sp|Q6L4S3|HIRL1_ORYSJ ----> Hypersensitive-induced response protein-like protein 1

Intron 1 GTAGATTTCA ... TCATGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.93	189	56	22.8
A2	17.81	209	45	10
A3	25.52	167.8	57	14.5
A4	21.47	117.5	32	6.5
A5	23.13	70.5	21	3
A6	14.58	447.3	76	28.5
A7	20.13	622.5	156	36.5
A8	20.22	550.8	139	16
A9	19.39	611.5	146	28.3
A10	21.55	522.5	143	28.8

>TRINITY_DN129374_c0_g2_i18 from sample A1 / Example spliced isoform

TGCGATGTGAGACAAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAAGGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGTTCAAGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAAT
GATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGGTAAATGAGTGAAAATCATTTTGTGTTTGGCCTATGCTTTTTTTTGGAGGATAAATACTAACTCAAAAAATACTTGCATATTTATTGCTTCATATTCAGTGGGGAAAATGCCTGTAATTTCTTTGCATCTTCCAGCATCATTGCATTGTTTATATTGCTTTTGT
TCTGGTTTTGGTACAATAATATTAGATTGTTCTCCACAATCATCTCTTCTATTTGGATATAGGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTATTGATATAGTACCCGCTGAAACTGTGAAGAAAGCAATGAATGAAATAAATGCAGCTGCAAGAATGAGGGTGGCAACACAAGATAAAGCTGAGGCA
GAGAAAATCTTGCAAAT

>TRINITY_DN129374_c0_g2_i14 from sample A1 / Example unspliced isoform:

TGCGATGTGAGACAAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAAGGGAGCAGATCCAAGCTTATGTCTTTGATGgtagatttcagaactatccctattaacaacatagtcccaaaattatgctgctggcc
acaaaccatggcaatttgtatctactaatttgtattttgtgaacattcatacttacattctgttttggattagttacatgctgccatttttctaattcactaaagcaaatggaatggagtgaccattgttaagaaggattagtaatcaatatttgaacttgtttgttatggttcatgttttttgcataggcagatcctaa
acaaagaacagaagcaatggtttctaagcatcgattgatagcagaaagcttgttaatttaggctaaatcagaagtttaatatgatgcctttctttattcatagtaatattataatatatagtttggttctgtgttggtgcaagatctcctttcttgttttatgcaaccggtgcactattatttgagctcatgtacatgtt
ctcatgtgcagTCATTCGTTCAAGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGGTAAATGAGTGAAAATCATTTTGTGTTTGGCCTATGCTTTTTTTTGGAGGATAAATACTAACTCAAAAAATACTTGCATATTTATTGCTTCATATTC
AGTGGGGAAAATGCCTGTAATTTCTTTGCATCTTCCAGCATCATTGCATTGTTTATATTGCTTTTGTTCTGGTTTTGGTACAATAATATTAGATTGTTCTCCACAATCATCTCTTCTATTTGGATATAGGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTATTGATATAGTACCCGCTGAAACTGTGAA
GAAAGCAATGAATGAAATAAATGCAGCTGCAAGAATGAGGGTGGCAACACAAGATAAAGCTGAGGCAGAGAAAATCTTGCAAAT

Intron 2 GTTATGACAA ... ATAAATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	72.32	65.7	171	172
A2	69.86	83.3	197.3	189
A3	68.69	73	156.3	164
A4	68.27	55	112.7	124
A5	67.15	42	82.7	89
A6	69.43	235	467.7	600
A7	70.42	305.7	682.7	773
A8	69.59	325.7	647	844
A9	70.04	328.7	730	807
A10	68.65	293.7	610.3	676

>TRINITY_DN120142_c1_g1_i18 from sample A2 / Example spliced isoform

TGCAGAGCAAGTTTCAGAGATCTCCCCAACTTCAAGTCCAGATTCAAGACCTGTGCATCATTCTTTATACCATCTCATCTTGACAGCTTTTTTGCACTTCAGGTACAGGAATCGATAGAAATGGGGCAATTACTCTGCTGTATACAAGTGGATCAGTCAAAAGTGGCTATGAAGGAGACATTTGGACGCTTTAGTGAGGT
TCTTGAACCAGGATGCCACTGTCTGCCATGGTGTTTTGGGCAACAAGTTGGTGGTTATCTTTCATTACGGGTACAAAAGCTGGATGTGCGATGTGAGACAAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAA
GGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGTTCATGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGCTGCGAGAATGAGGGTAGCAACAAAAGACAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGGTGAAG
CAGAAGCTAAGTATTTATCTGGATTGGGAATTGCTCGTCAACGGCAAGCAATTGTGGATGGCCTTAGGGACAGTGTACTTGCTTTCTCAGACAATGTGCCCGGGACAACTGCAAGAGAGGTGATGGACATGGTCTTGGTGACACAATATTTTGACACAATGAAAGAGATAGGAGCATCTTCAAAGGCAACGGCAGTATTC
ATCCCCCATGGACCTGGTGCAGTTCGTGATGTTGCCGAGGAGATTAGAAATGGATTACTTCAGGCACAGGCCCTTTAAACATCATGAAGTGTCGGATTTTGGAATAAAGGCAAAGTGTGTGCCACAATGTTTATAGCTTGCTGTTTATCTTTTAAGGAGTTATTTTTTGTTTTTAATTTTTTTTTGAAATAAGGAATTCT
GACAGATTCCTTGTATAATGTTCTGTAAGTATCAACTTCAAGTGCCAATTTACTATATAATAAGTAGGCACTCAACCTTGTATAATTGTTAATAAAAAATAGCATATAATGTGTGGTGGTGTGTCGCCATTTTTTCAGTTTTATTAATGAAGAAAAAAGTTCTGCATGGATGGGAGGATCGACAAGTATTAATTATAAGG
TGTTACATTTTGTGTCGTGAAAAGCTCAGCAAACACGGGGAATTGAATTACAGATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCTGGGGATAGATTTATAGATTGAAGTTACGGGAGATTAATTGAAGTTGCATTAATATGATTTGGGTTCTACTTATTTATGCTTTAAGAGTCTTGACAAT
TACATAACAAGGGCTTTCGTATAATTTTCTTTGGACTTTAACATTGACATTATGTCTTCAATCTCATGCTGCAAATGCCAAGCTTCTTACAAGGTCA

>TRINITY_DN120142_c1_g1_i17 from sample A2 / Example unspliced isoform:

TGCAGAGCAAGTTTCAGAGATCTCCCCAACTTCAAGTCCAGATTCAAGACCTGTGCATCATTCTTTATACCATCTCATCTTGACAGCTTTTTTGCACTTCAGGTACAGGAATCGATAGAAATGGGGCAATTACTCTGCTGTATACAAGTGGATCAGTCAAAAGTGGCTATGAAGGAGACATTTGGACGCTTTAGTGAGGT
TCTTGAACCAGGATGCCACTGTCTGCCATGGTGTTTTGGGCAACAAGTTGGTGGTTATCTTTCATTACGGGTACAAAAGCTGGATGTGCGATGTGAGACAAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAA
GGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGTTCATGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGgttatgacaaactacggatttgagatagtgcaaactctcattgttgatatagagcctgttgaaactgtgaagagagca
atgaatgaaataaatgcagCTGCGAGAATGAGGGTAGCAACAAAAGACAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGGTGAAGCAGAAGCTAAGTATTTATCTGGATTGGGAATTGCTCGTCAACGGCAAGCAATTGTGGATGGCCTTAGGGACAGTGTACTTGCTTTCTCAGACAATGTGCCCGG
GACAACTGCAAGAGAGGTGATGGACATGGTCTTGGTGACACAATATTTTGACACAATGAAAGAGATAGGAGCATCTTCAAAGGCAACGGCAGTATTCATCCCCCATGGACCTGGTGCAGTTCGTGATGTTGCCGAGGAGATTAGAAATGGATTACTTCAGGCACAGGCCCTTTAAACATCATGAAGTGTCGGATTTTGGA
ATAAAGGCAAAGTGTGTGCCACAATGTTTATAGCTTGCTGTTTATCTTTTAAGGAGTTATTTTTTGTTTTTAATTTTTTTTTGAAATAAGGAATTCTGACAGATTCCTTGTATAATGTTCTGTAAGTATCAACTTCAAGTGCCAATTTACTATATAATAAGTAGGCACTCAACCTTGTATAATTGTTAATAAAAAATAGC
ATATAATGTGTGGTGGTGTGTCGCCATTTTTTCAGTTTTATTAATGAAGAAAAAAGTTCTGCATGGATGGGAGGATCGACAAGTATTAATTATAAGGTGTTACATTTTGTGTCGTGAAAAGCTCAGCAAACACGGGGAATTGAATTACAGATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCT
GGGGATAGATTTATAGATTGAAGTTACGGGAGATTAATTGAAGTTGCATTAATATGATTTGGGTTCTACTTATTTATGCTTTAAGAGTCTTGACAATTACATAACAAGGGCTTTCGTATAATTTTCTTTGGACTTTAACATTGACATTATGTCTTCAATCTCATGCTGCAAATGCCAAGCTTCTTACAAGGTCA

Intron 3 GTGTGTGCCA ... ATTTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.85	38	97	20
A2	78.9	23	86	12
A3	74.11	29	83	15
A4	84	8	42	4
A5	96.43	1	27	5
A6	79.75	98	386	99
A7	75.95	159	502	137
A8	75.5	196	604	154
A9	71.4	157	392	140
A10	72.67	123	327	84

>TRINITY_DN46782_c4_g1_i8 from sample A8 / Example spliced isoform

CAGGTACAGGAATCGATAGAAATGGGGCAATTACTCTGCTGTATACAAGTGGATCAGTCAAAAGTGGCTATGAAGGAGACATTTGGACGCTTTAGTGAGGTTCTTGAACCAGGATGCCACTGTCTGCCATGGTGTTTTGGGCAACAAGTTGGTGGTTATCTTTCATTACGGGTACAAAAGCTGGATGTGCGATGTGAGAC
AAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAAGGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGTTCAAGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAAT
CTGTTGAAGAGCAACTTGAAAAGGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTGTTGATATAGAGCCTGTTGAAACTGTGAAGAGAGCAATGAATGAAATAAATGCAGCTGCAAGAATGAGGGTGGCAACACAAGATAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGCTGAAGCA
GAATCGAAGTATTTGTCTGGATTGGGTATTGCTCGTCAACGGCAAGCAATTGTGGATGGACTTCGGGAAAGTGTTCTTGCTTTCTCAGACAATGTGCCTGGGACAACTGCAAGAGAGGTAATGGACATGGTCTTGGTTACACAATATTTCGATACAATGAAAGAGATAGGAGCATCATCAAAGTCATCAGCAGTATTCAT
CCCCCATGGACCTGGTGCAGTTCGTGATGTTGCCGAGGAGATTAGAAATGGATTACTTCAGGCACAGGCCCTTTAAACATCATGAAGTGTCGGATTTTGGAATAAAGGCAAATTTTATTAATGAAGAAAAAAGTTCTGCATGGATGGGAGGATCGACAAGTATTAATTATAAGGTGTTACATTTTGTGTCGTGAAAAGCT
CAGCAAACACGGGGAATTGAATTACAGATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCTGGGGATAGATTTATAGATTGAAGTTACGGGAGATTAATTGAAGTTGCATTAATATGATTTGGGTTCTACTTATTTATGCTTTAAGAGTCTTGACAATTACATAACAAGGGCTTTCGTATAATT
TTCTTTGGACTTTAACATTGACATTATGTCTTCAATCTCATGCTGCAAATGCCAAGCTTCTTACAAGGTCTCAATTTTTTATCTTGTCCTTACATGAAAGACTGTCATTGCCCGTTTTTTATGTAAAGATTTAATGTGGAAAGCTTGTGTTTGTGT

>TRINITY_DN46782_c4_g1_i2 from sample A8 / Example unspliced isoform:

GGGCTTCACTGGTTGGTGAAGAGGGGGTGGTGATATTCCCCCCACCATAGTTCAACTCTCCCCCAACTGTATGGTATGTTTATCCTTCTAAAATAGCAAGGGTTGTGTAATGTCCCTTTTTTAGAAATTTATTAATATGGTGAAATTTTCAACATTTTTCCCTAGTTCGACCTTTGACTAGTTTTGATCTCTAGGTCCCA
AATTTGCCCCAAATGATCCCAAATCTTCTGAGAAGGTATATGAATGATATTAGAACATAAATATGTGTTTCAGGGATGCCTTTGTACCTTTAAAACACTTCTGCAAATACTCTTTCAATTCTGGTCAATGTAGGTAACTTTACTAGTGATTTCCCTTTGACTAGTATTGGTCTCTAGGTCTCAAATTGACTCCAAATGCC
TTCAAATATTCAAGGAAGGTTTATGAATGATATTAGGATTTGAATATGATGTTCAGGGATAACATATGGCCACCAAAAGACCTCTGCAATCTCTCTTAAGATTCTGGACCAAGTATGCAATTTTACTAGTAATTTGGGGTTCAAATCCCCCTGGGGTAAGTACTGAAAATGGCTTCCCAAATGCCTCCAAAGCCACTCAA
ATTTATGAACAGAGGTATGTAATGTGTTAAGTATGTTATTAAGGTCTCATATGCACCATTAATTGATTTTTAATACTGTTCTCACCCTCTCCCATTCAATTGCAAAAATCCCCAATTCGACCCTTGGGGAAATGGCACTATTTCACCTCCCAATACAACTAAACTGAGTAAAAATGCTTCAAATGCTCAAGTACAGTACA
TGAAACTTGTAAAATACATCCATGGCAGTCCATTAATCACAAATACATTAGAGAATCATCCATTCATTCGAAATCATCATCAATACATTGGTTCACAACAAGGTAGTGGGGAAATGGCATTGTTCTTCCATTAAAAATGAGATTTATACATTTCTACTTGGAATTTCGACCTGAAACTTTCTGGAGATGAAGAACAGAGT
ATTTACTTCATATTACAAAAGAAATGGGGCATTAGAAGCTCCCCCAAAGAGTACAATAGCTCACCAAAAACGCCCTCCCTCAAGGATCAAGAATATGCCATCAAAACTGGAAATGGTTGAAGGAGCGAGCTGCAATAGAAGAAACCATGAGCTGCCCTGTAGCTTACACCTGCAAATAAAGACTCCATTAAATCTCCAAA
TGAAAGGTCTGAATGGCCTTTCCAATTACCAACTTGGATGGGAATCTTTCACCCTCGAAATTGGCTAAGGCAAGAAACTAGTCATCCACTAGCTCTCCCTCTTCACAAATGCAATTGCAAATTCTACAAATGATCAAAAGCCATTCTCATACTTCATTTCTACATTTTATAACCATCATTATCCTTCTAAGGGTCTAAAT
CCTCTCAATAGATTCAATAGATTTCCATTTAGGAAATATTCCACATTTGCCACTTGTCTCCTAGTTCCAACCTTCCATCTTCTTCCAAATTTGATTTTGAGTCTCTTTGGCTTCTCCAACTCCCAAATTCGCCTTCCTTAAGCCTATTTTTGGGGCTGACATGTCATAGTGGTCAGATGTCAGAGGTCAGGTCTGCAATT
TGTCATAGTTGTCATAGATGCTCCATCATTGGTGTCATAGGGGCTAGGGAATCTAGCCCAAGTGTCCACAAACTTCCACTTTGACTCTTTATCTTCCATGGAGGTTACCAATCCTTCCCAATTCGACCTAAGATGCTCAATGACATGTGTTATGACTTACCAACTCACCCAAGAGTGTTCACATTCCCATTAATTCGAAT
TTGCAAAAGAGAGATACCATGTATTATGAAAAATCAAGCTAGTGTGGGTCCCACATCCTCCATATGTCTCCAAAACCATTTGTCACCTAGGATTTCTCTTGAATTTCTTTATTCACTCTATTTATTAAATACTTGAACCCTTCTAATGTCTAAACATAATTTATTATCCCCATTATTCCAAATCCCAAAGCTTCCACCCC
AAACCTAGGAAACTAGTAATTTTTCTCCTTGGCAATTATTTGACCTTTAGCATCAATTTGACAAACTCTAATGAATAGGGCCAATGTGATTAGGCCATTGTGACCCAATACCAAATTTGGGACATGACATATTTACTAGGGTCTGTGCATTCATGTATGGGTATGGGTGCAGCATACAAGAGAAAGAAAATGAAAGAAAT
TGACACAGATTTCAATTGATTCATTGGTGATTGTCCTTGGCTGTGTTCTTTAGTTTGGTGCAAGCTCCCCCTGCTGTTAGGTTGGACATATTTAAGGTAGAATATTAAAGGTCTGTAGCCTGTTTGGATTAAGCATAGCAATGACCTCTATACAATATGGTATTGGGTTTAATACCAATGGCATGCTCGATATCCCCGGT
TAAAATAATTGAGACTGTGTATGGTTTGTGGAGATAAAAAGGAAGCTCACTGATTTTATGAAAACAATTATTTTATTTGCTGCATCTCAAGATAAAGTTGGTTTTGTATATCTAACTCTGAAAAAAATTCCTCCTGTCCATTACTTTTCTAGCCAAGCACAGAATGTTTTCCGAAAAGACAAAAATAGTAATCCTTATCA
TTTCTAGTGTTTCTAGTGATGTACTTTATTTATATGAAATCAACTTAAGATACATCCATTTAACAAATACATGAAAACAGAGCAGGATGTAACTCCTCTTAACAACAGATGTACAGCTCCTAGTAGATTTTTCAGTTGATTAGTCAAGGTCCTAGGTCTACAGTGCTACATATTTAAATTGCCGTCTTTCGGTTTCCATT
TGCCAGTTTTGTGTTTGCTTATAGAAATTCATTATTTTAATGCGTTAAGACAGTTGAGTCTAATTATGCTATCAAGCAGGTACAGGAATCGATAGAAATGGGGCAATTACTCTGCTGTATACAAGTGGATCAGTCAAAAGTGGCTATGAAGGAGACATTTGGACGCTTTAGTGAGGTTCTTGAACCAGGATGCCACTGTC
TGCCATGGTGTTTTGGGCAACAAGTTGGTGGTTATCTTTCATTACGGGTACAAAAGCTGGATGTGCGATGTGAGACAAAGACAAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAAGGGAGCAGATCCAAGCTTATGTC
TTTGATGTCATTCGTTCAAGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTGTTGATATAGAGCCTGTTGAAACTGTGAAGAGAGCAATGAATGAAATAAATGCAGCTGC
AAGAATGAGGGTGGCAACACAAGATAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGCTGAAGCAGAATCGAAGTATTTGTCTGGATTGGGTATTGCTCGTCAACGGCAAGCAATTGTGGATGGACTTCGGGAAAGTGTTCTTGCTTTCTCAGACAATGTGCCTGGGACAACTGCAAGAGAGGTAATGG
ACATGGTCTTGGTTACACAATATTTCGATACAATGAAAGAGATAGGAGCATCATCAAAGTCATCAGCAGTATTCATCCCCCATGGACCTGGTGCAGTTCGTGATGTTGCCGAGGAGATTAGAAATGGATTACTTCAGGCACAGGCCCTTTAAACATCATGAAGTGTCGGATTTTGGAATAAAGGCAAAgtgtgtgccaca
atgtttatagcttgctgtttatcttttaaggagttattttttgtttttaatttttttttgaaataaggaattctgacagattccttgtataatgttctgtaagtatcaacttcaagtgccaatttactatataataagtaggcactcaaccttgtataattgttaataaaaaatagcatataatgtgtggtggtgtgtcg
ccattttttcagTTTTATTAATGAAGAAAAAAGTTCTGCATGGATGGGAGGATCGACAAGTATTAATTATAAGGTGTTACATTTTGTGTCGTGAAAAGCTCAGCAAACACGGGGAATTGAATTACAGATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCTGGGGATAGATTTATAGATTGAAG
TTACGGGAGATTAATTGAAGTTGCATTAATATGATTTGGGTTCTACTTATTTATGCTTTAAGAGTCTTGACAATTACATAACAAGGGCTTTCGTATAATTTTCTTTGGACTTTAACATTGACATTATGTCTTCAATCTCATGCTGCAAATGCCAAGCTTCTTACAAGGTCTCAATTTTTTATCTTGTCCTTACATGAAAG
ACTGTCATTGCCCGTTTTTTATGTAAAGATTTAATGTGGAAAGCTTGTGTTTGTGT

Intron 4 GTAAAGCGTG ... ATCAATTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	61.75	35	29	84
A2	58.38	36	31	70
A3	61.8	34	26	84
A4	61.84	29	22	72
A5	60.71	11	9	25
A6	56.52	85	48	173
A7	59.5	97	79	206
A8	60.73	43	34	99
A9	61.95	82	70	197
A10	62.01	68	66	156

>TRINITY_DN120142_c1_g1_i9 from sample A2 / Example spliced isoform

CGAAAACGCATCCTGCACACTGTGTTTCGAAACCGGGGGACTCTGCCAAAACATAGCTGGCATGGTACACAATCCGCTTGCTTTAAGGTCGGGCATTGGCTCTTAGCACAGTTTGCACATCGAGTTTTTTCGCATCTCAGACTTGTGAATCATTCTTCATACGATTTCAGCAGCTCTGTTACGCATAAGGTACAGTAATA
AAGAAAATGGGACAGTTATTCTGCTGTGTAAAAGTGGAACAGTCAACAGTGGCTATGAGAGAGAGATTTGGACGCTTTGATAAAGTTCTTGAGCCAGGCCTCCATTGTCTGCCATGGGTTTGTGGGAGTCAAATTGGAGGCCATCTTTCCTTACGGGTACAAAAGCTGGATGTGCGATGTGAGACGAAGACAAAGGATAA
TGTATTTGTGACTGTAATTGCATCTGTGCAATACCGTGCCATTTTAGAGAAATCTGTGGATGCTTTTTATAAGCTTAGCAATACAAAGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGGGCATGTGTCCCAAAGATGAACTTGGATGCAGTATTTGAGCAAAAGAATGACGTTGCTAAAGCTGTTGAAGCGGAAC
TCGAAAAGGCTATGACGAACTATGGATTTGAGATAGTGCAAACTCTCATTATTGATATAGTACCCGCTGAAACTGTGAAGAAAGCAATGAATGAAATAAATGCAGCTGCAAGAATGAGGGTGGCAACACAAGACAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGCTGAAGCAGAATCGAAGTATTTG
TCTGGATTGGGTATTGCTCGTCAACGGCAAGCAATTGTGGATGGACTTCGGGAAAGTGTTCTTGCTTTCTCAGACAATGTGCCTGGGACAACCGCAAAAGATGTCATGGACATGGTCTTGGTGACACAATATTTTGACACAATGAAAGAGATAGGAGCATCGTCAAAGTCATCAGCAGTATTCATCCCCCATGGACCTGG
TGCAGTTCGTGAAGTTGCTGCGCAGATCAGAGATGGATTACTTCAGGCACAGGCTCATGAAACATCATAATGGTTTCTGGCTACAGAACAAAAGTGTTTCATGTAACATATGTATCTTGGATTGCCATTTGCCTTTGTCTGATATTCTGATAGACCTGTAGCAGTTTTCATGAAGTGTTGAATTTTAGAATAAAAGCACA
TCATGTGCAACAATGTTTATAGTTTGCTTTTTGCCTTTTGAGGAATCCTTACAGAGCTGTAGTATTATTTTATAAGTGCTTATTAGTAAATACTTCAACCTTGTATATGAAGTTTGATTAGAAAATATGCATAAATGCACGACAGTCATTAGCCGT

>TRINITY_DN120142_c1_g1_i11 from sample A2 / Example unspliced isoform:

ATTATTATATATTTTTATTTTCGAAACCGGGGGACTCTGCCAGAACATAAGCTGGCATGGTACACAATCCGCTTGCTTTAAGgtaaagcgtggaatgcattcttccattcaattctgactgttccagtgattagccgtatcaattcagGTCGGGCATTGGCTCTTAGCACAGTTTGCACATCGAGTTTTTTCGCATCTCA
GACTTGTGAATCATTCTTCATACGATTTCAGCAGCTCTGTTACGCATAAGGTACAGTAATAAAGAAAATGGGACAGTTATTCTGCTGTGTAAAAGTGGAACAGTCAACAGTGGCTATGAGAGAGAGATTTGGACGCTTTGATAAAGTTCTTGAGCCAGGCCTCCATTGTCTGCCATGGGTTTGTGGGAGTCAAATTGGAG
GCCATCTTTCCTTACGGGTACAAAAGCTGGATGTGCGATGTGAGACGAAGACAAAGGATAATGTATTTGTGACTGTAATTGCATCTGTGCAATACCGTGCCATTTTAGAGAAATCTGTGGATGCTTTTTATAAGCTTAGCAATACAAAGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGGGCATGTGTCCCAAAG
ATGAACTTGGATGCAGTATTTGAGCAAAAGAATGACGTTGCTAAAGCTGTTGAAGCGGAACTCGAAAAGGCTATGACGAACTATGGATTTGAGATAGTGCAAACTCTCATTATTGATATAGTACCCGCTGAAACTGTGAAGAAAGCAATGAATGAAATAAATGCAGCTGCAAGAATGAGGGTGGCAACACAAGACAAAGC
TGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGCTGAAGCAGAATCGAAGTATTTGTCTGGATTGGGTATTGCTCGTCAACGGCAAGCAATTGTGGATGGACTTCGGGAAAGTGTTCTTGCTTTCTCAGACAATGTGCCTGGGACAACCGCAAAAGATGTCATGGACATGGTCTTGGTGACACAATATTTTGACA
CAATGAAAGAGATAGGAGCATCGTCAAAGTCATCAGCAGTATTCATCCCCCATGGACCTGGTGCAGTTCGTGAAGTTGCTGCGCAGATCAGAGATGGATTACTTCAGGCACAGGCTCATGAAACATCATAATGGTTTCTGGCTACAGAACAAAAGTGTTTCATGTAACATATGTATCTTGGATTGCCATTTGCCTTTGTC
TGATATTCTGATAGACCTGTAGCAGTTTTCATGAAGTGTTGAATTTTAGAATAAAAGCACATCATGTGCAACAATGTTTATAGTTTGCTTTTTGCCTTTTGAGGAATCCTTACAGAGCTGTAGTATTATTTTATAAGTGCTTATTAGTAAATACTTCAACCTTGTATATGAAGTTTGATTAGAAAATATGCATAAATGCA
CGACAGTCATTAGCCGT

Intron 5 GTAAATGAGT ... TTGGATATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	9.52	171	6	18
A2	2.97	196	2	6
A3	1.92	153	6	3
A4	5.79	114	1	7
A5	2.38	82	0	2
A6	1.5	461	1	7
A7	1.46	676	0	10
A8	2.57	645	3	17
A9	1.23	720	4	9
A10	2.88	607	2	18

>TRINITY_DN44568_c0_g1_i9 from sample A9 / Example spliced isoform

CAGGAATCGATAGAAATGGGGCAATTACTCTGCTGTATACAAGTGGATCAGTCAAAAGTGGCTATGAAGGAGACATTTGGACGCTTTAGTGAGGTTCTTGAACCAGGATGCCACTGTCTGCCATGGTGTTTTGGGCAACAAGTTGGTGGTTATCTTTCATTACGGGTACAAAAACTGGATGTGCGATGTGAGACAAAGAC
AAAGGATAATGTATTTGTAACAGTTGTTGCATCTGTGCAATATCGTGCCATTTTAGAGAAAGCAGTGGATGCTTTTTATACGCTTAGCAATACAAGGGAGCAGATCCAAGCTTATGTCTTTGATGTCATTCGTTCAAGTGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTG
AAGAGCAACTTGAAAAGGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTGTTGATATAGAGCCTGTTGAAACTGTGAAGAGAGCAATGAATGAAATAAATGCAGCTGCGAGAATGAGGGTAGCAACAAAAGACAAAGCTGAGGCAGAGAAAATCTTGCAAATTAAACGAGCGGAAGGTGAAGCAGAAGCT
AAGTATTTATCTGGATTGGGAATTGCTCGTCAACGGCAAGCAATTGTGGATGGCCTTAGGGATAGTGTACTTGCTTTCTCAGACAATGTGCCCGGGACAACTGCAAGAGAGGTGATGGACATGGTCTTGGTGACACAATATTTTGACACAATGAAAGAGATAGGAGCATCTTCAAAGGCAACGGCAGTATTCATCCCCCA
TGGACCTGGTGCAGTTCGTGATGTTGCCGAGGAGATTAGAAATGGATTACTTCAGGCACAGGCCCTTTAAACATCATGAAGTGTCGGATTTTGGAATAAAGGCAAAGTGTGTGCCACAATGTTTATAGCTTGCTGTTTATCTTTTAAGGAGTTATTTTTTGTTTTTAATTTTTTTTTGAAATAAGGAATTCTGACAGATT
CCTTGTATAATGTTCTGTAAGTATCAACTTCAAGTGCCAATTTACTATATAATAAGTAGGCACTCAACCTTGTATAATTGTTAATAAAAAATAGCATATAATGTGTGGTGGTGTGTCGCCATTTTTTCAGTTTTATTAATGAAGAAAAAAGTTCTGCATGGATGGGAGGATCGACAAGTATTAATTATAAGGTGTTACAT
TTTGTGTCGTGAAAAGCTCAGCAAACACGGGGAATTGAATTACAGATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCTGGGGATAGATTTATAGATTGAAGTTACGGGAGATTAATTGAAGTTCTGAGAGATTAATTTGAAGGTGTGAAAAACTCAGCAAACCTGGGGATAGATTTATAGATT
GAAGTTACGGGAGATTAATTGAAGTTGCATTAATATGATTTGGGTTCTACTTATTTATGCTTTAAGAGTCTTGACAATTACATAACAAGGGCTTTCGTATAATTTTCTTTGGACTTTAACATTGACATTATGTCTTCAATCTCATGCTGCAAATGCCAAGCTTCTTACAAGGTCTCAATTTTTTATCTTGTCCTTACATG
AAAGACTGTCATTGCCCGTTTTTTTATGTAAAGATTTAATGTGGAAAGC

>TRINITY_DN44568_c0_g1_i8 from sample A9 / Example unspliced isoform:

TGTCCCAAAGATGAACTTGGATGATTTTTTTGAGCAAAAGAATGATGTTGCTAAATCTGTTGAAGAGCAACTTGAAAAGgtaaatgagtgaaaatcattttgtgtttggcctatgcttttttttggaggataaatactaactcaaaaaatacttgcatatttattgcttcatattcagtggggaaaatgcctgtaatttc
tttgcatcttccagcatcattgcattgtttatattgcttttgttctggttttggtacaataatattagattgttctccacaatcatctcttctatttggatatagGTTATGACAAACTACGGATTTGAGATAGTGCAAACTCTCATTGTTGATATAGAGCCTGTTGAAACTGTGAAGAGAGCAATGAATGAAATAAATGC
AGGCAAGAATTCTTTGCCATATTGAAGTCACAATAGAATTATGTAGATGCAAGTACATCAAAGCTAATTTCTTGCTGTTAACTATT