sp|O48686|SNL3_ARATH ----> Paired amphipathic helix protein Sin3-like 3

Intron 1 GTAATGCAGA ... TGGTTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.09	17	4	6
A2	37.5	5	2	3
A3	27.78	13	5	5
A4	33.33	2	0	1
A5	33.33	2	1	1
A6	28.24	61	6	24
A7	38.25	134	31	83
A8	34.29	207	41	108
A9	32.37	326	42	156
A10	35.79	174	22	97

>TRINITY_DN40930_c0_g1_i5 from sample A8 / Example spliced isoform

AATCAATACATTTTTTTTCTCTCTTCTCAATTAATTCTCATATTCCGTCTATTCTTCCTGCAGGCTTGATACAGTTGATGTTATAATCCGATTAAAGCCTCTATTTAAGCGGCATCATTTTCTCATTTTCGGTTTGAATACTTTTCTCTCCAAAGATTATCAAATTTCGTTTCCTTTCCACGATGACCTAACAAGGTTGT
ACCACGATATAGAGTTTGAACAAGCCACGAAATATGTTAATAAGATTAAGACACGCTTCCAAAATGAAATAGTCTACCAGAAGTTTGGGGATATACTGGATAGGTATAGGTTTGGGGATATACTGGATAGGTATAGGATATTAGACACGTCAATCGATGAAGTATACGGAGAGGTCGAAGAACTGTTTTATCCTCATCAA
GATCTTATAGAGGAATTTCCTGGATTTCTACGCCACGGGTGAAATATCTGTTAATTTGTTATTTTGTTTTGCAATTGCTACACATGAACGTTGAGAGGGCAAACACTGAGATAGAACAGAGCTACT

>TRINITY_DN40930_c0_g1_i1 from sample A8 / Example unspliced isoform:

GTTTTGGTATAAGTTTTAATTTTGTGTTCTCATCAATGGACGTTGATACCATGATAACTTTTATGACATCTTTTGCGATCTTCTTGCTGAGGTCTTTGTCAAGTCTTTTGATAATAACATTCAAAACCTCTTTTGTAATCTGCTCTCATTTAAAATTGGAGGAAGTTATAATAATTAGTTAAGAATTTAATATTTTATTA
TAATTAATAGGTTGATCGAATCACTTTAAAGTAAATCGACTTTGGGCGTGTCTTCAAACCTAAATCTGCCTTCAGTGTGTTTGTTTTATTTTCCTTTCAACAGGCCTCTGTATCTCATCAATGGAACACGGAGAACAGCTAGGAGAAACCTCCACACTGCATCAAGATTCTGATGGATCAGAGAGGCCAACAATGGGTGA
TGCTTTGGCATATCTCAAGGTAGTCAAAGAAGTATTCAAGGATACTCCACACAAATATGACCAGTTTCTTGTGGTCATCAAAGCTTTCCATGCCCAAAGGCTTGATACAGTTGATGTTATAATCCGATTAAAGCCTCTATTTAAGCGGCATCATTTTCTCATTTTCGGTTTGAATACTTTTCTCTCCAAAGATTATCAAA
TTTCGTTTCCTTTCCACGATGACCTAACAAGGTTGTACCACGATATAGAGTTTGAACAAGCCACGAAATATGTTAATAAGATTAAGgtaatgcagatcacatattaatggttttaacatttgaaagctctgttctgtttacaaacatcaaatgtgttcttaaaatgctgaactggacttgggtaggccattgatagtgaa
ctggcattgagtgtttgaaaaaaattcaaacctatccacttgttttcacttacttgtaatttatggttttcagACACGCTTCCAAAATGAAATAGTCTACCAGAAGTTTGGGGATATACTGGATAGGTATAGGTTTGGGGATATACTGGATAGGTATAGGATATTAGACACGTCAATCGATGAAGTATACGGAGAGGTCG
AAGAACTGTTTTATCCTCATCAAGATCTTATAGAGGAATTTCCTGGATTTCTACGCCACGGGTGAAATATCTGTTAATTTGTTATTTTGTTTTGCAATTGCTACACATGAACGTTGAGAGGGCAAACACTGAGATAGAACAGAGCTACTAATATATGTTAGATATTCTAAATAATAGAATTATCAAGCAAAGACTATGAT
TATAATTCATGTTAGTTTTTAATCGTTGAAGCGTGATTGCATAAATATGGTAATGAAATATGGGTAAAGGTTGTTGGAGGGATTTGTGGTAAATATGTCACTATTATTTGGCCAAAATGTTTTCAAGTGAAAGTTGAATATGATAGCCATAAGATTTTGAACAAATTTATTTTCAATGATGTTTGTTTTAAATAAAAACT
GTTCTCCAC

Intron 2 GTATTATCTT ... CTATTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.43	1	3	2
A2	52.94	4	4	5
A3	28.21	14	4	7
A4	25	3	2	0
A5	20	8	1	3
A6	22.05	76	17	26
A7	22.26	227	53	77
A8	24.6	354	90	141
A9	23.03	463	89	188
A10	20.62	283	63	84

>TRINITY_DN67726_c0_g1_i1 from sample A2 / Example spliced isoform

CTTTTCTCTCCAAAGATTATCAAATTTCGTTTCCTTTCCACGATGACCCAACAAGGTTGTACCACGATATAGAGTTTGAACAAGCCACGAAATATGTTAATAAGATTAAGACACGCTTCCAAAATGAAATAGTCTACCAGAAGTTTGGGGATATACTGGATAGGTATAGGTTTGGGGATATACTGGATAGGTATAGGATA
TTAGACACGTCAATCGATGAAGTATACGGAGAGGTCGAAGAACTGTTTTATCCTCATCAAGATCTTATAGAGGAATTTCCTGGATTTCTACGCCACGGGTGAAATATCTGTTAATTTGTTATTTTGTTTTGCAATTGCTACACATGAACGTTGAGAGGGCAAACACTGAGATAGAACAGAGCGT

>TRINITY_DN67726_c0_g1_i2 from sample A2 / Example unspliced isoform:

CTTTTCTCTCCAAAGATTATCAAATTTCGTTTCCTTTCCACGATGACCCAACAAGGTTGTACCACGATATAGAGTTTGAACAAGCCACGAAATATGTTAATAAGATTAAGACACGCTTCCAAAATGAAATAGTCTACCAGAAGTTTGGGGATATACTGGATAGGTATAGGTTTGGGGATATACTGGATAGGTATAGGATA
TTAGACACGTCAATCGATGAAGTATACGGAGAGgtattatcttatccattgtttcccagaaatgaattatacattaatattattttctagttgtattaatgaattacacattaatattattcacataatttaattgtatttgtctatttgcagGTCGAAGAACTGTTTTATCCTCATCAAGATCTTATAGAGGAATTTCC
TGGATTTCTACGCCACGGGTGAAATATCTGTTAATTTGTTATTTTGTTTTGCAATTGCTACACATGAACGTTGAGAGGGCAAACACTGAGATAGAACAGAGCGT