sp|Q8GXS3|CFIS2_ARATH ----> Pre-mRNA cleavage factor Im 25 kDa subunit 2

Intron 1 GTAGGCACAG ... TCAAATTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	36.51	20	15	8
A2	29.73	13	5	6
A3	27.27	28	15	6
A4	23.81	24	8	7
A5	50	1	0	2
A6	25	60	16	24
A7	28.26	66	22	30
A8	24	19	3	9
A9	25.97	67	18	29
A10	24.32	28	8	10

>TRINITY_DN106170_c0_g2_i3 from sample A4 / Example spliced isoform

CTTTGAGTCGCCAAATGTCAATTCCATCACAATGCTTTCCAAACAACGCTAGAAGTCGGTGGGAAGATTTCCCAACAATACAGCAGCTGAAGGAGACGAGCTCCATTTATCATCATGTGGGTGTTGTGAACTTTACTCAGAATTATTTCTTACAGGGTACTTACATTAAAGATTCCATTAACTTCATACATTCGCGGCTT
CATTCTGTGCTATTCATCATCATTGTCTGGGCTGTTCGAGACAGTCACAGTTGAGAGAGTGTGGGTGTTGTGAAATTCATTCAGAATTATCCCTTACAGGGTTAGAGGTTTCTGTTTGCAGAAGATCAAGGAAGACATCATAAAAATATGAGTTCTCATTTAGTTGTGAAAGTTCACCCTCTATCCTGCTACTCATATGG
GAAGAAGGAAGCCAAGGTGGATAAAGACATTTTTCTCTCAGACAGGCTGGACAGAATCAGAGCCAATTTCATGAGAGAGGGTATGCGGACATATGTGGAAGGGATACTTCTGGTACATGAGTATGGTCACCCACATTTGCTGCTACTTCAAAAAGGAAATAAGATTATCAGGCTGCCTGGTGGGCGCTTAAGGCCTGGCG
AAAATGAGATTGAAGGATTGAAGCGCAAACTCACTAGTAAACTCATTTCCAGTTCAAGCTCAGCCCAACCAGACTGGCAGATTGGAGAGTGTGTTGGAGTGTGGTGGAGGCCTAATTTTGAGACCTTGATGTATCCATATTGTCCACCACATATCAATAAACCAAAGGAATGCAAAAAAATGTTTTTTGTTCATTTATCT
GAAAACCAATGCTTCGAAGTACCCAAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTTGATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTA
GAAAGTATGCCAGGAGCCTTTTAAAAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGTGCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGC
TTCTGGTGGTTCTTATTAATGTGGCTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAATTGTAGTTTTGTTTTTGAG

>TRINITY_DN106170_c0_g2_i2 from sample A4 / Example unspliced isoform:

CTTTGAGTCGCCAAATGTCAATTCCATCACAATGCTTTCCAAACAACGCTAGAAGTCGGTGGGAAGATTTCCCAACAATACAGCAGCTGAAGGAGACGAGCTCCATTTATCATCATGTGGGTGTTGTGAACTTTACTCAGAATTATTTCTTACAGGGTACTTACATTAAAGATTCCATTAACTTCATACATTCGCGGCTT
CATTCTGTGCTATTCATCATCATTGTCTGGGCTGTTCGAGACAGTCACAGTTGAGAGAGTGTGGGTGTTGTGAAATTCATTCAGAATTATCCCTTACAGGgtaggcacagtagagattacatcaattttatacattcaaagctttattctctgctctttatgttttttcattagacggtaaagattttactatatgtaca
gataagttgcctggctggatgttaggtaatttgattgagagctttgtgaattcttaccaaagaatttcaaattcagGTTAGAGGTTTCTGTTTGCAGAAGATCAAGGAAGACATCATAAAAATATGAGTTCTCATTTAGTTGTGAAAGTTCACCCTCTATCCTGCTACTCATATGGGAAGAAGGAAGCCAAGGTGGATAA
AGACATTTTTCTCTCAGACAGGCTGGACAGAATCAGAGCCAATTTCATGAGAGAGGGTATGCGGACATATGTGGAAGGGATACTTCTGGTACATGAGTATGGTCACCCACATTTGCTGCTACTTCAAAAAGGAAATAAGATTATCAGGCTGCCTGGTGGGCGCTTAAGGCCTGGCGAAAATGAGATTGAAGGATTGAAGC
GCAAACTCACTAGTAAACTCATTTCCAGTTCAAGCTCAGCCCAACCAGACTGGCAGATTGGAGAGTGTGTTGGAGTGTGGTGGAGGCCTAATTTTGAGACCTTGATGTATCCATATTGTCCACCACATATCAATAAACCAAAGGAATGCAAAAAAATGTTTTTTGTTCATTTATCTGAAAACCAATGCTTCGAAGTACCC
AAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTTGATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTAGAAAGTATGCCAGGAGCCTTTTAA
AAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGTGCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGCTTCTGGTGGTTCTTATTAATGTGG
CTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAATTGTAGTTTTGTTTTTGAG

Intron 2 GTAGGCACAG ... CTGTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	36.36	21	15	9
A2	28.21	14	5	6
A3	28.89	32	15	11
A4	26.32	28	8	12
A5	50	1	0	2
A6	26.19	62	16	28
A7	28.78	73	22	37
A8	25.37	25	3	14
A9	26.32	70	18	32
A10	25.58	32	8	14

>TRINITY_DN106170_c0_g2_i1 from sample A4 / Example spliced isoform

CTTTGAGTCGCCAAATGTCAATTCCATCACAATGCTTTCCAAACAACGCTAGAAGTCGGTGGGAAGATTTCCCAACAATACAGCAGCTGAAGGAGACGAGCTCCATTTATCATCATGTGGGTGTTGTGAACTTTACTCAGAATTATTTCTTACAGGGTACTTACATTAAAGATTCCATTAACTTCATACATTCGCGGCTT
CATTCTGTGCTATTCATCATCATTGTCTGGGCTGTTCGAGACAGTCACAGTTGAGAGAGTGTGGGTGTTGTGAAATTCATTCAGAATTATCCCTTACAGGAAGATCAAGGAAGACATCATAAAAATATGAGTTCTCATTTAGTTGTGAAAGTTCACCCTCTATCCTGCTACTCATATGGGAAGAAGGAAGCCAAGGTGGA
TAAAGACATTTTTCTCTCAGACAGGCTGGACAGAATCAGAGCCAATTTCATGAGAGAGGGTATGCGGACATATGTGGAAGGGATACTTCTGGTACATGAGTATGGTCACCCACATTTGCTGCTACTTCAAAAAGGAAATAAGATTATCAGGCTGCCTGGTGGGCGCTTAAGGCCTGGCGAAAATGAGATTGAAGGATTGA
AGCGCAAACTCACTAGTAAACTCATTTCCAGTTCAAGCTCAGCCCAACCAGACTGGCAGATTGGAGAGTGTGTTGGAGTGTGGTGGAGGCCTAATTTTGAGACCTTGATGTATCCATATTGTCCACCACATATCAATAAACCAAAGGAATGCAAAAAAATGTTTTTTGTTCATTTATCTGAAAACCAATGCTTCGAAGTA
CCCAAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTTGATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTAGAAAGTATGCCAGGAGCCTTT
TAAAAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGTGCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGCTTCTGGTGGTTCTTATTAATG
TGGCTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAATTGTAGTTTTGTTTTTGAG

>TRINITY_DN106170_c0_g2_i2 from sample A4 / Example unspliced isoform:

CTTTGAGTCGCCAAATGTCAATTCCATCACAATGCTTTCCAAACAACGCTAGAAGTCGGTGGGAAGATTTCCCAACAATACAGCAGCTGAAGGAGACGAGCTCCATTTATCATCATGTGGGTGTTGTGAACTTTACTCAGAATTATTTCTTACAGGGTACTTACATTAAAGATTCCATTAACTTCATACATTCGCGGCTT
CATTCTGTGCTATTCATCATCATTGTCTGGGCTGTTCGAGACAGTCACAGTTGAGAGAGTGTGGGTGTTGTGAAATTCATTCAGAATTATCCCTTACAGGgtaggcacagtagagattacatcaattttatacattcaaagctttattctctgctctttatgttttttcattagacggtaaagattttactatatgtaca
gataagttgcctggctggatgttaggtaatttgattgagagctttgtgaattcttaccaaagaatttcaaattcaggttagaggtttctgtttgcagAAGATCAAGGAAGACATCATAAAAATATGAGTTCTCATTTAGTTGTGAAAGTTCACCCTCTATCCTGCTACTCATATGGGAAGAAGGAAGCCAAGGTGGATAA
AGACATTTTTCTCTCAGACAGGCTGGACAGAATCAGAGCCAATTTCATGAGAGAGGGTATGCGGACATATGTGGAAGGGATACTTCTGGTACATGAGTATGGTCACCCACATTTGCTGCTACTTCAAAAAGGAAATAAGATTATCAGGCTGCCTGGTGGGCGCTTAAGGCCTGGCGAAAATGAGATTGAAGGATTGAAGC
GCAAACTCACTAGTAAACTCATTTCCAGTTCAAGCTCAGCCCAACCAGACTGGCAGATTGGAGAGTGTGTTGGAGTGTGGTGGAGGCCTAATTTTGAGACCTTGATGTATCCATATTGTCCACCACATATCAATAAACCAAAGGAATGCAAAAAAATGTTTTTTGTTCATTTATCTGAAAACCAATGCTTCGAAGTACCC
AAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTTGATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTAGAAAGTATGCCAGGAGCCTTTTAA
AAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGTGCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGCTTCTGGTGGTTCTTATTAATGTGG
CTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAATTGTAGTTTTGTTTTTGAG

Intron 3 GTACAAAGAG ... TTTCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25	6	0	2
A2	45.83	13	1	11
A3	10	9	0	1
A4	28.57	20	0	8
A5	12.5	7	0	1
A6	25	30	0	10
A7	23.81	32	1	10
A8	23.81	32	0	10
A9	22.97	57	0	17
A10	12.5	35	0	5

>TRINITY_DN46166_c0_g1_i1 from sample A7 / Example spliced isoform

GCCAAATGTCAATTCCATCACAATGCTTTCCAAACAACGCTAGAAGTCGGTGGGAAGATTTCCCAACAATACAGCAGCTGAAGGAGACGAGCTCCATTTATCATCATGTGGGTGTTGTGAACTTTACTCAGAATTATTTCTTACAGGGTACTTACATTAAAGATTCCATTAACTTCATACATTCGCGGCTTCATTCTGTG
CTATTCATCATCATTGTCTGGGCTGTTCGAGACAGTCACAGTTGAGAGAGTGTGGGTGTTGTGAAATTCATTCAGAATTATCCCTTACAGGGTTAGAGGTTTCTGTTTGCAGAAGATCAAGGAAGACATCATAAAAATATGAGTTCTCATTTAGTTGTGAAAGTTCACCCTCTATCCTGCTACTCATATGGGAAGAAGGA
AGCCAAGGTGGATAAAGACATTTTTCTCTCAGACAGGCTGGACAGAATCAGAGCCAATTTCATGAGAGAGGGTATGCGGACATATGTGGAAGGGATACTTCTGGTACATGAGTATGGTCACCCACATTTGCTGCTACTTCAAAAAGGAAATAAGATTATCAGGCTGCCTGGTGGGCGCTTAAGGCCTGGCGAAAATGAGA
TTGAAGGATTGAAGCGCAAACTCACTAGTAAACTCATTTCCAGTTCAAGCTCAGCCCAACCAGACTGGCAGATTGGAGAGTGTGTTGGAGTGTGGTGGAGGCCTAATTTTGAGACCTTGATGTATCCATATTGTCCACCACATATCAATAAACCAAAGGAATGCAAAAAAATGTTTTTTGTTCATTTATCTGAAAACCAA
TGCTTCGAAGTACCCAAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTTGATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTAGAAAGTATG
CCAGGAGCCTTTTAAAAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGTGCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGCTTCTGGTGG
TTCTTATTAATGTGGCTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAATTGTAGTTTTGTTTTTGAGAATAATGAGTTATGCTCTATGGCCATAAGAACCATAGTAAGCAAACTAAACTCTGCATGCATCTTATCGCCTTCTCAAGTAGAACATATTCACTTTACCTATTCTGCAGTAACAACATGAATTT
TTAG

>TRINITY_DN46166_c0_g1_i2 from sample A7 / Example unspliced isoform:

ACCACATATCAATAAACCAAAGgtacaaagagtattgttaaccagctcagttgtaacctcaagaaagaactttctgctgaataatatatcttttcttgcagGAATGCAAAAAAATGTTTTTTGTTCATTTATCTGAAAACCAATGCTTCGAAGTACCCAAGAACTTGAAAATTCTTGCTGTTCCATTGTTTGAACTCTTT
GATAATGTCAAGAAATATGGTCCAGAAATCTCAAGTATTCCACAGCAACTCTCCAGGTTTTCTTTCGATCTAGTGTAAAAATGAGTTGTCTCACTTGAATGATCAGAAAGTGTCTCAGCAGAAAATAAACTGTAGAAAGTATGCCAGGAGCCTTTTAAAAGAATTGTACTATTTAAAGCATGATGATATCATGGAAGAGT
GCGAGTGGGAGAGTCGATGATTCTCTTCGGACAACTTTATATGGAGGCAAGTATAACATTGATGGAAGAAAAACACTGGCCCGCATCTGAGGCCTTATTACGTTTACACTTGTATATTTGTGCAGTGATGTTGCTTCTGGTGGTTCTTATTAATGTGGCTCCATGCTTTGTATGTAATAAGATGTGTAATTTGCATTCAA
TTGTAGTTTTGTTTTTGAGAATAATGAGTTATGCTCTATGGCCATAAGAACCATAGTAAGCAAACTAAACTCTGCATGCATCTTATCGCCTTCTCAAGTAGAACATATTCACTTTACCTATTCTGCAGTAACAACATGAATTTTTAG