sp|Q9CAI5|CKL2_ARATH ----> Casein kinase 1-like protein 2

Intron 1 GTATACATAA ... ACATCAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	96.4	1.3	7	27
A2	85	4	6	20
A3	76.5	6	3	19.3
A4	89.65	5.7	5	35.3
A5	90.52	1.3	6	14
A6	86.41	6	8	33.3
A7	87.11	12	6	67
A8	93.33	3.7	8	31.3
A9	88.85	9	5	40
A10	91.42	2.7	8	28.7

>TRINITY_DN42939_c1_g4_i9 from sample A9 / Example spliced isoform

GAAGAAGCAGCTGAGAGAAGGTACCCTCAGTCCTTGATAAGAAACTCCAAGTCACGTGCTGTTGAATTCGGTTCTCATTATTTTTGAACGTGGGCACTTGGATTTGGAGGCAAAACCTGACTGGGTTTTGCTCAGTGATAATTTATGAATACATGTGGGTACTCAGATTAAAATATTCTATATAGGAATACAAGCAAAGC
CCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATT
TATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAA
GCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGC
AAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGA
GCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGCTTTCAGTTTGATTATATATTTGATTGGAATCCGTTAAAATACCAACGGGCCCAAAGTGCTGCTGCTAATCCTCGTCCACATATTGGAAGTGGGAAGGGGCACGAGAATGCTAATATCCTAATGGA
AGGGATTTTAGCTGGGCAGGGGATTCATCAGCGAGTTTCAGGAATAGGTGAATGGTCTCAAAGGACTATTGGAGGTAATGCTGTAACTCGTAGAATACCAGATCATTCTAAAGACACGACTTACAGGCAGGACGACCATTCAGCATACAAGGAAGAGGGGTTACATACTGAACCAATACACTCGTCATCTATGCAGATAG
GGAATTCATTAAAGAAACCAGTGGTCTCGGGAAACAGAGCAGCCTCCTCTGGTGGAACTTTTGAACGAACTCGTTTTGCAACAACTAGGATTTCTCCTTCCAATCATCACACTTCATCTGAACAGCCACGTTCTTCTGTGGTGGCTACATCTGGTTCTAAAAGGCCAGTCCATGTTCATCATAAAATACCAAAGATTGTT
GATGCTGACATTCTAACTGATTTCCAGTTCCTTGGTGTTGAATCAGACCAACAATGAGTGTTTCCCATTCTTACATTTGTCTTCTAGTAAAATTGCAACAGCATTGCTTATATTTCTAGGATTTTGTACACCTTATATTGATCTTCTAGTAATGCTGCAAGGGCATCTCTCCATTGGAATTGCTGATTGCACAGTATTTT
TTTTCCTTCTCTGCTTCCACTCGTTGAGTAAGATTACATACAACTAACAGTGGTACTATAAGGAGTACTAATCTCAGTCTCTAAATAAAATCAATGCAACTGATTTCATAACATGTTTTTCTGAATTTTTGGTGTTCCTTAATATTTATATACTTGTGTTTAG

>TRINITY_DN42939_c1_g4_i7 from sample A9 / Example unspliced isoform:

CTATGGAGACGAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGgtatacataatcatcggaacacttgttggccttaacttttcttgcttgttcttcttctgcaaacccatatgcagatttttgcctcatattttttctctaagtttccagttttttcctctgtcccttctatttcttccaaccaa
actatctctaaaatcctggagaattggcgctgttgctggcagattaatgggctggagtggttactagtctttcatattttttcaattgtgattatggggtggcagtgcccaatctcctgagaagtaattagtcttttatcatttcaaatgcatgggatataaacatcaacagGTACCCTCAGTCCTTGATAAGAAACTCC
AAGTCACGTGCTGTTGAATTCGGTTCTCATTATTTTTGAACGTGGGCACTTGGATTTGGAGGCAAAACCTGACTGGGTTTTGCTCAGTGATAATTTATGAATACATGTGGGTACTCAGATTAAAATATTCTATATAGGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAG
TGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTAT
GGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCT
TGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACT
TCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATA
TTTCGTGATCTATTTATTCGAGAGAGCTTTCAGTTTGATTATATATTTGATTGGAATCCGTTAAAATACCAACGGGCCCAAAGTGCTGCTGCTAATCCTCGTCCACATATTGGAAGTGGGAAGGGGCACGAGAATGCTAATATCCTAATGGAAGGGATTTTAGCTGGGCAGGGGATTCATCAGCGAGTTTCAGGAATAGG
TGAATGGTCTCAAAGGACTATTGGAGGTAATGCTGTAACTCGTAGAATACCAGATCATTCTAAAGACACGACTTACAGGCAGGACGACCATTCAGCATACAAGGAAGAGGGGTTACATACTGAACCAATACACTCGTCATCTATGCAGATAGGGAATTCATTAAAGAAACCAGTGGTCTCGGGAAACAGAGCAGCCTCCT
CTGGTGGAACTTTTGAACGAACTCGTTTTGCAACAACTAGGATTTCTCCTTCCAATCATCACACTTCATCTGAACAGCCACGTTCTTCTGTGGTGGCTACATCTGGTTCTAAAAGGCCAGTCCATGTTCATCATAAAATACCAAAGATTGTTGATGCTGACATTCTAACTGATTTCCAGTTCCTTGGTGTTGAATCAGAC
CAACAATGAGTGTTTCCCATTCTTACATTTGTCTTCTAGTAAAATTGCAACAGCATTGCTTATATTTCTAGGATTTTGTACACCTTATATTGATCTTCTAGTAATGCTGCAAGGGCATCTCTCCATTGGAATTGCTGATTGCACAGTATTTTTTTTCCTTCTCTGCTTCCACTCGTTGAGTAAGATTACATACAACTAAC
AGTGGTACTATAAGGAGTACTAATCTCAGTCTCTAAATAAAATCAATGCAACTGATTTCATAACATGTTTTTCTGAATTTTTGGTGTTCCTTAATATTTATATACTTGTGTTTAG

Intron 2 GTACCCTCAG ... TTCTATATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	31.13	32	23.2	13.8
A2	40.07	24.3	17.4	16
A3	49.89	19.4	18.6	19
A4	37.93	44.9	29	27
A5	51.15	9.7	15.5	10
A6	27.63	48.7	24.2	18
A7	29.76	94.6	50.4	39
A8	31.3	42.9	24.1	19
A9	34.26	74.2	21.3	38
A10	21.84	42.6	20.3	11

>TRINITY_DN115923_c0_g1_i5 from sample A1 / Example spliced isoform

GAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGATATAAACATCAACAGGAATACAAGCAAAGCCCATCAAA
CTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAAT
TGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTA
TTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGG
AGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCG
CTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGC

>TRINITY_DN115923_c0_g1_i3 from sample A1 / Example unspliced isoform:

GAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGGTATACATAATCATCGGAACACTTGTTGGCCTTAACTTTTCTTGCTTGTTCTTCTTCTGCAAACCCATATGCAGATTTTTGCCTCATATTTTTTCTCTAAGTTTCCAGTTTTTTCCTCTGTCCCTTCTATTTCTTCCAACCAAACTATCTCTA
AAATCCTGGAGAATTGGCGCTGTTGCTGGCAGATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGATATAAACATCAACAGgtaccctcagtccttgataagaaactccaagtcacgtg
ctgttgaattcggttctcattatttttgaacgtgggcacttggatttggaggcaaaacctgactgggttttgctcagtgataatttatgaatacatgtgggtactcagattaaaatattctatatagGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAA
GTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAG
GCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGA
GCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGG
AAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATC
TATTTATTCGAGAGAGC

Intron 3 GTGGGTATCT ... GTGGTTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.89	32	14	5
A2	21.21	26	8	6
A3	22.45	38	16	6
A4	32.56	29	17	11
A5	26.32	7	4	1
A6	21.52	31	10	7
A7	18.78	80	24	13
A8	21.1	43	14	9
A9	23.27	61	23	14
A10	22.52	86	30	20

>TRINITY_DN45347_c0_g3_i14 from sample A7 / Example spliced isoform

TAATGACGAAACTGTAAGAATACGGCCACTATGGAGACGAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGGTATACATAATCATCGGAACACTTGTTGGCCTTAACTTTTCTTGCTTGTTCTTCTTCTGCAAACCCATATGCAGATTTTTGCCTCATATTTTTTCTCTAAGTTTCCAGTTTTTTC
CTCTGTCCCTTCTATTTCTTCCAACCAAACTATCTCTAAAATCCTGGAGAATTGGCGCTGTTGCTGGCAGATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGATATAAACATCAACAG
GTACCCTCAGTCCTTGATAAGAAACTCCAAGTCACGTGCTGTTGAATTCGGTTCTCATTATTTTTGAACGTGGGCACTTGGATTTGGAGGCAAAACCTGACTGGGTTTTGCTCAGTGATAATTTATGAATACATGTGGGTACTCAGATTAAAATATTCTATATAGGAATACAAGCAAAGCCCATCAAACTTAATTGTGAA
AATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGG
AACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTATTCATCGTGATG
TAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGGAGAGATGATCTA
GAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCGCTTTGATGATAA
GCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGCTTTCAGTTTGATTATATATTTGATTGGAATCCGTTAAAATACCAACGGGCCCAAAGTGCTGCTGCTAATCCTCGTCCACATATTGGAAGTGGGAAGGGGCACGAGAATGCTAATATCCTAATGGAAGGGATTTTAGCTGGGCAGG
GGATTCATCAGCGAGTTTCAGGAATAGGTGAATGGTCTCAAAGGACTATTGGAGGTAATGCTGTAACTCGTAGAATACCAGATCATTCTAAAGACACGACTTACAGGCAGGACGACCATTCAGCATACAAGGAAGAGATAGGGAATTCATTAAAGAAACCAGTGGTCTCGGGAAACAGAGCAGCCTCCTCTGGTGGAACT
TTTGAACGAACTCGTTTTGCAACAACTAGGATTTCTCCTTCCAATCATCACACTTCATCTGAACAGCCACGTTCTTCTGTGGTGGCTACATCTGGTTCTAAAAGGCCAGTCCATGTTCATCATAAAATACCAAAGATTGTTGATGCTGACATTCTAACTGATTTCCAGTTCCTTGGTGTTGAATCAGACCAACAATGAGT
GTTTCCCATTCTTACATTTGTCTTCTAGTAAAATTGCAACAGCATTGCTTATATTTCTAGGATTTTGTACACCTTATATTGATCTTCTAGTAATGCTGCAAGGGCATCTCTCCATTGGAATTGCTGATTGCACAGTATTTTTTTTCCTTCTCTGCTTCCACTCGTTGAGTAAGATTACATACAACTAACAGTGGTACTAT
AAGGAGTACTAATCTCAGTCTCTAAATAAAATCAATGCAACTGATTTCATAACATGTTTTTCTGAATTTTTGGTGTTCCTTAATATTTATATACTTGTGTTTAGATGCG

>TRINITY_DN45347_c0_g3_i12 from sample A7 / Example unspliced isoform:

TAATGACGAAACTGTAAGAATACGGCCACTATGGAGACGAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGA
TATAAACATCAACAGGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAG
CACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCT
Agtgggtatctttgctctttgttccagcttgtgcaacattagttgcataagtatttattttctttcagcatcacggagtaggctgtagttgcattaagaaaacattgaatttgcagttttgcatctataacacgtggagcaatgatttttgcacaatggattattcattattaatttatttccctttctatttgtcgtga
tgtctttattggaagtgatgactatgagtttcctagtttgtggttttagATTAACAGGATTGAGTATGTCCATTCAAAGCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGC
ATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAA
AAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGCTTTCAGTTTGATTATATATTTGATTGGAATCCGTTAAAATACCAACG
GGCCCAAAGTGCTGCTGCTAATCCTCGTCCACATATTGGAAGTGGGAAGGGGCACGAGAATGCTAATATCCTAATGGAAGGGATTTTAGCTGGGCAGGGGATTCATCAGCGAGTTTCAGGAATAGGTGAATGGTCTCAAAGGACTATTGGAGGTAATGCTGTAACTCGTAGAATACCAGATCATTCTAAAGACACGACTT
ACAGGCAGGACGACCATTCAGCATACAAGGAAGAGATAGGGAATTCATTAAAGAAACCAGTGGTCTCGGGAAACAGAGCAGCCTCCTCTGGTGGAACTTTTGAACGAACTCGTTTTGCAACAACTAGGATTTCTCCTTCCAATCATCACACTTCATCTGAACAGCCACGTTCTTCTGTGGTGGCTACATCTGGTTCTAAA
AGGCCAGTCCATGTTCATCATAAAATACCAAAGATTGTTGATGCTGACATTCTAACTGATTTCCAGTTCCTTGGTGTTGAATCAGACCAACAATGAGTGTTTCCCATTCTTACATTTGTCTTCTAGTAAAATTGCAACAGCATTGCTTATATTTCTAGGATTTTGTACACCTTATATTGATCTTCTAGTAATGCTGCAAG
GGCATCTCTCCATTGGAATTGCTGATTGCACAGTATTTTTTTTCCTTCTCTGCTTCCACTCGTTGAGTAAGATTACATACAACTAACAGTGGTACTATAAGGAGTACTAATCTCAGTCTCTAAATAAAATCAATGCAACTGATTTCATAACATGTTTTTCTGAATTTTTGGTGTTCCTTAATATTTATATACTTGTGTTT
AGATGCG

Intron 4 GTATACATAA ... TTCTATATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	77.78	4	7	14
A2	66.67	8	6	16
A3	82.61	4	3	19
A4	64.29	15	5	27
A5	83.33	2	6	10
A6	60	12	8	18
A7	60	26	6	39
A8	63.33	11	8	19
A9	60.32	25	5	38
A10	73.33	4	8	11

>TRINITY_DN42939_c1_g4_i8 from sample A9 / Example spliced isoform

CTATGGAGACGAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACA
AACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCG
CAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTA

>TRINITY_DN42939_c1_g4_i13 from sample A9 / Example unspliced isoform:

CTATGGAGACGAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGgtatacataatcatcggaacacttgttggccttaacttttcttgcttgttcttcttctgcaaacccatatgcagatttttgcctcatattttttctctaagtttccagttttttcctctgtcccttctatttcttccaaccaa
actatctctaaaatcctggagaattggcgctgttgctggcagattaatgggctggagtggttactagtctttcatattttttcaattgtgattatggggtggcagtgcccaatctcctgagaagtaattagtcttttatcatttcaaatgcatgggatataaacatcaacaggtaccctcagtccttgataagaaactcc
aagtcacgtgctgttgaattcggttctcattatttttgaacgtgggcacttggatttggaggcaaaacctgactgggttttgctcagtgataatttatgaatacatgtgggtactcagattaaaatattctatatagGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAG
TGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTAT
GGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAGTGGGTATCTTTGCTCTTTGTTCCAGCTTGTGCAACATTAGTTGCATAAGTATTTATTTTCTTTCAGCATCACGGAG
TAGGCTGTAGTTGCATTAAGAAAACATTGAATTTGCAGTTTTGCATCTATAACACGTGGAGCAATGATTTTTGCACAATGGATTATTCATTATTAATTTATTTCCCTTTCTATTTGTCGTGATGTCTTTATTGGAAGTGATGACTATGAGTTTCCTAGTTTGTGGTTTTAGATTAACAGGATTGAGTATGTCCATTCAAA
GCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGC
AAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGA
GCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGCTTTCAGTTTGATTATATATTTGATTGGAATCCGTTAAAATACCAACGGGCCCAAAGTGCTGCTGCTAATCCTCGTCCACATATTGGAAGTGGGAAGGGGCACGAGAATGCTAATATCCTAATGGA
AGGGATTTTAGCTGGGCAGGGGATTCATCAGCGAGTTTCAGGAATAGGTGAATGGTCTCAAAGGACTATTGGAGGTAATGCTGTAACTCGTAGAATACCAGATCATTCTAAAGACACGACTTACAGGCAGGACGACCATTCAGCATACAAGGAAGAGGGGTTACATACTGAACCAATACACTCGTCATCTATGCAGATAG
GGAATTCATTAAAGAAACCAGTGGTCTCGGGAAACAGAGCAGCCTCCTCTGGTGGAACTTTTGAACGAACTCGTTTTGCAACAACTAGGATTTCTCCTTCCAATCATCACACTTCATCTGAACAGCCACGTTCTTCTGTGGTGGCTACATCTGGTTCTAAAAGGCCAGTCCATGTTCATCATAAAATACCAAAGATTGTT
GATGCTGACATTCTAACTGATTTCCAGTTCCTTGGTGTTGAATCAGACCAACAATGAGTGTTTCCCATTCTTACATTTGTCTTCTAGTAAAATTGCAACAGCATTGCTTATATTTCTAGGATTTTGTACACCTTATATTGATCTTCTAGTAATGCTGCAAGGGCATCTCTCCATTGGAATTGCTGATTGCACAGTATTTT
TTTTCCTTCTCTGCTTCCACTCGTTGAGTAAGATTACATACAACTAACAGTGGTACTATAAGGAGTACTAATCTCAGTCTCTAAATAAAATCAATGCAACTGATTTCATAACATGTTTTTCTGAATTTTTGGTGTTCCTTAATATTTATATACTTGTGTTTAG

Intron 5 GTATACATAA ... TTGCTGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	60.04	16	7	24
A2	52.97	24	6	27
A3	54.69	9.9	3	12
A4	57.58	14	5	19
A5	61.54	10	6	16
A6	64.76	12	8	22
A7	56.54	40	6.2	52
A8	42.07	24.8	8	18
A9	52.92	32.9	5	37
A10	57.89	24	8	33

>TRINITY_DN115923_c0_g1_i5 from sample A1 / Example spliced isoform

GAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGATATAAACATCAACAGGAATACAAGCAAAGCCCATCAAA
CTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAAGTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAAT
TGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAGGCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTA
TTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGAGCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGG
AGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGGAAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCG
CTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATCTATTTATTCGAGAGAGC

>TRINITY_DN115923_c0_g1_i3 from sample A1 / Example unspliced isoform:

GAAAAGAAGAGCAAAGAGCAAATGAGAGAAGAAGCAGCTGAGAGAAGgtatacataatcatcggaacacttgttggccttaacttttcttgcttgttcttcttctgcaaacccatatgcagatttttgcctcatattttttctctaagtttccagttttttcctctgtcccttctatttcttccaaccaaactatctcta
aaatcctggagaattggcgctgttgctggcagATTAATGGGCTGGAGTGGTTACTAGTCTTTCATATTTTTTCAATTGTGATTATGGGGTGGCAGTGCCCAATCTCCTGAGAAGTAATTAGTCTTTTATCATTTCAAATGCATGGGATATAAACATCAACAGGTACCCTCAGTCCTTGATAAGAAACTCCAAGTCACGTG
CTGTTGAATTCGGTTCTCATTATTTTTGAACGTGGGCACTTGGATTTGGAGGCAAAACCTGACTGGGTTTTGCTCAGTGATAATTTATGAATACATGTGGGTACTCAGATTAAAATATTCTATATAGGAATACAAGCAAAGCCCATCAAACTTAATTGTGAAAATCAACCCCGAGCAATGGAGGCCATAGTGGGAGAAAA
GTATAGACTTGGCCGAAAAATTGGCAACGGTTCGTTTGGTGAAATCTATCTGGGGGTCAATATTCAGACAAACGAAGAAGTGGCCGTTAAACTGGAAGATGCAGAGACTAAGCACCCTCAACTTTCATACGAGGCCAAGATTTATAGAATTGTTCAAGAAGGAACTGGAATCCCAAATGTAAGATGGTATGGTGGGGAAG
GCAATCATAATGTGATGGTTCTTGACCTCCTTGGACCAAGTCTTGAAGATTTATTCGACTGTTGTGATCGCAAATTCTCTTTGAAAACTATACTAATGCTTGCTGATCAGCTAATTAACAGGATTGAGTATGTCCATTCAAAGCACATTATTCATCGTGATGTAAAGCCTGACAATTTTCTCATGGGTCTTGGGCGAAGA
GCAAATCAGGTCTACATCATAGATTTTGGGCTTGCCAAAAAATATCGAGATGCTACTCATAAGCATATTCCCTATAGGGAAAACAAAAATCTCACTGGTACTGCTCGCTATGCTAGTGTCAATGCCCACATTGGGATAGAGCAAAGCAGGAGAGATGATCTAGAATCTCTAGGCTATATGCTGATGTACTTCTTAAGAGG
AAGCCTTCCATGGCAGGGATTAAAAGCTGCAACCAAAAAGCAAAAGTATGATAAGATCAGTGAAAAGAAAATATCAACTCCAATAGAGGTATTGTGCAAGTCTTACCCGTCTGAGTTTGCCTCATATTTCCGTTACTGTCGAGCACTGCGCTTTGATGATAAGCCAGATTATGCTTACTTGAAGAGGATATTTCGTGATC
TATTTATTCGAGAGAGC