCCTTGCCTTGGGTTATTCCAGCATTGGATTCGTGTACTCCGGTTTTCTCTTCATCATTCACAATGGAGTTGATCAGAAGACGGTTAAAGGAGTTCAGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTT
GAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATGTGAAGATGGAACAATTTTCCATACTGGAGACTGGAAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGGTAATTTAATCTCATTATATGTT
TACAGTGGCCATCCTTGAAGAAGACTGCAAAATGGTGTTTATTGTGGTAATTATTGTCTCGACCAACTCTTTTGTCCAACCAACCATTGCAGGGTGTCCTTGAACAAGAACATGATGAGTGACTCAACCAACAT

>TRINITY_DN107503_c1_g1_i2 from sample A5 / Example unspliced isoform:

TGTCAAACTAGCATATTTGAGATCATAGCTTGTCATTTCTCTTTGGATCTTGATCTATGGTCTTCCAAATCATATCTTAGCCAGCTCAGGTAAGACCTTTTAGGACCGACCCATTCTTTGTAATTTTCTGTCTCGAGTCTGCAGAAATGGCCTTTTTCCATTTTATCCTGGTCTGCATAAATAATCTCAGGTCTATGAAC
AGGTGCTGTCCTGAACCTCCTACTGCAGTGTGTTTTCTTTCCAGTTTCACGTTCATTTTCTTTTCTTTTAAGCCCTCATTTGGTTCTAAAGTTGCTAAATATTTCTAGAGATAAAACAATCGTTCAATTGATTTCTAGGGTTTTCTATTTATAAAAAATATTAAGCAAATACTTTTCTCTTCATTTCTTTATCGGTTGCC
ACCTGTGGCTAGGCCATCCTTGAAGAAGACTGCAAAATGGTGTTTATTGTGGTAATTATTGTCTCGACCAACTCTTTTGTCCAACCAACCATTGCAGGGTGTCCTTGAACAAGAACgtaggtttggaaatgaagttcctgtactgattttttatttatgtatttggattctgttacttttaagggatgaatatctggatc
caaaattttatcttccatattaaccttgctctattgttgtctgtttctgttctattactacggtaccagATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTATTGCATCTGCAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGT
TCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTATGAAATAGTGTACATATCTCTGAGTTCATGCATTTGCCAATGTGCCCCACACTGTATGCTTTGT
CTTAATCTTCATCTAGATCCC

Intron 3 GTACTGGGCC ... TGTGTTCTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	53.24	11.6	13	13.2
A2	25.24	20.7	8.7	5.3
A3	36.95	36	19.4	22.8
A4	25.2	23.8	5.9	10.2
A5	48.89	6.3	7.8	4.1
A6	12.75	9.9	0	2.9
A7	24.16	15.8	6.8	3.3
A8	43.65	7.6	6.9	4.8
A9	1.84	8.7	0	0.4
A10	17.08	12	3	1.9

>TRINITY_DN117943_c1_g1_i5 from sample A1 / Example spliced isoform

CTCCAACAAATAGCCGATACGATTCCACTCTTTTCTGGTACATTCTCAGCTTCATTGCAGCTCCACATTTGATATTTTCAAATGAATGCGTTGAGGTGCGAGGGGATGCTCTTCCCAACAAAGGACTACCATGGCTGGTGGCCGACTATCCTTACCCCGAACAGATATTCAGGGTTCCGGCTTGGCATCATCACTAGAAG
AAAAAATGTGTGCAGATTTGCCAAGGCAGATTCACAACATTATAATAAATCTCGAAATAGTTCTAGGAGCCTGGAAGGGCCTCGAAGGAGCATTGAGGATGGAGTACATCGTAAATTGAAGCAGTTCCATGAAGGATCTGAAGGACCACCTTTACGCATCCTGCCATTAGGAGGTCTGGGGGAAATAGGGATGAACTGTA
TGCTTGTAGGTCATTATGATCGGTATATTATTGTGGATGCTGGCCTCATGTTTCCAGACTATGATGAACTTGGCATCCAGAAAGTATTACCTGACACAACTTTCATTCGACGCTGGAGTCATAAGATAGAAGCAGTTGTTATAACACATGGCCATGAGGATCACATTGGAGCCTTGCCTTGGGTTATTCCAGCATTGGAT
TCGTGTACTCCGGTTTTCTCTTCATCATTCACAATGGAGTTGATCAGAAGACGGTTAAAGGAGTTCAGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATGTGAAGA
TGGAACAATTTTCCATACTGGAGACTGGAAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTATTGCATCTG
CAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGTTCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTCAAACCTGAAGACATGGATGCTTAT
GCACCTAAAGATCTCCTTGTGGTGACAACAGGATCACAGGTAGTGCTTTGAAGGAGTCAGAATATAGTATTTGGTTAAAATCCATTTCCTATCAAGGTCTTCGCATTAAACATAACGGAAGCCCATTTTGAGACAGGCAGAACCTCGTGCAGCTCTGAATCTTGCATCATTTGGAAGCAGTCACTCCCTCC

>TRINITY_DN117943_c1_g1_i11 from sample A1 / Example unspliced isoform:

TCTCTTCATCATTCACAATGGAGGTATGCTTTCTGATGTAAATATTTGGACTTGCCGTATGCAGATTATTTGCATTTCTGTTCGAGTGTTGCATGATGAACTGAATTCATCAGATGGAGTGTGAAGGAAGTATCTTTTTAAAGTCCTAAAGTATTCTACATCTTATAAACTGATCGATGAGAAAATTTTCCTTTGAGTTC
ACATAGTTCTTAAAATGGAAGTATACAGGCAAATTTGCTTCCTTTGGCCTTATGATAAGGGCATATAGCTCAACAATGTTAGGAGCACAATTCGGTCCTTCAAAGCTCATCATTCTTAGATCTATTTTAGAACCTGACTATGGACTAATACCTCAAGTATCACTATTACGCAGTTGATCAGAAGACGGTTAAAGGAGTTC
AGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATGTGAAGATGGAACAATTTTCCATACTGGAGACTGGAAGgtactgggccactggaagaacattatagaaacagc
caggaacttaattcaattgcttctgataaatgtatgtctgtgttctagATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGGTAATTTAATCTCATTATATGTTTACAGTGGTACTTTGAAACACCTTTACCTCCCCCTCTACAATTTGAATATT
GTTTTGTTGACATTTCTGTCTTTCAAGAAAATGAGTCCTAGTCTGTTACTGGTATGTGCAACATTGACAGATCAATTCTATGTGATACATTCATATTTTGAAAGAAAAACAAAACTTTCTTTCCATTGGAAGTTTATAATATTACTTAAACAGTAGAATAGTGTAGGCTGTTATATGTTAATGCCAATAACAGCTTTACC
CTGCCAGAATAGTGATGTTGTATACAATATCTCAGTTTAATCTTAGTTTATGGGAAGCCATCCAATATGATATAAATTAGTCTATATACTTTTGAAGTTTTTAGAAAGGAAAAATTAAACAATTAAATTTATGGTGTACAGGACTAAATGGTGCAAGCTGATGTCTCACGTAACTCTCTTTAAAAGTTTAATCATAATGC
ATAGTATAAATTAATAGAAATAATGGTTACAACATGAAAAACATAGTAATTCTGCTTGGTCCTTTTTTCACCTGCTGTTTTATCAGGCCACAAATACTGGTTGACCTAGTTGTTGGGTACAACCTTTTCTAATTTCTATGAGGAACCTTTGTAAGTGACATGGTAGCCCTTTCCCTGTAGTTGTATTATATATGTTCTCA
TCTCTAAAAGAATCAACATTTTGACTTTAATGTGGTTGTCAAACTAGCATATTTGAGATCATAGCTTGTCATTTCTCTTTGGATCTTGATCTATGGTCTTCCAAATCATATCTTAGCCAGCTCAGGTAAGACCTTTTAGGACCGACCCATTCTTTGTAATTTTCTGTCTCGAGTCTGCAGAAATGGCCTTTTTCCATTTT
ATCCTGGTCTGCATAAATAATCTCAGGTCTATGAACAGGTGCTGTCCTGAACCTCCTACTGCAGTGTGTTTTCTTTCCAGTTTCACGTTCATTTTCTTTTCTTTTAAGCCCTCATTTGGTTCTAAAGTTGCTAAATATTTCTAGAGATAAAACAATCGTTCAATTGATTTCTAGGGTTTTCTATTTATAAAAAATATTAA
GCAAATACTTTTCTCTTCGTTTCTTTATCGGTTGCCACCTGTGGCTAGGCCATCCTTGAAGAAGACTGCAAAATGGTGTTTATTGTGGTAATTATTGTCTCGACCAACTCTTTTGTCCAACCAACCATTGCAGGGTGTCCTTGAACAAGAACGTAGGTTTGGAAATGAAGTTCCTATACTGATTTTTTATTTATGTATTT
GGATTCTGTTACTTTTAAGGTATGAATATCTGGATCCAAAATT

Intron 4 GTAGTGCTTT ... TTTGAGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	37.24	12.8	5	10
A2	43.06	6.3	7	2
A3	58.45	7.2	9	11
A4	32.98	3.5	1.4	2
A5	66.67	3	9	3
A6	61.11	1.2	0	2
A7	26.39	8.9	5	1
A8	24.75	5.2	2.2	1.2
A9	24.18	5.3	3	0
A10	33.53	8.1	5	2

>TRINITY_DN107885_c1_g1_i10 from sample A2 / Example spliced isoform

ATTGCACTCCAACAAATAGCCGATACGATTCCACTCTTTTCTGGTACATTCTCAGCTTCATTGCAGCTCCACATTTGATATTTTCAAATGAATGCGTTGAGGTGCGAGGGGATGCTCTTCCCAACAAAGGACTACCATGGCTGGTGGCCGACTATCCTTACCCCGAACAGATATTCAGGGTTCCGGCTTGGCATCATCAC
TAGAAGAAAAAATGTGTGCAGATTTGCCAAGGCAGATTCACAACATTATAATAAATCTCGAAATAGTTCTAGGAGCCTGGAAGGGCCTGGAAGGAGCATTGAGGATGGAGTACATCGTAAATTGAAGCAGTTCCATGAAGGATCTGAAGGACCACCTTTACGCATCCTGCCATTAGGAGGTCTGGGGGAAATAGGGATGA
ACTGTATGCTTGTAGGTCATTATGATCGGTATATTATTGTGGATGCTGGCCTCATGTTTCCAGACTATGATGAACTTGGCATCCAGAAAGTATTACCTGACACAACTTTCATTCGACGCTGGAGTCATAAGATAGAAGCAGTTGTTATAACACATGGCCATGAGGATCACATTGGAGCCTTGCCTTGGGTTATTCCAGCA
TTGGATTCGTGTACTCCGGTTTTCTCTTCATCATTCACAATGGAGTTGATCAGAAGACGGTTAAAGGAGTTCAGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATG
TGAAGATGGAACAATTTTCCATACTGGAGACTGGAAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTATTG
CATCTGCAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGTTCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTCAAACCTGAAGACATGGAT
GCTTATGCACCTAAAGATCTCCTTGTGGTGACAACAGGATCACAGGCAGAACCTCGTGCAGCTCTGAATCTTGCATCATTTGGAAGCAGTCACTCTCTCAAGCTTAACAAAGATGATCTGGTATTGTATTCTGCTAGGATGATACCTGGGAATGAAACTCGTGTAATGAAAATGCTTAACCGTATATCAGAGCTTGGGCC
AATGATAGTGATGGGAAGAGGAGAGACGTTGCATACTTCTGGTCATGCTTACCGTGGAGAGCTGGAGGAAGTTCTCAAGCTGGTAA

>TRINITY_DN107885_c1_g1_i4 from sample A2 / Example unspliced isoform:

ATTTGGATTCTGTTACTTTTAAGGTATGAATATCTGGATCCAAAATTTTATCTTCCATATTAACCTTGCTCTATTGTTGTCTGTTTCTGTTCTATTACTACGGTACCAGATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTATTGCATCTG
CAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGTTCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTCAAACCTGAAGACATGGATGCTTAT
GCACCTAAAGATCTCCTTGTGGTGACAACAGGATCACAGgtagtgctttgaaggagtcagaatatagtatttggttaaaatccatttcctatcaaggtcttcgcattaaacataacggaagcccattttgagacagGCAGAACCTCGTGCAGCTCTGAATCTTGCATCATTTGGAAGCAGTCACTCTCTCAAGCTTAACA
AAGATGATCTGGTATTGTATTCTGCTAGGATGATACCTGGGAATGAAACTCGTGTAATGAAAATGCTTAACCGTATATCAGAGCTTGGGCCAATGATAGTGATGGGAAGAGGAGAGACGTTGCATACTTCTGGTCATGCTTACCGTGGAGAGCTGGAGGAAGTTCTCAAGCTGGTAA

Intron 5 GTTTTGTATC ... TGTGATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	38.74	6	6.6	1
A2	60	2	4	2
A3	0	6	0	0
A4	75	1	4	2
A5	100	0	0	2
A6	25	12	2	6
A7	23.08	30	13	5
A8	19.86	25	3.4	9
A9	20	34	9	8
A10	14.29	15	1	4

>TRINITY_DN45612_c3_g4_i8 from sample A7 / Example spliced isoform

AGGACCACCTTTACGCATCCTGCCATTAGGAGGTCTGGGGGAAATAGGGATGAACTGTATGCTTGTAGGTCATTATGATCGGTATATTATTGTGGATGCTGGCCTCATGTTTCCAGACTATGATGAACTTGGCATCCAGAAAGTATTACCTGACACAACTTTCATTCGACGCTGGAGTCATAAGATAGAAGCAGTTGTTA
TAACACATGGCCATGAGGATCACATTGGAGCCTTGCCTTGGGTTATTCCAGCATTGGATTCGTGTACTCCGGTTTTCTCTTCATCATTCACAATGGAGGTATGCTTTCTGATGTAAATATTTGGACTTGCCGTATGCAGATTATTTGCATTTCTGTTCGTGTGTTGCATGATGAACTGAATTCATCAGATGGAGTGTGAA
GGAAGTATCTTTTTAAAGTCCTAAAGTATTCTACATCTTATACACTGATCGATGAGAAAATTTTCCTTTGAGTTCACATAGTTCTTAAAATGGAAGTATACAGGCAAATTTGCTTCCTTTGGCCTTATGATAAGGGCATATAGCTCAACAATGTTAGGAGCACAATTCTGTCCTTCAAAGCTCATCATTCTTAGATCTAT
TTTAGAACCTGACTATGGACTAATACCTCAAGTATCACTATTACGCAGTTGATCAGAAGACGGTTAAAGGAGTTCAGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAG
ATGTGAAGATGGAACAATTTTCCATACTGGAGACTGGAAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTA
TTGCATCTGCAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGTTCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTCAAACCTGAAGACATG
GATGCTTATGCACCTAAAGATCTCCTTGTGGTGACAACAGGATCACAGGCAGAACCTCGTGCAGCTCTGAATCTTGCATCATTTGGAAGCAGTCACTCTCTCAAGCTTAACAAAGATGATCTGGTATTGTATTCTGCTAGGATGATACCTGGGAATGAAACTCGTGTAATGAAAATGCTTAACCGTATATCAGAGCTTGG
GCCAATGATAGTGATGGGAAGAGGAGAGACGTTGCATACTTCTGGTCATGCTTACCGTGGAGAGCTGGAGGAAGTTCTCAAGCTGGTAAAGCCTCAACATTTCCTACCTGTTCACGGCGAATTCACTTACCTTAAAGAGCATGAGCTGCTCGGGAAGTCTACTGGTATTCGTCACACAAGTGTGATTAAAAATGGGGAGA
TGCTTGGAGTTTCTCCCCTGAGAAACAGAAGAGTCCTTTCTAATGGTTTTGCTTCCCTAGGCAAGGAGAATTTACAGTTGATGTACAATGATGGAGATAAAGCTTTTGGAACATCAACAGATCTTTGCATTGATGAGCGGATGAAAATAGCCCTTGATGGCATTATAATTGCAAGTGTGGAATTTATGCGGCCTCAGAAT
GTACCTTCAGATTCAGTAGCAGATGGCAAATTTGAATCACAGGCACTACTAACAGGAAATATAAAGATCACAACTCGTTGCCTATGGGTTGACAAAGGCAAACTTCTAGAAGCACTACAGAAAGCTGCACATTTGGCATTGGCAGGATGCCCTCCAAATTGTCCAATTGGTCATATAGAGCGCACCATTTCTACAGTACT
TAGAAAGGTGGTACGCAAGTACAATAGCAAACGGCCAGAAGTGATTGTAATGGCCGTTGAAAATATTTCTGGCTTCTCTGCTAAAGATTTAAAGTCAAAAAGATCCAGAAAAGACCACAATGTGGTTGGGAGTTTTGAGGATAGTGCACCAAAATTGACTTCTTTGCAAGGTGCAACAAATACATCAGTGGCAGCATCAA
CAACACCTAAAAAAAATTGTAAAAGTCAACAAAGAATCGATCATGTATCTCCTTCAGTGCCTCCTATAACATTGGCTAACACATCAAAAGTTTCAGATGAGAAATGTGCTGATGGAGTTTCTCAGGTGCCCACTGAAACATTGCATACAGAGTCATCAGTTATATCTCCAGCTAAGAAGCACCGCAAATGGAAGAAACAC
GAGACTCTGAAGTTGATTGAAATGCGTGGGAATATGGAAAATCAGTTTAAAACAGAGAAGGAAAAGGTACTCTGGGAAGAGATTTCAGCATCTTTGTTGGGGCATGGAATTGATCGTGGTCCAGACCAATGCAAATCTCTTTGGGTATCACTGGTTACGAAGTATGAGAGCCTTCTTCAAGGAGAGAAAAGTAAAAAGAC
ATGGCCTTTTTTGGCTGAGATGGACAAAATCTTATCGTGTCAGTCAAGAAGAGTATAAAAATATCAGTTGCCTTTAAATGGGATGATACATAGGAGATCACCAAATCATTATTTTATTGGTGATCTCCTTATGTGCCATATCTTGTGTGAAAAATAGGGATGTAAAGAGAAGTGCTCACCAATTTGGTCGACATCCTCTA
TACAATGTCATCACAACAGGTGACCAGAAAGGTATAATTCTGGTTGAATAACAAACGCAAAAAAATTGGGAAGCCAAATTCTTCTTGGGCAGCCTTATAGAGGAAAATGGCCACAACCATTTACTGGAAAGTCAAGGGACTTTGATGCCAAGAAAGATTTTGCCTTTCTATGCCCTAGTTCTAGATCTCTTATGATGTTT
TCTGGAATTAATGCTCTTTTGCTAGTCATAGATTAATAAATGTTCAAAGGGATTTTGCAAGGTTGATGTCGATCCCATCCCTTGTTTCAGTTTCCCCGAGTGTAGCAGAGTTGGTCAATTATAGACGTGTACTTAGTGACCAACATTGCTATTTGTACTGTGCTGTTGAAATTCTGCTAAAATGAAGGCAAAAGGTATGT
ATTTATTTGCACTTAATGATTTGTTTATTGCAAGTCAGATTTAGAGTCCCACAAATTCCGTGGACTTTAAGTTTTTATTGGAAATAATAAATTTGGGG

>TRINITY_DN45612_c3_g4_i4 from sample A7 / Example unspliced isoform:

GTCATTCTACATCATGCTTTCTGTTGAAACCTGAATGGGGATGGCACTGAAATGTTGTTTACAAAATTGAAATTTACAGAGCCTTCTTCAAGGAGAGAAAAGTAAAAAGACATGGCCTTTTTTGGCTGAGATGGACAAAATCTTATCGTGTCAGTCAAGAAGAGTATAAAAATATCAGTTGCCTTTAAATGGGATGATAC
ATAGGAGATCACCAAATCATTATTTTATTGGTGATCTCCTTATGTGCCATATCTTGTGTGAAAAATAGGGATGTAAAGAGAAGTGCTCACCAATTTGGTCGACATCCTCTATACAATGTCATCACAACAGgttttgtatctgattgccacattgtattttgttattgtattcctttcatactgggttccacgagcaacta
aatgtttaccaattctgaaggatccgtttatatcttaatattttgtgatgcagGTGACCAGAAAGGTATAATTCTGGTTGAATAACAAACGCAAAAAAATTGGGAAGCCAAATTCTTCTTGGGCAGCCTTATAGAGGAAAATGGCCACAACCATTTACTGGAAAGTCAAGGGACTTTGATGCCAAGAAAGATTTTGCCTT
TCTATGCCCTAGTTCTAGATCTCTTATGATGTTTTCTGGAATTAATGCTCTTTTGCTAGTCATAGATTAATAAATGTTCAAAGGGATTTTGCAAGGTTGATGTCGATCCCATCCCTTGTTTCAGTTTCCCCGAGTGTAGCAGAGTTGGTCAATTATAGACGTGTACTTAGTGACCAACATTGCTATTTGTACTGTGCTGT
TGAAATTCTGCTAAAATGAAGGCAAAAGGTATGTATTTATTTGCACTTAATGATTTGTTTATTGCAAGTCAGATTTAGAGTCCCACAAATTCCGTGGACTTTAAGTTTTTATTGGAAATAATAAATTTGGGG

Intron 6 GTATGCTTTC ... TATTACGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.44	10	2.4	8
A2	0	5	5.4	0
A3	20	12	3.8	3
A4	50	10	4.1	10
A5	11.11	8	1.1	1
A6	-1	0	0	0
A7	42.86	4	1.4	3
A8	0	4	1.6	0
A9	0	6	0.6	0
A10	66.67	1	0	2

>TRINITY_DN117943_c1_g1_i5 from sample A1 / Example spliced isoform

CTCCAACAAATAGCCGATACGATTCCACTCTTTTCTGGTACATTCTCAGCTTCATTGCAGCTCCACATTTGATATTTTCAAATGAATGCGTTGAGGTGCGAGGGGATGCTCTTCCCAACAAAGGACTACCATGGCTGGTGGCCGACTATCCTTACCCCGAACAGATATTCAGGGTTCCGGCTTGGCATCATCACTAGAAG
AAAAAATGTGTGCAGATTTGCCAAGGCAGATTCACAACATTATAATAAATCTCGAAATAGTTCTAGGAGCCTGGAAGGGCCTCGAAGGAGCATTGAGGATGGAGTACATCGTAAATTGAAGCAGTTCCATGAAGGATCTGAAGGACCACCTTTACGCATCCTGCCATTAGGAGGTCTGGGGGAAATAGGGATGAACTGTA
TGCTTGTAGGTCATTATGATCGGTATATTATTGTGGATGCTGGCCTCATGTTTCCAGACTATGATGAACTTGGCATCCAGAAAGTATTACCTGACACAACTTTCATTCGACGCTGGAGTCATAAGATAGAAGCAGTTGTTATAACACATGGCCATGAGGATCACATTGGAGCCTTGCCTTGGGTTATTCCAGCATTGGAT
TCGTGTACTCCGGTTTTCTCTTCATCATTCACAATGGAGTTGATCAGAAGACGGTTAAAGGAGTTCAGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATGTGAAGA
TGGAACAATTTTCCATACTGGAGACTGGAAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGATGATGAGTGACTCAACCAACATTCTTTCTCCTGGAAGAACTGTTAGTGAATCAGATGTAGCAGAGGGTTTGCTACGACGTATTGCATCTG
CAAAGGGAAGAGTGATAACAACACAGTTTGCCTCCAATGTTCATCGTCTTGGTAGTGTGAAAGCCGCAGCTGAAGTTACTGGCCGAAAGCTGGTCTTTGTTGGCATGTCATTGAGGACATACTTGGATGCTGCTTGGAAGGACGGGCAAGCACCCTTTGATCCATCTACCCTGGTCAAACCTGAAGACATGGATGCTTAT
GCACCTAAAGATCTCCTTGTGGTGACAACAGGATCACAGGTAGTGCTTTGAAGGAGTCAGAATATAGTATTTGGTTAAAATCCATTTCCTATCAAGGTCTTCGCATTAAACATAACGGAAGCCCATTTTGAGACAGGCAGAACCTCGTGCAGCTCTGAATCTTGCATCATTTGGAAGCAGTCACTCCCTCC

>TRINITY_DN117943_c1_g1_i11 from sample A1 / Example unspliced isoform:

TCTCTTCATCATTCACAATGGAGgtatgctttctgatgtaaatatttggacttgccgtatgcagattatttgcatttctgttcgagtgttgcatgatgaactgaattcatcagatggagtgtgaaggaagtatctttttaaagtcctaaagtattctacatcttataaactgatcgatgagaaaattttcctttgagttc
acatagttcttaaaatggaagtatacaggcaaatttgcttcctttggccttatgataagggcatatagctcaacaatgttaggagcacaattcggtccttcaaagctcatcattcttagatctattttagaacctgactatggactaatacctcaagtatcactattacgcagTTGATCAGAAGACGGTTAAAGGAGTTC
AGTATTCCGGTGCAGAACAGACTTAAAATATTTAAAATGAGAGAGAGGTTTAGAGCGGGGCCATTTGAGATAGAGCCCATTCGGGTTACTCATTCAATTCCAGATTGCTGTGGGTTGGTGCTTAGATGTGAAGATGGAACAATTTTCCATACTGGAGACTGGAAGGTACTGGGCCACTGGAAGAACATTATAGAAACAGC
CAGGAACTTAATTCAATTGCTTCTGATAAATGTATGTCTGTGTTCTAGATTGATGAGTCACCAGTTGATGGAAAAGCTTTTGATCGGCCGGCTCTAGAAGAACTTGCAAAGGAAGGTGTTACCTTGGTAATTTAATCTCATTATATGTTTACAGTGGTACTTTGAAACACCTTTACCTCCCCCTCTACAATTTGAATATT
GTTTTGTTGACATTTCTGTCTTTCAAGAAAATGAGTCCTAGTCTGTTACTGGTATGTGCAACATTGACAGATCAATTCTATGTGATACATTCATATTTTGAAAGAAAAACAAAACTTTCTTTCCATTGGAAGTTTATAATATTACTTAAACAGTAGAATAGTGTAGGCTGTTATATGTTAATGCCAATAACAGCTTTACC
CTGCCAGAATAGTGATGTTGTATACAATATCTCAGTTTAATCTTAGTTTATGGGAAGCCATCCAATATGATATAAATTAGTCTATATACTTTTGAAGTTTTTAGAAAGGAAAAATTAAACAATTAAATTTATGGTGTACAGGACTAAATGGTGCAAGCTGATGTCTCACGTAACTCTCTTTAAAAGTTTAATCATAATGC
ATAGTATAAATTAATAGAAATAATGGTTACAACATGAAAAACATAGTAATTCTGCTTGGTCCTTTTTTCACCTGCTGTTTTATCAGGCCACAAATACTGGTTGACCTAGTTGTTGGGTACAACCTTTTCTAATTTCTATGAGGAACCTTTGTAAGTGACATGGTAGCCCTTTCCCTGTAGTTGTATTATATATGTTCTCA
TCTCTAAAAGAATCAACATTTTGACTTTAATGTGGTTGTCAAACTAGCATATTTGAGATCATAGCTTGTCATTTCTCTTTGGATCTTGATCTATGGTCTTCCAAATCATATCTTAGCCAGCTCAGGTAAGACCTTTTAGGACCGACCCATTCTTTGTAATTTTCTGTCTCGAGTCTGCAGAAATGGCCTTTTTCCATTTT
ATCCTGGTCTGCATAAATAATCTCAGGTCTATGAACAGGTGCTGTCCTGAACCTCCTACTGCAGTGTGTTTTCTTTCCAGTTTCACGTTCATTTTCTTTTCTTTTAAGCCCTCATTTGGTTCTAAAGTTGCTAAATATTTCTAGAGATAAAACAATCGTTCAATTGATTTCTAGGGTTTTCTATTTATAAAAAATATTAA
GCAAATACTTTTCTCTTCGTTTCTTTATCGGTTGCCACCTGTGGCTAGGCCATCCTTGAAGAAGACTGCAAAATGGTGTTTATTGTGGTAATTATTGTCTCGACCAACTCTTTTGTCCAACCAACCATTGCAGGGTGTCCTTGAACAAGAACGTAGGTTTGGAAATGAAGTTCCTATACTGATTTTTTATTTATGTATTT
GGATTCTGTTACTTTTAAGGTATGAATATCTGGATCCAAAATT