sp|Q9SRS9|CHIP_ARATH ----> E3 ubiquitin-protein ligase CHIP

Intron 1 GCTTTGGAGC ... TCCTAATGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	65.31	51	94	98
A2	66.36	54	95	118
A3	66.56	54	93	122
A4	65.87	43	72	94
A5	60.63	25	38	39
A6	64.41	100	102	260
A7	67.35	208	274	584
A8	64.67	206	220	534
A9	65.13	231	302	561
A10	65.12	188	230	472

>TRINITY_DN39047_c0_g1_i2 from sample A6 / Example spliced isoform

GTCGAACCTTTGATAGGAAAAAAAAAAAGGAATAGAGTGTTCAACATTAACGGTGGTATTTAAAAAGCCTATTAAAAACATCTCCGAAAGGGTGATTTTCTTGTTTGCATAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAG
AGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCG
TGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCT
TTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGGTACCTGAATATCTGTGTTGCAAAATTACATTGGACATCTTTCGGGACCCGGTAATCACTCCTAGTGGAGTTACATATGAGAGGGCAGTTATTCTAGAACA
TATACGGAAGGTTGGCAACTTTGATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGA
GAGTTTTGGAGATGGCGTCATAAAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAAT
GTGTGAATTCTTTGATCCAAATGTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTG
GCTTTGGAATGTTTAGCTACATGGTAATGAAATGGCAGTCGTTTCTTCTTCAATTATCACTCTATTCCTAAGTCATGGCGGCTTGGAAGTTAATGTTCCCAACCGCATTCCCTGTTGATCCGTGAGTCTAATGGGCTTTACTTTGAAATATGTACTTGAGGAAAGAATGATAGGCGTAGCTGCATCTGTTACACAAGGCA
ATATTTGTTGCAGTCATGGGAATGACATGCATGCATGCGACTGCTGCTTATTATAATTTTCTAGGTGAGAAAGACTATTGTTTCATTCATATTATTATTATCAATGAATATACCATAGTATAGAAGTTGACATATATAGGTTCAGCTTTTGGCACCAACTTGAAAGAAACCACATCAAGGTGCA

>TRINITY_DN39047_c0_g1_i1 from sample A6 / Example unspliced isoform:

GTCGAACCTTTGATAGGAAAAAAAAAAAGGAATAGAGTGTTCAACATTAACGGTGGTATTTAAAAAGCCTATTAAAAACATCTCCGAAAGGGTGATTTTCTTGTTTGCATAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAG
AGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCG
TGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCT
TTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGgctttggagcttgggagaggagcaaatccatcaagttatatggtggaggagatctggcaggaacttgcaaaagcaaaatatttagagtgggagtcttcttc
acaccttcgttttaaaaaacaacaagagttgagaggaatttgtgaaagggctctccagcaagaatttgaaagtactcgtatgcaagacagtgaaactggtatccagcctacgaccgctacgtatcataatgggggtacagcaagcacacacagtgatggtacggaatcaaatgacgtggaaggagaatctagaagtcgtg
aaaactctctgaaagtggtgtcagaaattacttacaaagaacgaattaaaatactctctgacgtgtttaacaaagcagcagaggcggatattcctaatgagGTACCTGAATATCTGTGTTGCAAAATTACATTGGACATCTTTCGGGACCCGGTAATCACTCCTAGTGGAGTTACATATGAGAGGGCAGTTATTCTAGAA
CATATACGGAAGGTTGGCAACTTTGATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCA
GAGAGTTTTGGAGATGGCGTCATAAAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATA
ATGTGTGAATTCTTTGATCCAAATGTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTAT
TGGCTTTGGAATGTTTAGCTACATGGTAATGAAATGGCAGTCGTTTCTTCTTCAATTATCACTCTATTCCTAAGTCATGGCGGCTTGGAAGTTAATGTTCCCAACCGCATTCCCTGTTGATCCGTGAGTCTAATGGGCTTTACTTTGAAATATGTACTTGAGGAAAGAATGATAGGCGTAGCTGCATCTGTTACACAAGG
CAATATTTGTTGCAGTCATGGGAATGACATGCATGCATGCGACTGCTGCTTATTATAATTTTCTAGGTGAGAAAGACTATTGTTTCATTCATATTATTATTATCAATGAATATACCATAGTATAGAAGTTGACATATATAGGTTCAGCTTTTGGCACCAACTTGAAAGAAACCACATCAAGGTGCA

Intron 2 GCTTTGGAGC ... TATACGGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	58.64	67	94	96
A2	55.63	69	95	78
A3	60.22	71	93	122
A4	58.27	53	72	76
A5	48.39	40	38	37
A6	56.9	153	102	302
A7	56.54	314	274	543
A8	57.69	278	220	538
A9	56.91	318	302	538
A10	56.25	294	230	526

>TRINITY_DN97533_c0_g1_i1 from sample A4 / Example spliced isoform

GTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAGAGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGG
ATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCGTGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCC
CAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGGTTGGCAACTTT
GATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGAGAGTTTTGGAGATGGCGTCATA
AAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAATGTGTGAATTCTTTGATCCAAAT
GTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTGGCTTTGGAATGTTTAGCTACAT
GGTAATGAAATGGCAGTCGT

>TRINITY_DN97533_c0_g1_i3 from sample A4 / Example unspliced isoform:

GTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAGAGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGG
ATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCGTGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCC
CAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGgctttggagctt
gggagaggagcaaatccatcaagttatatggtggaggagatctggcaggaacttgcaaaagcaaaatatttagagtgggagtcttcttcacaccttcgttttaaaaaacaacaagagttgagaggaatttgtgaaagggctctccagcaagaatttgaaagtactcgtatgcaagacagtgaaactggtatccagcctac
gaccgctacgtatcataatgggggtacagcaagcacacacagtgatggtacggaatcaaatgacgtggaaggagaatctagaagtcgtgaaaactctctgaaagtggtgtcagaaattacttacaaagaacgaattaaaatactctctgacgtgtttaacaaagcagcagaggcggatattcctaatgaggtacctgaat
atctgtgttgcaaaattacattggacatctttcgggacccggtaatcactcctagtggagttacatatgagagggcagttattctagaacatatacggaagGTTGGCAACTTTGATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAG
CATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGAGAGTTTTGGAGATGGCGTCATAAAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGT
TCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAATGTGTGAATTCTTTGATCCAAATGTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGA
GCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTGGCTTTGGAATGTTTAGCTACATGGTAATGAAATGGCAGTCGT

Intron 3 GTCATTTCCA ... TTCTGCGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	0.92	108	0	1
A2	0.74	134	0	1
A3	0.71	140	0	1
A4	5.3	125	1	7
A5	0	54	0	0
A6	0	172	0	0
A7	0.22	455	0	1
A8	0.77	258	0	2
A9	0.51	391	0	2
A10	0	399	0	0

>TRINITY_DN97533_c0_g1_i1 from sample A4 / Example spliced isoform

GTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAGAGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGG
ATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCGTGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCC
CAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGGTTGGCAACTTT
GATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGAGAGTTTTGGAGATGGCGTCATA
AAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAATGTGTGAATTCTTTGATCCAAAT
GTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTGGCTTTGGAATGTTTAGCTACAT
GGTAATGAAATGGCAGTCGT

>TRINITY_DN97533_c0_g1_i4 from sample A4 / Example unspliced isoform:

AGCCATCGAGGCTTATACACAGgtcatttccattatgcttttaaactcacagagacaattgtaaggtttcaatgttatcataagctaattgatccactctatttctgcgcagGCTATAACTCTCTGCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGAGTAAGATAGCCATTTATTGC
AGTTGCGGTGATCATTTTACTCAGTAGGTTTTTTATTGTTATTATCTTCACTTGTCTTCTGCAGCGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTCAAGGTCAGTATTAATGCTGTTTTGAACATGTCATCAAGGAGTAAATGACATCAAACGCTTTCAGCCCTTGAGATT
GACTTTGAAAGTATGTAGCTAGCGGATGTAGGAAACCCTAAATGGGCATCAAAAGGGTACAAACAGCAAGTTATACATGGAATGCAGAGGATATATATGAAGTACAAAAGTGTTTTCCAAATTTTTATTTATGTTGTAGTCAATGCCGATCATGTCCATGTATCTATTTAATGCCTTTTGGGTGGTTTGCCTGTTCTTAT
TGGACAAATTGGAGGACACATCGGCACATGTATTTAATTTATCCGCAAAAGCTCTATGGAATTACATTTGGCTTTGTCGAAGATGCATGTTAATGTCTATAGAGTGCCATATTATATTGTTAATATGGATTTCTGTAACTTATGGGTTACATAATCCCTCCTGTCCATAGATTTCTATTTATTTGTGCATACAAAGTTGT
AGACTCTAATTTTGTTTAGTTCATAGATTCTGTTATGTATTTCAAAGTATATGTGTAAGATGGTGGAATCATATAGCCACTATTAACATATCATCTGACTGTTTTTTTTCTAAGTTGGGTTCTAATTCACTATTAAAATACAAAATAAAGAGTTACATCATTAAAGACCTGATTATCTCCTTAAAGAGATAATGTCCGAG
TTTTTCCAGCAGAGATATGCATTCAAGACTAAAATGCCATAGTATTCAGAAATATCACTGCATCTAATGTTTGACAGAGTTAACACTAAATTGGACCCAAAAGTAAGAGCTGTCTTATAGACGATGACTATCTTACTTCCTCAAACTAGTAAACACAG

Intron 4 GTAAGATAGC ... TCTTCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	24.94	105	35.4	21.4
A2	26.72	74	27.7	7.3
A3	28.67	85	35	14
A4	26.51	71	26.1	9.2
A5	30.84	26	12	6.4
A6	21.43	130	36.4	20.6
A7	25.78	308	110.8	37.3
A8	22.44	175	52	28.2
A9	23.99	301	98	42.7
A10	24.59	264	89	38.1

>TRINITY_DN120808_c6_g1_i3 from sample A1 / Example spliced isoform

TAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAGAGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACG
GGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCGTGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTG
CCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGGTAAGAGCGC
ACATCAAATGCATTTACAAGTGAAGTACTTAAATTGTTGGAAGAATTCATTATATTTTTTTTATCGCCACATTTTATATTGATTCTACATAGTATTGTCAAGGATATTGTGTTCCATTGTGAAATATGTAATTGGGGCAAATTATCTTATTTTCATGTAAGAGTATGGTAAAGAGTTTTGTTAAAACAGTAACTCGAAAA
AGTAAAAGGAACTTGAATTTCCTTATAAAAACATCTTTTGAGAAAGAAAATAAAATATGAATGTACAAGGATCATTGAAGTTTGTTGATTGTAGTAGGAACTCCACCATTTAGAATAGATCAAGGTAGTGCAGACGTCTTTTATCTGAATACAAGAACTATTAAAAAATATGACAATATGACATTGTATAACTATGGGGT
AGAGAAAGCACTGTCCGTCTATCCCGTGAAGTGTTATATAACTCTTGAAGATAAAGAGAACTGTTCATCTTTTTGAATTGTGATAAGGTCTATTGAAACTCTTGTATGGTGTCATTTGCTGAAGATTATATATTCAAGTGTATGTTGTGTAGATTGAGTGACAGAGGTCATTGACTCTAATACTTTCTGTACACTTGTGT
CCCATTGACCTATTTCTGGGTACTTGTGGACATTGATATAATTTCTTTATTTTGTTTTACTTTTCTTGTGCACATGAAAGGTGTCTCTCTTATCATCCAAGGCAGCTTCCCCAG

>TRINITY_DN120808_c6_g1_i4 from sample A1 / Example unspliced isoform:

TAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAGAGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGAC
GGGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCGTGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCT
GCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGAgtaagatagccatttattgcagttgcggtgatcattttactcagtaggttttttattgttattatcttcacttgtcttctgcagCGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCTTTAGAGCTCGACGTCAATTCTGTC
AAGGTCAGTATTAATGCTGTTTTGAACATGTCATCAAGGAGTAAATGACATCAAACGCTTTCAGCCCTTGAGATTGACTTTGAAAGTATGTAGCTAGCGGATGTAGGAAACCCTAAATGGGCATCAAAAGGGTACAAACAGCAAGTTATACATGGAATGCAGAGGATATATATGAAGTACAAAAGTGTTTTCCAAATTTT
TATTTATGTTGTAGTCAATGCCGATCATGTCCATGTATCTATTTAATGCCTTTTGGGTGGTTTGCCTGTTCTTATTGGACAAATTGGAGGACACATCGGCACATGTATTTAATTTATCCGCAAAAGCTCTATGGAATTACATTTGGCTTTGTCGAAGATGCATGTTAATGTCTATAGAGTGCCATATTATATTGTTAATA
TGGATTTCTGTAACTTATGGGTTACATAATCCCTCCT

Intron 5 GTACCTGAAT ... TATACGGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	51.8	67	51	93
A2	48.31	69	54	75
A3	54.92	71	54	119
A4	52.68	53	43	75
A5	43.66	40	25	37
A6	56.47	153	100	297
A7	54.13	314	208	533
A8	56.56	278	206	518
A9	54.11	318	231	519
A10	54.59	294	188	519

>TRINITY_DN39047_c0_g1_i4 from sample A6 / Example spliced isoform

GTCGAACCTTTGATAGGAAAAAAAAAAAGGAATAGAGTGTTCAACATTAACGGTGGTATTTAAAAAGCCTATTAAAAACATCTCCGAAAGGGTGATTTTCTTGTTTGCATAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAG
AGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCG
TGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCT
TTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGGTTGGCAACTTTGATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCA
TGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGAGAGTTTTGGAGATGGCGTCATAAAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTC
AACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAATGTGTGAATTCTTTGATCCAAATGTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGC
ATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTGGCTTTGGAATGTTTAGCTACATGGTAATGAAATGGCAGTCGTTTCTTCTTCAATTATCACTCTATTCCTAAGTCATGGCGGCTTGGAAGTTAATGTTCCCAACCGCATTCC
CTGTTGATCCGTGAGTCTAATGGGCTTTACTTTGAAATATGTACTTGAGGAAAGAATGATAGGCGTAGCTGCATCTGTTACACAAGGCAATATTTGTTGCAGTCATGGGAATGACATGCATGCATGCGACTGCTGCTTATTATAATTTTCTAGGTGAGAAAGACTATTGTTTCATTCATATTATTATTATCAATGAATAT
ACCATAGTATAGAAGTTGACATATATAGGTTCAGCTTTTGGCACCAACTTGAAAGAAACCACATCAAGGTGCA

>TRINITY_DN39047_c0_g1_i2 from sample A6 / Example unspliced isoform:

GTCGAACCTTTGATAGGAAAAAAAAAAAGGAATAGAGTGTTCAACATTAACGGTGGTATTTAAAAAGCCTATTAAAAACATCTCCGAAAGGGTGATTTTCTTGTTTGCATAGTTATAGCCATGAAGGAAGGAAGGATGTGAGTCCGAGCAGGAGTACGATTCAAGAATGAAAAAAGGGTACAATTCAAGAAAAAAAATAG
AGACGAGAACATACGTGAAGGGTCAGAGAAAGGAGATCTTTGTTTCGTGATGGGCAAAGCAAACCGGGTATATGTTCAATCCTCTCTCCCGGCGAGAGCGTAAGCGACGGGATTCAAAGGATCGGGAAACGACCCCATCGTCGTTGTGGATCGAATCATAGGATCAAGAAGAATAATGGCTCCAGGATTGGACGTTCCCG
TGAACGTGGCAAAACAGGCGGAATTACTGAAGCAAGATGGCAATACTTACTTCAAGAAAGATCGTCTAGGCGCAGCCATCGAGGCTTATACACAGGCTATAACTCTCTGCCCAAGTGTTACCGTTTATTGGACTAACAGAGCTCTTTGTCATAGGAAACGCGACGATTGGGAAAAGGTTGAAGCTGATTGCAGAAAAGCT
TTAGAGCTCGACGTCAATTCTGTCAAGGCTCATTACATGTTAGGTCTTGCATTGCTTCAACATAAGCGATATGCAGAAGGTGTAAAGCAACTTGAGAAGgtacctgaatatctgtgttgcaaaattacattggacatctttcgggacccggtaatcactcctagtggagttacatatgagagggcagttattctagaaca
tatacggaagGTTGGCAACTTTGATCCTATTACACGGGAGCCACTTAAACCTGAGCAATTGGTATCAAATTTGGCGATTAAGGAGGCTGTTCAAGACTACTTAGGCAAGCATGGCTGGGCTTACAAAATGACATGAAACTAAAACATCTGAAGACTTCCTTTGTATATTAATGTTGACTTCTTTGGGAGCATGAATCAGA
GAGTTTTGGAGATGGCGTCATAAAATATGTGATCTTACATGTATGTCAACCAATCGAGTGGTAACATGGTCTTTGGATTATATTGGTTTATTGATATACTGCAAAGGGTTCAACACACGAGGTTTTGGTTTTCATGACAAAAGATGTACATAATATCCATCAGTGCCTGAATACAATGTTGCAGTCCGTCATACAATAAT
GTGTGAATTCTTTGATCCAAATGTACAGCAGTTCGATGAGCAAGTAATCAACTAGTATATCTTATCAATTTTTTGGTTGAGCTGGGAGTGTAGCACTGAGCAGTCGTGAGCATATTATTTATTTAGTTTTATAACCAGTGGTCTATAAGGATGTTTAAACAAGTCATTTATCAATATCCAATGTCCGTGTTATTTTATTG
GCTTTGGAATGTTTAGCTACATGGTAATGAAATGGCAGTCGTTTCTTCTTCAATTATCACTCTATTCCTAAGTCATGGCGGCTTGGAAGTTAATGTTCCCAACCGCATTCCCTGTTGATCCGTGAGTCTAATGGGCTTTACTTTGAAATATGTACTTGAGGAAAGAATGATAGGCGTAGCTGCATCTGTTACACAAGGCA
ATATTTGTTGCAGTCATGGGAATGACATGCATGCATGCGACTGCTGCTTATTATAATTTTCTAGGTGAGAAAGACTATTGTTTCATTCATATTATTATTATCAATGAATATACCATAGTATAGAAGTTGACATATATAGGTTCAGCTTTTGGCACCAACTTGAAAGAAACCACATCAAGGTGCA