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

Intron 1 ATAAGAGAAT ... CAATGGCGAC

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	65.98	24	36	53.1
A2	60.65	23.4	28	41.3
A3	59.7	28.3	26	52.9
A4	67.8	11	22	23.7
A5	57.62	15.4	14	26.3
A6	54.66	126.9	108.2	176.8
A7	55.06	157.1	134.2	227.7
A8	54.56	181.4	137.2	266.7
A9	54.06	164.4	137	224.5
A10	58.47	107.9	112.7	171.8

>TRINITY_DN103652_c0_g1_i4 from sample A2 / Example spliced isoform

CGGGTATGAGAATTACGAAACCGAAAGAAACCAGAACCAGAAACAGAAACAGAAACCGAAACCATTCCGATTCCTTCCAGAACCTCAACAGATTATAGAAGATTCGAGCTCTGGATCCCTTGAGACTCTTAGAGCAAAATTTTCAAACGTCATTGCCTGCTGGAAAATTTGCTCTGCTGGAAGTCTCTGGCTGTTGTGGA
AGGAAGGAGGGAGGGAAATCATGGTGCTGGGTCCAGTGGTGAATTTGTTCAAGCCATCCAACTACAGCTTCGACTGGAAGGAGTCCAGGATTGAGAAAGACGCCTCAAGCGCCGAATTCTTGATCCGCTTCAAGAACAATTATCTGAACAAAGGGATGCGCACAAGTGTGCATGGAATATTGTTGGTTCAAGAGCATAAT
CATCCACATATTCTCCTTTTGAAAAATAGAAACGAAGTTTATACATTGCCTGGTGGACGATTGTTTCCTGGAGAAAATGAGATCAAGGGTTTGAAGCGCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGAGATTCGGTGCTGTGATTTCTGCTATTCCACTCCAACTCTCCAGATT
CACTTTCAATGCAATGTAATGGCTGAAATTCTGAGAAATCTAAATCAAGTTTTGTACATCTCGACTAAAAGTGGCATATCATTGTTGTTAATGTACAACCCATTCTATGTACTACTTCTTCCAAACTTGGGAAATTTGAGATATTGTATTGAAGGCTCGCTGCAAAATTTTCAGATTTTGTATATTAAGAGGATTCCACA
AAGATGCACATACACAATCATCCTGATTGATCTATACAACGCCATTTATGTTCTTTCTACTTGGTCCAAGCTCCTCTCCCAAACTACACTCATGTGGCGTATTCAGACTTTAGCCGGCAAATTGAAATCTCTTGAAGAATTATCTGGAAATGGAAATTGAGGTATAATTACCTCTTATGGAATTTCTTCTACTTTTCACT
AATGTCTTGACTACGTTAACTTGGCGAATAAAGAAGGCTAGAGTCTCGTCTTCCTTCTTTTAAGGTTTTGCTTCATTATTTTTACTTATAAAACTTAAAATCTCAGTTTGGCCAATTTTCCAGTCTTTCACAATAATGTAATAAAAGCTTTTCA

>TRINITY_DN103652_c0_g1_i1 from sample A2 / Example unspliced isoform:

CGGGTATGAGAATTACGAAACCGAAAGAAACCAGAACCAGAAACAGAAACAGAAACCGAAACCATTCCGATTCCTTCCAGAACCTCAACAGATTATAGAAGATTCGAGCTCTGGATCCCTTGAGACTCTTAGAGCAAAATTTTCAAACGTCATTGCCTGCTGGAAAATTTGCTCTGCTGGAAGTCTCTGGCTGTTGTGGA
AGGAAGGAGGGAGGGAAATCATGGTGCTGGGTCCAGTGGTGAATTTGTTCAAGCCATCCAACTACAGCTTCGACTGGAAGGAGTCCAGGATTGAGAAAGACGCCTCAAGCGCCGAATTCTTGATCCGCTTCAAGAACAATTATCTGAACAAAGGGATGCGCACAAGTGTGCATGGAATATTGTTGGTTCAAGAGCATAAT
CATCCACATATTCTCCTTTTGAAAAATAGAAACGAAGTTTATACATTGCCTGGTGGACGATTGTTTCCTGGAGAAAATGAGATCAAGGGTTTGAAGCGCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGataagagaatgtgttggagtatggtggaggccgaattttgagactct
gatgtacccttactgcccaccccatataacaaaacctaaggagtgcaaaaagttgtttattgtccagctacccgaagggcagcgctttgttattcctgaaaacctgaagctcttggctgttccattatttgagttgcaggacaatggcgacAGATTCGGTGCTGTGATTTCTGCTATTCCACTCCAACTCTCCAGATTCA
CTTTCAATGCAATGTAATGGCTGAAATTCTGAGAAATCTAAATCAAGTTTTGTACATCTCGACTAAAAGTGGCATATCATTGTTGTTAATGTACAACCCATTCTATGTACTACTTCTTCCAAACTTGGGAAATTTGAGATATTGTATTGAAGGCTCGCTGCAAAATTTTCAGATTTTGTATATTAAGAGGATTCCACAAA
GATGCACATACACAATCATCCTGATTGATCTATACAACGCCATTTATGTTCTTTCTACTTGGTCCAAGCTCCTCTCCCAAACTACACTCATGTGGCGTATTCAGACTTTAGCCGGCAAATTGAAATCTCTTGAAGAATTATCTGGAAATGGAAATTGAGGTATAATTACCTCTTATGGAATTTCTTCTACTTTTCACTAA
TGTCTTGACTACGTTAACTTGGCGAATAAAGAAGGCTAGAGTCTCGTCTTCCTTCTTTTAAGGTTTTGCTTCATTATTTTTACTTATAAAACTTAAAATCTCAGTTTGGCCAATTTTCCAGTCTTTCACAATAATGTAATAAAAGCTTTTCA

Intron 2 GCAAGTGATA ... AAACATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	13.99	49.3	5.8	8.1
A2	18.97	25.1	3.5	5.8
A3	10.31	49.8	9.8	5.7
A4	7.2	35.7	5.4	2.8
A5	3.95	31.2	3.1	1.3
A6	16.96	171.6	23.4	35.2
A7	18.22	226.8	29.5	50.4
A8	16.74	201.5	33.2	40.3
A9	12.71	225.8	35.2	32.8
A10	18.57	199.6	47.9	45

>TRINITY_DN39152_c0_g1_i5 from sample A8 / Example spliced isoform

AGGAGATTCTGAAGGAAGGAGAAGAGCTCCAAGTCTTAAAAAGCAAGGATGAAGGAAGGAGAATTTATGGCAAGGGAGGAGGCATTCACACCAGGATTCCTGGTTCAAGAGCATAATCATCCACATATTCTCCTTTTGAAAAATAGAAACGAAGTTTATACATTGCCTGGTGGACGATTGTTTCCTGGAGAAAATGAGAT
CAAGGGTTTGAAGCGCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGAGATTCGGTGCTGTGATTTCTGCTATTCCACTCCAACTCTCCAGATTCACTTTCAATGCAATGTAATGGCTGAAATTCTGAGAAATCTAAATCAAGTTTTGTACATCTCGACTAAAAGTGGCATATCATT
GTTGTTAATGTACAACCCATTCTATGTACTACTTCTTCCAAACTTGGGAAATTTGAGATATTGTATTGAAGGCTCGCTGCAAAATTTTCAGATTTTGTATATTAAGAGGATTCCACAAAGATGCACATACACAATCATCCTGATTGATCTATACAACGCCATTTATGTTCTTTCTACTTGGTCCAAGCTCCTCTCCCAAA
CTACACTCATGTGGCGTATTCAGACTTTAGCCGGCAAATTGAAATCTCTTGAAGAATTATCTGGAAATGGAAATTGAGG

>TRINITY_DN39152_c0_g1_i4 from sample A8 / Example unspliced isoform:

TGTTTCCTGGAGAAAATGgcaagtgataataacaagttcatgttatgcatgcaaatctgaagtgtaactagctaattattgtcacccaactcttttcttcttgaaaacatgcagAGATCAAGGGTTTGAAGCGCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGGAGTGCAAAAAG
TTGTTTATTGTCCAGCTACCCGAAGGGCAGCGCTTTGTTATTCCTGAAAACCTGAAGCTCTTGGCTGTTCCATTATTTGAGTTGCAGGACAATGGCGACGACCACGAAGTAGAAGCTATTCACTAAAAGTTCGTTAACAAAAATGCTGAGGAATTCCTCGTCAACATTTTTGTTCAATGACTCGAGAGGAAATCATTTTG
TTACTGTGGATTTTTTCTATGACCACTAGTGGATTCAAAGAACACCATGAGAGTAACAGAGAAGCACGAGCTAAGAAGAGTAGTATGAGAGCTGCAAGTTTTGGAAAATGTATCCCAACATTTACTATCACAGCTAAAACATATGGTTGTTGTTTTGAAGGGACATGTCTCATATTTTGAAAATGTTTAATTTTCTCCTA
AATCGAGGAAATCGATTCGATGCATTTCATTGTATGAATAAATTAACTATGGACATGAAAAGACTCGTGCCAATTTTACCTTTGAATACAATCTATTGTTAGTACATTACTGGTGTTATTTGTGTGTTGTTAATTAGGGGATTGTCCAACACTTTGTAGAGTATAAGGGCCCACTCTGTAGTTCTATTGGATTGAC

Intron 3 GTAATGGCTG ... GGAAATTGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	78.72	13	48.3	6
A2	87.39	5	34.7	6
A3	84.2	9	48	8
A4	72.61	12	32	17
A5	89.77	3	27	2
A6	86.81	36	237.3	24
A7	84.2	46	245.3	20
A8	90.1	39.3	358.3	51
A9	88.02	41	301.7	28
A10	88.98	24	194.3	14

>TRINITY_DN105992_c0_g1_i5 from sample A3 / Example spliced isoform

GAAGATTCGAGCTCTGGATCCCTTGAGACTCTTAGAGCAAAATTTTCAAACGTCATTGCCTGCTGGAAAATTTGCTCTGCTGGAAGTCTCTGGCTGTTGTGGAAGGAAGGAGGGAGGGAAATCATGGTGCTGGGTCCAGTGGTGAATTTGTTCAAGCCATCCAACTACAGCTTCGACTGGAAGGAGTCCAGGATTGAGAA
AGACGCCTCAAGCGCCGAATTCTTGATCCGCTTCAAGAACAATTATCTGAACAAAGGGATGCGCACAAGTGTGCATGGAATATTGTTGGTTCAAGAGCATAATCATCCACATATTCTCCTTTTGAAAAATAGAAACGAAGTTTATACATTGCCTGGTGGACGATTGTTTCCTGGAGAAAATGAGATCAAGGGTTTGAAGC
GCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGATAAGAGAATGTGTTGGAGTATGGTGGAGGCCGAATTTTGAGACTCTGATGTACCCTTACTGCCCACCCCATATAACAAAACCTAAGGAGTGCAAAAAGTTGTTTATTGTCCAGCTACCCGAAGGGCAGCGCTTTGTTATTCCT
GAAAACCTGAAGCTCTTGGCTGTTCCATTATTTGAGTTGCAGGACAATGGCGACAGATTCGGTGCTGTGATTTCTGCTATTCCACTCCAACTCTCCAGATTCACTTTCAATGCAATGACCACGAAGTAGAAGCTATTCACTAAAAGTTCGTTAACAAAAATGCTGAGGAATTCCTCGTCAACATTTTTGTTCAATGACTC
GAGAGGAAATCATTTTGTTACTGTGGATTTTTTCTATGACCACTAGTGGATTCAAAGAACACCATGAGAGTAAC

>TRINITY_DN105992_c0_g1_i7 from sample A3 / Example unspliced isoform:

GAAGATTCGAGCTCTGGATCCCTTGAGACTCTTAGAGCAAAATTTTCAAACGTCATTGCCTGCTGGAAAATTTGCTCTGCTGGAAGTCTCTGGCTGTTGTGGAAGGAAGGAGGGAGGGAAATCATGGTGCTGGGTCCAGTGGTGAATTTGTTCAAGCCATCCAACTACAGCTTCGACTGGAAGGAGTCCAGGATTGAGAA
AGACGCCTCAAGCGCCGAATTCTTGATCCGCTTCAAGAACAATTATCTGAACAAAGGGATGCGCACAAGTGTGCATGGAATATTGTTGGTTCAAGAGCATAATCATCCACATATTCTCCTTTTGAAAAATAGAAACGAAGTTTATACATTGCCTGGTGGACGATTGTTTCCTGGAGAAAATGAGATCAAGGGTTTGAAGC
GCAAGTTAACCAGCAAATTTGAATCTAAGTCATCACCCATTCCACATGATTGGAAGATAAGAGAATGTGTTGGAGTATGGTGGAGGCCGAATTTTGAGACTCTGATGTACCCTTACTGCCCACCCCATATAACAAAACCTAAGGAGTGCAAAAAGTTGTTTATTGTCCAGCTACCCGAAGGGCAGCGCTTTGTTATTCCT
GAAAACCTGAAGCTCTTGGCTGTTCCATTATTTGAGTTGCAGGACAATGGCGACAGATTCGGTGCTGTGATTTCTGCTATTCCACTCCAACTCTCCAGATTCACTTTCAATGCAATgtaatggctgaaattctgagaaatctaaatcaagttttgtacatctcgactaaaagtggcatatcattgttgttaatgtacaac
ccattctatgtactacttcttccaaacttgggaaatttgagatattgtattgaaggctcgctgcaaaattttcagattttgtatattaagaggattccacaaagatgcacatacacaatcatcctgattgatctatacaacgccatttatgttctttctacttggtccaagctcctctcccaaactacactcatgtggcg
tattcagactttagccggcaaattgaaatctcttgaagaattatctggaaatggaaattgagGACCACGAAGTAGAAGCTATTCACTAAAAGTTCGTTAACAAAAATGCTGAGGAATTCCTCGTCAACATTTTTGTTCAATGACTCGAGAGGAAATCATTTTGTTACTGTGGATTTTTTCTATGACCACTAGTGGATTCA
AAGAACACCATGAGAGTAAC