sp|Q6YXH8|CCD41_ORYSJ ----> Cyclin-D4-1

Intron 1 GTTAGTTGTG ... TTGCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	37.93	27	26	7
A2	33.93	37	34	4
A3	31.43	24	14	8
A4	35.85	17	10	9
A5	16.67	25	6	4
A6	19.37	281	52	83
A7	17.56	338	93	51
A8	19.49	382	80	105
A9	19.57	339	80	85
A10	13.73	201	44	20

>TRINITY_DN44437_c3_g1_i4 from sample A9 / Example spliced isoform

GTTCCATCACGCTCTCTTCGATTACTTTGCTCACAGGGATGTTCACTATATTTACCACAACTAATAATTTCTTTACTGAAGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGGGTGTTT
AGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGGTGATTAGGCTTTTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCG
TATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCT
TTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAAA

>TRINITY_DN44437_c3_g1_i3 from sample A9 / Example unspliced isoform:

GTTCCATCACGCTCTCTTCGATTACTTTGCTCACAGGGATGTTCACTATATTTACCACAACTAATAATTTCTTTACTGAAGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGGGTGTTT
AGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGgttagttgtgactcttttgggtctcatccttgttcagtttcaggagggaaatataattggttctaacttttaatctcttggaattcatatacaacataacttcaattgacca
cacaaatatggttctaaattgcttcatggaaacaatggtggccatctggattggattactagatacaaaattccaatacaaaaggattttgctatcttcacaatgattgtctttcattttaactagaaaacatatttccgttgatttcttcatatacttgcaatgagtggttggttttgttctcatgggttaaatcaaat
ggaatttcaatggatttctaaccactactcttatgttgttcagctgttcaatatgcagatcagtgcgttctacattttactattgttccttcttagctatgctctactctatagctctactctactcatagctataagtttctttatgtgtatagattaattgtattacagtctttttggttcatctcaaattaatcata
tgtttgttttgcttgcagGTGATTAGGCTTTTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCAT
GGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAAA

Intron 2 GTATGTTTTG ... TGTTGTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	0	5
A2	40	6	0	4
A3	43.75	9	2	7
A4	76.92	3	0	10
A5	0	1	0	0
A6	60.98	16	1	25
A7	47.06	36	1	32
A8	61.54	25	2	40
A9	37.29	37	0	22
A10	46.97	35	0	31

>TRINITY_DN48143_c1_g2_i9 from sample A7 / Example spliced isoform

GTTTTTATGTAGGGATTTTGCAGAGTGAGGTTTTTATGTAGGGATTTTGCAGAGTGAGGTTTTTATGTAGGGATTTTGCAGTCATGGAGGAGGATGAAATCATAGGGATTAAAAACCATTTAATGGAATTAGATGACTTCGGTAAAGCCATTCACACAATAAAACTTGCAGATTTCCGCTTACATGGCCGCTACATTCGA
TTGATATGCAAAAGATCTGGTGAAGACACGGACCCATGACAGGCTCAAGAATTTTCTCGGCTTCTTCGCAAGGAAATGTATGGAGGGCGGTTTCAACAAGACGATCAGACCATTGATCAGCTCACAGTTCCTATGCGATTATGCTGAAGAATGTTAGCTCGATACATAATGTGGACCGATCATGCAAATGGCTATGATAT
TTCATAGATATAAATCTCATTCCACACATCTAATAACTTCTACTTCGGGCCTCTGAAATCGCCACAACAATGCGAATCAGGTTCAATAATAGCATAACCTCGGCCCATCTCAAATCATGTCACAAAACAGGTCCGAAGTGGAATGTTCCTCCAATAAAAGCGTGATAAGGGTGAACGCATTCCTTGAGATCCTCATAGCT
TCCAAAAGATGGATGTTCCAAACAAGAATGGACCCAAAAATACACCAAACTACAGCATATGCCCTTTCCATCCAAATCAGAGATCAATAGCTCTGCAGTGATCAGATCCAATGTAAAACTGAGGAAACAGGGGTTTCTCGCTTACTGCTGAAGTAGATCCACCTAATGTTAAATGAGATAACCGCAGGCTGCTCAGAAAT
TATACCCGAAATGCTAATTACTATTGATTACTATTGATTGATGGTTGCTACAACTTCCAAATCATCTAGGCGTCACCAGAAAAGGCGTTACTGCTGCTCAATAGCTTTTAGCCTATCAGACAGAGCTTTTTGTGCCCAGATTTGCAATTTTAATGTCGTCTATAGTCTCTTCACGGCTGATTCACCCCACATATATTCTC
AGATTAAGATTTATATTGCCATTTGATTTTAAATCAGGGTTGCCACTACAAGGAAGATGCCCACATTATGCGCAGAACCAATCCTTCTGCTGTTAGAGGGTTCTACTCCAGCTATGTTTCATCTGTCTGAAGAAAAATTACCCTGGTGCTGTCCTTAAACGGTGTCTAAAGTGAAAGAATTATCACCCATTTACTGCTGC
TATCGACCTGTTTGAAAAGGGAGTTATATCCAGCCAGTTTCACACCCTAAGCATGTCCAAATTTGAATCGGATCTCTCAGATATCATGCTCAGAAATTTTCACAACCTCAGGCCCACTGATTTGGACCACATTCACGCTCAGAAGCCCTGGGAATTCTATATGCACATCCCCCTGAAATATAGCATTGCTTTACGCACAA
ATGAAATTAGAATCACAAAAACCTTGATTTCCATTGATTTCTTCTTAATCTTTAAAAAGCCTATCAAGTGGTTTAACAATTTACAATTTTCCCCTAATAATGTTGACAGTTGAATGGTTAAACTTATGACCAATTATGAAGGATCCTTGGAGAATTTTTGAGTTCCTCTTCACTGGATCTTGTACTTCCCACGACATTTG
GTTTGTTCCAGCATTTTGAGCTAGCTCATATCAGGAGGAATTAGTTCCTGCGTTAATCAGGGCAAAATCAGAGTTAAATTCTTGGTACAAAGCATGAATAGAAACTGACAAAAAAAAGCATGAATAGAAACTGACAAAAAAAGCATAAATTGAAATTTAAGAAAAGCATGAGAGTCACGTTTGGATTTACCAGATAATCA
TCTGCGAACGGTTCTGTCCGCTGACACATCTTCTTTTTGGGATTTTCTTTCCGTTACAAAGGTGGGAAAAGTCTTAATTCATTGAGAAGAAAGCAATTTTTTCTTATCCTCAACGTTTCATTGCAAAGGTGGCAAACTATGTATCCGTTGGAAAGGAAGGATATATATATCTAAAATCTCATACAATTTCAACATTTACC
TCCTCCTTCGGCCTCTATCAATGGTCTGGTGTGTCTATGTGATTGGGTGTTGATCTGATTGGTCTTGTCTCTGAGTCTGTGTATGGTCCAAGACTCTGAGTCTGTGTATGGTCCTCTGTCTGAGTCTCTATCTGATAGAGGAGGCTGGACTGGAGGCAGCTATATTTGGATCAGCCTTTGGAGCAAACGAAATTTAAGGA
AATGGAGGAATCAACTTAACTGTTCAACATTCAGATCAATGCTCTCCTCAATAATCACAGGGATTTGGTTCCAGCTGTTCAATATGCAGGTCAATGCTTTCTCCCAATCATCGTTGCTTCATTTCCAGTTACGTTTTACTATTGTTCCTTCTTAGCTATGCTCTACTCTTCTCTCAAAAGCCCTGTAAACCTTAGCCCTT
TAATCTCAGCAATTTACGTTGATTTCTACAGCCTTGTATGAATGGCAATGTGAGCTTGGTTATGTTCTGAATAACACCAGGAATTAATGGAAAAATGATTTCGATGGATTTTATATGGAGAAACCCTTCCTTCACAAACCAAATCTCTCCATCCCTTCCTTCAACAAATCAAATCTCTCTAAATATTTGGGTTCTCTGTA
TTTCAAAATGTGTTACACAAAATTTACTCCCAAATCAAAACGCACTCAACTCCGATTCTCCTGCCTCTGCATTGTTTAGTTAATAAATTTAAGCTCTCCTTG

>TRINITY_DN48143_c1_g2_i19 from sample A7 / Example unspliced isoform:

CAGGGATTTGGTTCCAGgtatgttttgttattcatctctctaatctcttaatctcttatctatgctctgttctactctcaaaaatcctagttctttcattttaactagcaaacacatttccgttgatttcttcatatacttgcaatgagtggttggttttgttctcatgggttaaataaaatggaatttcaatggatttc
tataagcaaagtctaaccactactcttatgttgttcagCTGTTCAATATGCAGATCAGTGCGTTCTCCCAATCATCGTTGCTTCATTTCCAGTTACGTTTTACTATTGTTCCTTCTTAGCTATGCTCTACTCTTCTCTCAAAAGCCCTGTAAACCTTAGCCCTTTAATCTCAGCAATTTACGTTGATTTCTACAGCCTTG
TATGAATGGCAATGTGAGCTTGGTTATGTTCTGAATAACACCAGGAATTAATGGAAAAATGATTTCGATGGATTTTATATGGAGAAACCCTTCCTTCACAAACCAAATCTCTCCATCCCTTCCTTCAACAAATCAAATCTCTCTAAATATTTGGGTTCTCTGTATTTCAAAATGTGTTACACAAAATTTACTCCCAAATC
AAAACGCACTCAACTCCGATTCTCCTGCCTCTGCATTGTTTAGTTAATAAATTTAAGCTCTCCTTG

Intron 3 GCAGGGACAT ... TTACAGATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80.72	8	32	35
A2	76.74	10	28	38
A3	78.38	8	29	29
A4	88.24	3	21	24
A5	75	2	2	10
A6	63.6	85	140	157
A7	61.51	97	117	193
A8	61.11	98	119	189
A9	73.73	75	176	245
A10	66.12	62	113	129

>TRINITY_DN44437_c3_g1_i11 from sample A9 / Example spliced isoform

GTTCCATCACGCTCTCTTCGATTACTTTGCTCACAGGGATGTTCACTATATTTACCACAACTAATAATTTCTTTACTGAAGGGTGTTTAGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTTAAAAAAGACCTCTTACAAGAAAGCTGTTCAATATGCAGATCAGTGCG
TTCTCCCAATCATCGTTGCTTCATTTACAGGTGATTAGGCTTTTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGAT
GTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAA
A

>TRINITY_DN44437_c3_g1_i1 from sample A9 / Example unspliced isoform:

GTTCCATCACGCTCTCTTCGATTACTTTGCTCACAGGGATGTTCACTATATTTACCACAACTAATAATTTCTTTACTGAAGgcagggacatcaggctttcacatggcctttgctgagtaatgacatcaggacaaagaacttgaggttttggacctggacttatgagataagatgagtagtggattacagatagGGTGTTT
AGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGGTTAGTTGTGACTCTTTTGGGTCTCATCCTTGTTCAGTTTCAGGAGGGAAATATAATTGGTTCTAACTTTTAATCTCTTGGAATTCATATACAACATAACTTCAATTGACCA
CACAAATATGGTTCTAAATTGCTTCATGGAAACAATGGTGGCCATCTGGATTGGATTACTAGACACAAAATTGCAATACAAAAGGATTTTGCTATCTTCACAATGATTGTCTTTCATTTTAACTAGAAAACATATTTCCGTTGATTTCTTCATATACTTGCAATGAGTGGTTGGTTTTGTTCTCATGGGTTAAATCAAAT
GGAATTTCAATGGATTTCTATAAGCAAAGTCTAACCACTACTCTTATGTTGTTCAGCTGTTCAATATGCAGATCAGTGCGTTCTCCCAATCATCGTTGCTTCATTTACAGGTGATTAGGCTTTTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGA
GCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACC
CTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAAA

Intron 4 GTTAGTTGTG ... TCATTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	40	27	24	18
A2	32.73	37	25.5	18
A3	45.45	24	12.5	20
A4	55.26	17	7.5	21
A5	21.88	25	5	7
A6	47.67	281	32.5	256
A7	37.75	338	68	205
A8	46.12	382	60	327
A9	42.25	339	52	248
A10	35.16	201	36	109

>TRINITY_DN44437_c3_g1_i4 from sample A9 / Example spliced isoform

GTTCCATCACGCTCTCTTCGATTACTTTGCTCACAGGGATGTTCACTATATTTACCACAACTAATAATTTCTTTACTGAAGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGGGTGTTT
AGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGGTGATTAGGCTTTTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCG
TATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCT
TTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAAA

>TRINITY_DN44437_c3_g1_i2 from sample A9 / Example unspliced isoform:

AAAATATTTTGGTGGTTTTGTTTTTGGATGGCATATCTGAAGAGATATTCTATATATATGCTATATTGCAGGGTGTTTAGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGgttagttgtgactcttttgggtctcatccttgtt
cagtttcaggagggaaatataattggttctaacttttaatctcttggaattcatatacaacataacttcaattgaccacacaaatatggttctaaattgcttcatggaaacaatggtggccatctggattggattactagatacaaaattccaatacaaaaggattttgctatcttcacaatgattgtctttcattttaa
ctagaaaacatatttccgttgatttcttcatatacttgcaatgagtggttggttttgttctcatgggttaaatcaaatggaatttcaatggatttctataagcaaagtctaaccactactcttatgttgttcagctgttcaatatgcagatcagtgcgttctcccaatcatcgttgcttcatttacagGTGATTAGGCTT
TTGAGAGACGCTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGC
GAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGGTTCTCTGCATTTTAATTCTGCATTTCAAAATGTGTTACACAAAA

Intron 5 GTATAATGGA ... TATATTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	51.75	34.5	52	22
A2	35.66	37	36	5
A3	50.93	27.5	50	7
A4	58.76	22.5	53	11
A5	60	10	25	5
A6	20.64	152	64	15
A7	29.07	191.5	115	42
A8	27.31	185	76	63
A9	22.79	244	109	35
A10	34.59	130.5	106	32

>TRINITY_DN48143_c1_g2_i15 from sample A7 / Example spliced isoform

ATTTAACTTTTGCAGAATGACTTTGAGGTCCTAGAGGTGTGCACTCTCTTTGGGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGGGTGTTTAGCTGTGGAGGCTCTACTTGTCGCAGT
GATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGGTTAGTTGTGACTCTTTTGGGTCTCATCCTTGTTCAGTTTCAGGAGGGAAATATAATTGGTTCTAACTTTTAATCTCTTGGAATTCATATACAACATAACTTCAATTGACCACACAAATATGGTTCTAAATTGCTTCAT
GGAAACAATGGTGGCCATCTGGATTGGATTACTAGACACAAAATTGCAATACAAAAGGATTTTGCTATCTTCACAATGATTGTCTTTCATTTTAACTAGAAAACATATTTCCGTTGATTTCTTCATATACTTGCAATGAGTGGTTGGTTTTGTTCTCATGGGTTAAATAAAATGGAATTTCAATGGATTTCTAACAGGTG
ATTAGGCTTTTGAGAGACGTTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGT
TTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGG

>TRINITY_DN48143_c1_g2_i14 from sample A7 / Example unspliced isoform:

TTACAACTAAGACCGTAAAGTTACAGTAACCATTCGATAACAACATCCAAATTGGTTGGAATTTGACGGGCATTTTGGAAAACCGAAGTGGGCAATGGCGTGATATGCTATTTGGTGTTGGAGGGCTGCGAGAATTGGAACGGAGGAATTTGGTCAAAGAAAAGAGGAGGAGCGGCGGCGTTGGCCTGTGATAGCAAAAA
TGTCTGTTAAATAGCAGCGGCAGCCCGACGGTAGTGAGTGCGAATAAGACGGGGCATGTGCATCCTGGCGGGCCGTTCACATTCGATCTCTTCAGCTGGTCGAAGGGGCCTCCCAATAGCGCACAGATTCGAACCCCCGCGAGGCCTTCCGCGAGCACAGACAGCAACGCCTTCGGTCAAACTGCAAAAGCATTTCCCAT
CGGTCGTCCAACCATCAGTAACTGGCCACTGACTGGTCCTTCGCACAAATCTCGGATTGGCAGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGgtataatggatttcatgaatcgtct
gattgagggcattggatgccccatttgctggaatagttgtctttggagttcattttgatgttaaagttcaacaacaatacttatatttacaggataattattgtatttggaaaatattttggtggttttgtttttggatggcatatctgaagagatattctatatatatgctatattgcagGGTGTTTAGCTGTGGAGGC
TCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGGTTAGTTGTGACTCTTTTGGGTCTCATCCTTGTTCAGTTTCAGGAGGGAAATATAATTGGTTCTAACTTTTAATCTCTTGGAATTCATATACAACATAACTTCAATTGACCACACAAATATGGT
TCTAAATTGCTTCATGGAAACAATGGTGGCCATCTGGATTGGATTACTAGACACAAAATTGCAATACAAAAGGATTTTGCTATCTTCACAATGATTGTCTTTCATTTTAACTAGAAAACATATTTCCGTTGATTTCTTCATATACTTGCAATGAGTGGTTGGTTTTGTTCTCATGGGTTAAATAAAATGGAATTTCAATG
GATTTCTAACAGGTGATTAGGCTTTTGAGAGACGTTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAA
ATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGG

Intron 6 GTTAGTTGTG ... TGTTGTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	38.82	27.7	23.1	12
A2	28.99	47	21.9	16.7
A3	24.5	29.3	11.9	7
A4	30.29	23.4	6.4	14
A5	47.19	3.7	4.6	2
A6	17.06	339.6	24.1	115.4
A7	18.41	307	57.3	81.6
A8	22.99	385.7	51.9	178.3
A9	19.27	294.3	40	100.9
A10	16.37	228	32.6	56.6

>TRINITY_DN48143_c1_g2_i3 from sample A7 / Example spliced isoform

TTACAACTAAGACCGTAAAGTTACAGTAACCATTCGATAACAACATCCAAATTGGTTGGAATTTGACGGGCATTTTGGAAAACCGAAGTGGGCAATGGCGTGATATGCTATTTGGTGTTGGAGGGCTGCGAGAATTGGAACGGAGGAATTTGGTCAAAGAAAAGAGGAGGAGCGGCGGCGTTGGCCTGTGATAGCAAAAA
TGTCTGTTAAATAGCAGCGGCAGCCCGACGGTAGTGAGTGCGAATAAGACGGGGCATGTGCATCCTGGCGGGCCGTTCACATTCGATCTCTTCAGCTGGTCGAAGGGGCCTCCCAATAGCGCACAGATTCGAACCCCCGCGAGGCCTTCCGCGAGCACAGACAGCAACGCCTTCGGTCAAACTGCAAAAGCATTTCCCAT
CGGTCGTCCAACCATCAGTAACTGGCCACTGACTGGTCCTTCGCACAAATCTCGGATTGGCAGGCAGGGACATCAGGCTTTCACATGGCCTTTGCTGAGTAATGACATCAGGACAAAGAACTTGAGGTTTTGGACCTGGACTTATGAGATAAGATGAGTAGTGGATTACAGATAGGTATAATGGATTTCATGAATCGTCT
GATTGAGGGCATTGGATGCCCCATTTGCTGGAATAGTTGTCTTTGGAGTTCATTTTGATGTTAAAGTTCAACAACAATACTTATATTTACAGGATAATTATTGTATTTGGAAAATATTTTGGTGGTTTTGTTTTTGGATGGCATATCTGGAGAGATCTTCTATATATATGCTATATTGCAGGGTGTTTAGCTGTGGAGGC
TCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGCTGTTCAATATGCAGATCAGTGCGTTCTCCCAATCATCGTTGCTTCATTTACAGGTGATTAGGCTTTTGAGAGACGTTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGT
TGAGTAGCTTATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATC
CATTCTCTACTGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGG

>TRINITY_DN48143_c1_g2_i2 from sample A7 / Example unspliced isoform:

GGGCCACTTTTAATCTACTCTATTTTTCAATATTTGTTACTGGTGTTTATTAATGAATGTACACTATTGGATAATTATTGTATTTGGATAATACAACAATACTTATATTTACAGGATAATTATTGTATTTGGAAAATATTTTGGTGGTTTTGTTTTTGGATGGCATATCTGGAGAGATCTTCTATATATATGCTATATTG
CAGGGTGTTTAGCTGTGGAGGCTCTACTTGTCGCAGTGATTGTTTTCCTGTTGTTTCAAAAGAGTTTCCAGCCTAAAAAAAGACCTCTTACAAGAAAGgttagttgtgactcttttgggtctcatccttgttcagtttcaggagggaaatataattggttctaacttttaatctcttggaattcatatacaacataactt
caattgaccacacaaatatggttctaaattgcttcatggaaacaatggtggccatctggattggattactagacacaaaattgcaatacaaaaggattttgctatcttcacaatgattgtctttcattttaactagaaaacatatttccgttgatttcttcatatacttgcaatgagtggttggttttgttctcatgggt
taaataaaatggaatttcaatggatttctataagcaaagtctaaccactactcttatgttgttcagCTGTTCAATATGCAGATCAGTGCGTTCTCCCAATCATCGTTGCTTCATTTACAGGTGATTAGGCTTTTGAGAGACGTTATGCACACGATGGATATTATATTACTCCTTCAACCGAAGACGTTGTTGAGTAGCTT
ATAGTGCAGAGCTGGATATCTACTGAACGTCGTATTGTTTTTATGAATATTGTCATGAATTTTGTTATTTTTATAATAAAATCTTATGATGTTATGGCCCATGGGGAAATATATATTCTCTGTTTGACACGCGAAAGCTTCTTGTATTCTGTTAGTTTCAGAAAATAAAGAATAAGGATACATCATCATCCATTCTCTAC
TGCTCCAACCCTTCCGTCAACAAACCAAATCTTTCTAAATATTTGGG