sp|Q8VZ10|SOQ1_ARATH ----> Protein SUPPRESSOR OF QUENCHING 1, chloroplastic

Intron 1 GTGAGAGTAA ... TCTTCAGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80	3	13	11
A2	71.43	6	15	15
A3	53.85	6	7	7
A4	65.85	7	11	16
A5	46.15	7	10	2
A6	63.38	13	23	22
A7	76.12	8	23	28
A8	55.56	16	18	22
A9	55.1	22	19	35
A10	58.76	20	26	31

>TRINITY_DN95722_c0_g2_i3 from sample A4 / Example spliced isoform

ATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGCTTGCCCCATTGGAAGCATCTGTCCAACAAATAAAAATAATCTAAGCTAGGTTCGAATTTTTTGATGTCAGAT
TCTAAAATTTCAAAAGCCCATGCATTGTTTTGAACAAGTCAATCACCACACCCATCAATGTGGAAATCTCAAGTTTCAGCCAGATTGCCCACATCATTCTTATTCTTATGGAGAACCACATTAGTCCAGAAGCAGTTAGCAGGGAGACTTGGTTATGAAAGAATTAGCAAGGATCAAAGCAAGGGAAAAGATACGAAGCT
CTTTTGCTGGATGCAGGAGGGACACTGTTGCAGACAGTGAAGCCTGTTGAAGAGACATATGCAACTATTGGTTCAAAATATGGGGTGAGGGCATCTTCAGGGGAAATCAAACAAGGTTTCAAAAAAGCATTTGCTGAACCATGGCCAGACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGT
ACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTGGCTGTTGTATCAAACTTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTGT
TCAATGCAATCATAATATCGTCGGAAGTTGGATATGAAAAGCCTGCACCTCAAATATTTGAAATGGCTCTAGATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAAAATTGGTGCCAATGCTCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAAGAG
ATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGATGCTTCTGG

>TRINITY_DN95722_c0_g2_i1 from sample A4 / Example unspliced isoform:

ATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGCTTGCCCCATTGGAAGCATCTGTCCAACAAATAAAAATAATCTAAGCTAGGTTCGAATTTTTTGATGTCAGAT
TCTAAAATTTCAAAAGCCCATGCATTGTTTTGAACAAGTCAATCACCACACCCATCAATGTGGAAATCTCAAGTTTCAGCCAGATTGCCCACATCATTCTTATTCTTATGGAGAACCACATTAGTCCAGAAGCAGTTAGCAGGGAGACTTGGTTATGAAAGAATTAGCAAGgtgagagtaagagcccagatttctcaacc
atctagatcatattcttcagaagGATCAAAGCAAGGGAAAAGATACGAAGCTCTTTTGCTGGATGCAGGAGGGACACTGTTGCAGACAGTGAAGCCTGTTGAAGAGACATATGCAACTATTGGTTCAAAATATGGGGTGAGGGCATCTTCAGGGGAAATCAAACAAGGTTTCAAAAAAGCATTTGCTGAACCATGGCCAG
ACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTGGCTGTTGTATCAAAC
TTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTGTTCAATGCAATCATAATATCGTCGGAAGTTGGATATGAAAAGCCTGCACCTCAAATATTTGAAATGGCTCTAGATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAAAATTGGTGCCAATGC
TCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAAGAGATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGATGCTTCTGG

Intron 2 GTTCAATGCA ... ATGGCTCTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	87.1	2	9	18
A2	89.74	2	21	14
A3	81.78	2	10.5	7.5
A4	100	0	5	14
A5	60	1	2	1
A6	88.71	7	43	67
A7	81.82	7	34	29
A8	79.26	14	52	55
A9	90.96	4	33	47.5
A10	70	12	22	34

>TRINITY_DN42923_c0_g1_i2 from sample A10 / Example spliced isoform

CTGAACCATGGCCAGACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTG
GCTGTTGTATCAAACTTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTGTTCAATGCAATCATAATATCGTCGGAAGTTGGATATGAAAAGCCTGCACCTCAAATATTTGAAATGGCTCTAGATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAA
AATTGGTGCCAATGCTCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAAGAGATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGCAGGGAGACTTGG
TTATGAAAGAATTAGCAAGGTGAGAGTAAGAGCCCAGATTTCTCAACCATCTAGATCATATTCTTCAGAAGGATCAAAGCAAGGGAAAAGATACGAAGCTCTTTTGCTGGATGCAGGAGGGACACTGTTGCAGACAGTGAAGCCTGTTGAAGAGACATATGCAACTATTGGTTCAAAATATGGGGTGAGGGCATCTTCAG
GGGAAATCAAACAAGGTTTCAAAAAAGCATTTGCTGAACCATGGCCAGACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTT
CTCAGTCATTTGAAGGATGCTGGAGTGAAATTGGCTGTTGTATCAAACTTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAAAATTGGTGCCAATGCTCTCGGAATTGAT

>TRINITY_DN42923_c0_g1_i1 from sample A10 / Example unspliced isoform:

CTGAACCATGGCCAGACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTG
GCTGTTGTATCAAACTTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTgttcaatgcaatcataatatcgtcggaagttggatatgaaaagcctgcacctcaaatatttgaaatggctctagATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAA
AATTGGTGCCAATGCTCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAAGAGATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGATGCTTCTGGTTA
CCTATGTAAAATTTACATAATTTCTTTCTTTCTTTGTAATCTTTGCCTTTGGTTATTTGGATGTTTGTTGTGAAGTAATGAAATACTGTATTGTAGTTGCGCAATGGCTACTGCTTATTAAATGAAGAAAAACTGGTTTGGCATTTCCAATGTGTATGGTGACATAGAAGCACAATGAAACCTAAAGCCATGTGCATCAT
TTATTATAGTGATTACGTACATTATCATAACTAGTGCAAGGTATAAAGAGTAATCATCGTGTTCCCGTA

Intron 3 GTGAGAGTAA ... TATTCTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	86.21	2	13	12
A2	68.18	7	15	15
A3	53.85	6	7	7
A4	65.85	7	11	16
A5	50	6	10	2
A6	67.16	11	23	22
A7	74.29	9	23	29
A8	54.05	17	18	22
A9	55.1	22	19	35
A10	58.76	20	26	31

>TRINITY_DN106035_c1_g1_i1 from sample A2 / Example spliced isoform

ATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGCTTGCCCCATTGGAAGCATCTGTCCAACAAATAAAAATAATCTAAGCTAGGTTCGAATTTTTTGATGTCAGAT
TCTAAAATTTCAAAAGCCCATGCATTGTTTTGAACAAGTCAATCACCACACCCATCAATGTGGAAATCTCAAGTTTCAGCCAGATTGCCCACATCATTCTTATTCTTATGGAGAACCACATTAGTCCAGAAGCAGTTAGCAGGGAGACTTGGTTATGAAAGAATTAGCAAGAAGGATCAAAGCAAGGGAAAAGATACGAA
GCTCTTTTGCTGGATGCAGGAGGGACACTGTTGCAGACAGTGAAGCCTGTTGAAGAGACATATGCAACTATTGGTTCAAAATATGGGGTGAGGGCATCTTCAGGGGAAATCAAACAAGGTTTCAAAAAAGCATTTGCTGAACCATGGCCAGACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGT
TGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTGGCTGTTGTATCAAACTTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAAC
TGTTCAATGCAATCATAATATCGTCGGAAGTTGGATATGAAAAGCCTGCACCTCAAATATTTGAAATGGCTCTAGATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAAAATTGGTGCCAATGCTCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAA
GAGATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGATGCTTCTGGTTACCTATGTAAAATTTACATAATTTCTTTCTTTCTTTGTAATCTTTGCCTTTGGTTATTTGGATGT
TTGTTGTGAAGTAATGAAATACTGTATTGTAGTTGCGCAATGGCTACT

>TRINITY_DN106035_c1_g1_i5 from sample A2 / Example unspliced isoform:

ATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGAGTGTTGTAAACAGGCTCCAAGAGTGTATATTGTTAGACTGGGACAAGCTCGCTTGCCCCATTGGAAGCATCTGTCCAACAAATAAAAATAATCTAAGCTAGGTTCGAATTTTTTGATGTCAGAT
TCTAAAATTTCAAAAGCCCATGCATTGTTTTGAACAAGTCAATCACCACACCCATCAATGTGGAAATCTCAAGTTTCAGCCAGATTGCCCACATCATTCTTATTCTTATGGAGAACCACATTAGTCCAGAAGCAGTTAGCAGGGAGACTTGGTTATGAAAGAATTAGCAAGgtgagagtaagagcccagatttctcaacc
atctagatcatattcttcagAAGGATCAAAGCAAGGGAAAAGATACGAAGCTCTTTTGCTGGATGCAGGAGGGACACTGTTGCAGACAGTGAAGCCTGTTGAAGAGACATATGCAACTATTGGTTCAAAATATGGGGTGAGGGCATCTTCAGGGGAAATCAAACAAGGTTTCAAAAAAGCATTTGCTGAACCATGGCCAG
ACCGACTGCGCTATCAGGGAGATGGAAGGCCTTTCTGGAGACACATAGTTGTACAAGCAACAGGTTGTGCTAGCAATGATTATTTTGAGGAACTATACAATCATTTCTCGCGAGGTGATGTATGGACGCTTCCAACTGGAGCATATGAAGTTCTCAGTCATTTGAAGGATGCTGGAGTGAAATTGGCTGTTGTATCAAAC
TTCGACAATCGTTTGAGACCAATCTTGGAAGAGTTGAATGTCGCAAAACTGTTCAATGCAATCATAATATCGTCGGAAGTTGGATATGAAAAGCCTGCACCTCAAATATTTGAAATGGCTCTAGATCAGCTTGGTGTGGATGTGAGTAAAGCAATACATGTTGGAGATGACCCACGTAATGATAAAATTGGTGCCAATGC
TCTCGGAATTGATTCATGGTTATGGGGTAAGGAAGTGCACACATTTCAAGAGATTTTAGATCGCATCATAGAATCAAACGTGGAATAATTTCAAAGGATTCGTGAGTGCAACCTAAAAATGTATACTTTCATTCATGTCTCTCCCTTGTTTTGTTGTACACAATGCAGTTAGATGCTTCTGGTTACCTATGTAAAATTTA
CATAATTTCTTTCTTTCTTTGTAATCTTTGCCTTTGGTTATTTGGATGTTTGTTGTGAAGTAATGAAATACTGTATTGTAGTTGCGCAATGGCTACT