sp|Q9SRY4|LPA1_ARATH ----> Protein LOW PSII ACCUMULATION 1, chloroplastic

Intron 1 GTTGTTTCTT ... AATGGGAAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.28	29	21	27
A2	50	9	9	9
A3	48.28	15	14	14
A4	43.4	15	11	12
A5	52	6	7	6
A6	48.57	54	47	55
A7	44.71	81	63	68
A8	48.21	87	78	84
A9	46.34	55	40	55
A10	46.67	44	36	41

>TRINITY_DN113528_c0_g1_i5 from sample A1 / Example spliced isoform

TATTATCGTACTTGTGGCACTCTTCCTCTGGGATAATAGGAAAGAAGAGGAACAAATTGCCCAAATTTCCCGGGATGAAACTCTTTCAAGGTTGCCTTTGCGCCTATCAACTGATCGTGTTGTAGAACTTGTGCAGTTACGGGATACAACTCGGCCTGTAATTTTGGCAGGGGCAAACGATGTGGTAAATAGAGCAGTTC
AAAGAGCTGAGAAGTTTCGCAACGATCTTGTCAAAAGGGGAGTTCTTCTAGTACCTTTAGTTTGGAGCAGTGAAAGTAAAAGTAAAGGTTCTATCAGAAAGAAAGGTTTTGGAAGTTTACGGAAGCCAGCAATTTCTAGTCTTTCATCCAGTGGTGAATTTGAGAAACGAACACAGAATATTGCTTCCAAGTCAATAGCA
CAAGTTGAAAAACGATTCAAGGCAGAGTTGGGTTCGTGAGCAACAAGAGTCTGAAGGAGTAACACCGGGAGAAGATGTGTATATTGTCTTGCGTTTGGATGGTCGTGTTCGAAAATCTGGTCAGGGAATGCCTGACTGGAAAGAGTTAATTAACGAGTTGCCGCCATTAGAATCCTTTGTCAGCAAACTGGAAAAATAAT
ACAGTTATTCAACAACCATTTAATCCCTTGTCTGTAGCTTATAAACGGGATAGGAATGTGAGTTTTATCATTAACTAACTGAGTCATTGCTGTTTGTATTTCCTCCTGCTTTTGGTAGCTGAATAAGAGAAATACTAAAGTAAACGCTGGGATTGGAAAATATATAGGACATTTATCAAGGTGATGGTAGATTCTTCTTA
CAAAAGGTTTATTACATTGGAATTTCCATATTTCATCCCAAAAAACTTAAATGCAAGTATAGCTTGTAAATAGGTTAGCAAATGTCCATTTAGTTCATTGTATATAGCTTGTAAATGGC

>TRINITY_DN113528_c0_g1_i4 from sample A1 / Example unspliced isoform:

AATCGATATTCTCATTCATGGATCGTCCTGGCCATTATTATATTTTCTAACGAGTATAGGATGGCGATGGCTACTGTGCCTGGGCAACAGTAGTCCATATCATTATCCACAAGCACTGGCGATGGCCATGGCCATTGCAAATGGCGTCATTAATATGAATGTAATACCTCAATTCTCAGCACCCACCTGCAAATTTACTA
ATGTACCTCTTGACGGAAGAAGAAAACCATTATTCAAAATCAAGTTCAACAGATGGAATTTGGAAGTACCCAAGACAATTGGGTACATTGAGAGTAAAGAATGGAGTTTGGTTGTTGCTGCCTCGACAGGAGCAGAAGCAGATACAGAGACTCCATCGATGGACACTGCAACTGCCAGGGATGCTGTCAATTTGGGGCTT
TCTCTCTTCTCGAAAGGCCAGGTAAGAGATGCCCTTGTTCAATTTGAAAAGGCACTTTCTCTAGACCCAGATCCAGAGGAAGCCGCAGCTGCTCTATACAATAAAGCCTGTTGCCATGCCTACAGAGAAGAAGGAAGAAAAACTGCAGAAGCTTTACGGAAGGCTTTGCGGGATTATGATCTTAAATTTAGTGTGATTCT
CAATGATCCAGACATGGCTCCCTTTCGGGCTATGCCTGAGTTCAAGCAACTTCAAGTAGAGGTATTATCGTACTTGTGGCACTCTTCCTCTGGGATAATAGGAAAGAAGAGGAACAAATTGCCCAAATTTCCCGGGATGAAACTCTTTCAAGGTTGCCTTTGCGCCTATCAACTGATCGTGTTGTAGAACTTGTGCAGTT
ACGGGATACAACTCGGCCTGTAATTTTGGCAGGGGCAAACGATGTGGTAAATAGAGCAGTTCAAAGAGCTGAGAAGTTTCGCAACGATCTTGTCAAAAGGGGAGTTCTTCTAGTACCTTTAGTTTGGAGCAGTGAAAGTAAAAGTAAAGGTTCTATCAGAAAGAAAGGTTTTGGAAGTTTACGGAAGCCAGCAATTTCTA
GTCTTTCATCCAGTGGTGAATTTGAGAAACGAACACAGAATATTGCTTCCAAGTCAATAGCACAAGTTGAAAAACGATTCAAGGCAGAGgttgtttcttctaatgaatgggaaagTTGGGTTCGTGAGCAACAAGAGTCTGAAGGAGTAACACCGGGAGAAGATGTGTATATTGTCTTGCGTTTGGATGGTCGTGTTCGA
AAATCTGGTCAGGGAATGCCTGACTGGAAAGAGTTAATTAACGAGTTGCCGCCATTAGAATCCTTTGTCAGCAAACTGGAAAAATAATACAGTTATTCAACAACCATTTAATCCCTTGTCTGTAGCTTATAAACGGGATAGGAATGTGAGTTTTATCATTAACTAACTGAGTCATTGCTGTTTGTATTTCCTCCTGCTTT
TGGTAGCTGAATAAGAGAAATACTAAAGTAAACGCTGGGATTGGAAAATATATAGGACATTTATCAAGGTGATGGTAGATTCTTCTTACAAAAGGTTTATTACATTGGAATTTCCATATTTCATCCCAAAAAACTTAAATGCAAGTATAGCTTGTAAATAGGTTAGCAAATGTCCATTTAGTTCATTGTATATAGCTTGT
AAATGGC

Intron 2 GCTAGAATGG ... AACATTGGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52.73	13	17	12
A2	61.11	7	8	14
A3	47.06	27	22	26
A4	65.85	7	9	18
A5	64.29	5	2	16
A6	54.29	16	14	24
A7	50.56	22	10	35
A8	54.43	18	8	35
A9	57.69	11	13	17
A10	64.71	9	6	27

>TRINITY_DN113528_c0_g1_i4 from sample A1 / Example spliced isoform

AATCGATATTCTCATTCATGGATCGTCCTGGCCATTATTATATTTTCTAACGAGTATAGGATGGCGATGGCTACTGTGCCTGGGCAACAGTAGTCCATATCATTATCCACAAGCACTGGCGATGGCCATGGCCATTGCAAATGGCGTCATTAATATGAATGTAATACCTCAATTCTCAGCACCCACCTGCAAATTTACTA
ATGTACCTCTTGACGGAAGAAGAAAACCATTATTCAAAATCAAGTTCAACAGATGGAATTTGGAAGTACCCAAGACAATTGGGTACATTGAGAGTAAAGAATGGAGTTTGGTTGTTGCTGCCTCGACAGGAGCAGAAGCAGATACAGAGACTCCATCGATGGACACTGCAACTGCCAGGGATGCTGTCAATTTGGGGCTT
TCTCTCTTCTCGAAAGGCCAGGTAAGAGATGCCCTTGTTCAATTTGAAAAGGCACTTTCTCTAGACCCAGATCCAGAGGAAGCCGCAGCTGCTCTATACAATAAAGCCTGTTGCCATGCCTACAGAGAAGAAGGAAGAAAAACTGCAGAAGCTTTACGGAAGGCTTTGCGGGATTATGATCTTAAATTTAGTGTGATTCT
CAATGATCCAGACATGGCTCCCTTTCGGGCTATGCCTGAGTTCAAGCAACTTCAAGTAGAGGTATTATCGTACTTGTGGCACTCTTCCTCTGGGATAATAGGAAAGAAGAGGAACAAATTGCCCAAATTTCCCGGGATGAAACTCTTTCAAGGTTGCCTTTGCGCCTATCAACTGATCGTGTTGTAGAACTTGTGCAGTT
ACGGGATACAACTCGGCCTGTAATTTTGGCAGGGGCAAACGATGTGGTAAATAGAGCAGTTCAAAGAGCTGAGAAGTTTCGCAACGATCTTGTCAAAAGGGGAGTTCTTCTAGTACCTTTAGTTTGGAGCAGTGAAAGTAAAAGTAAAGGTTCTATCAGAAAGAAAGGTTTTGGAAGTTTACGGAAGCCAGCAATTTCTA
GTCTTTCATCCAGTGGTGAATTTGAGAAACGAACACAGAATATTGCTTCCAAGTCAATAGCACAAGTTGAAAAACGATTCAAGGCAGAGGTTGTTTCTTCTAATGAATGGGAAAGTTGGGTTCGTGAGCAACAAGAGTCTGAAGGAGTAACACCGGGAGAAGATGTGTATATTGTCTTGCGTTTGGATGGTCGTGTTCGA
AAATCTGGTCAGGGAATGCCTGACTGGAAAGAGTTAATTAACGAGTTGCCGCCATTAGAATCCTTTGTCAGCAAACTGGAAAAATAATACAGTTATTCAACAACCATTTAATCCCTTGTCTGTAGCTTATAAACGGGATAGGAATGTGAGTTTTATCATTAACTAACTGAGTCATTGCTGTTTGTATTTCCTCCTGCTTT
TGGTAGCTGAATAAGAGAAATACTAAAGTAAACGCTGGGATTGGAAAATATATAGGACATTTATCAAGGTGATGGTAGATTCTTCTTACAAAAGGTTTATTACATTGGAATTTCCATATTTCATCCCAAAAAACTTAAATGCAAGTATAGCTTGTAAATAGGTTAGCAAATGTCCATTTAGTTCATTGTATATAGCTTGT
AAATGGC

>TRINITY_DN113528_c0_g1_i2 from sample A1 / Example unspliced isoform:

AATCGATATTCTCATTCATGGATCGTCCTGGCCATTATTATATTTTCTAACGAGTATAGGATGGCGATGGCTACTGTGCCTGGGCAACAGTAGTCCATATCATTATCCACAAGCACTGGCGATGGCCATGGCCATTGCAAATGGCGTCATTAATATGAATGTAATACCTCAATTCTCAGCACCCACCTGCAAATTTACTA
ATGTACCTCTTGACGGAAGAAGAAAACCATTATTCAAAATCAAGTTCAACAGATGGAATTTGGAAGTACCCAAGACAATTGGGTACATTGAGAGTAAAGAATGGAGTTTGGTTGTTGCTGCCTCGACAGGAGCAGAAGCAGATACAGAGACTCCATCGATGGACACTGCAACTGCCAGGGATGCTGTCAATTTGGGGCTT
TCTCTCTTCTCGAAAGGCCAGGTAAGAGATGCCCTTGTTCAATTTGAAAAGGCACTTTCTCTAGACCCAGATCCAGAGGAAGCCGCAGCTGCTCTATACAATAAAGCCTGTTGCCATGCCTACAGAGAAGAAGGAAGAAAAACTGCAGAAGCTTTACGGAAGGCTTTGCGGGATTATGATCTTAAATTTAGTGTGATTCT
CAATGATCCAGACATGGCTCCCTTTCGGGCTATGCCTGAGTTCAAGCAACTTCAAGTAGAGgctagaatggggggtcaagacataggaagcagtttcagaagggacttgaagcttattagtgaagtccaagctcctttccgtggtgttcggagatttttctacatagctttaggtgctgctgcaggaatttcaacagttt
tcaccatacctaggctgactagtgcaattcgggggggtagtggtgctcctgatctttgggagactgctgggaatgctgcaattaacattggagGTATTATCGTACTTGTGGCACTCTTCCTCTGGGATAATAGGAAAGAAGAGGAACAAATTGCCCAAATTTCCCGGGATGAAACTCTTTCAAGGTTGCCTTTGCGCCTA
TCAACTGATCGTGTTGTAGAACTTGTGCAGTTACGGGATACAACTCGGCCTGTAATTTTGGCAGGGGCAAACGATGTGGTAAATAGAGCAGTTCAAAGAGCTGAGAAGTTTCGCAACGATCTTGTCAAAAGGGGAGTTCTTCTAGTACCTTTAGTTTGGAGCAGTGAAAGTAAAAGTAAAGGTTCTATCAGAAAGAAAGG
TTTTGGAAGTTTACGGAAGCCAGCAATTTCTAGTCTTTCATCCAGTGTAAGAAACAAAAATGTGGTGAATCATGCAATGCCAGGTTATCATTCTTCAGTTAAGGAACAGAAATGGCAACAGATTAACAATTTGCTTCCATGGCTTATTCCGAGTATTATGAACTTTTCTGTTGGTTGTTATCTTACTGCTGGTTTTAACA
TCCCTACTATTCAGACGTGGGATTTTTTAATTAGTTAGCGATTGAAACAATCACGCCCCAAAAGGAAAAAGAATACTCAGAGAAAGATTTATAGTCTTGCATGGAAGATTCACAAGTAGAAACCATTGGGCGTTTATTTCATGTTTGGGTGCTTAAAGAGTGACATTTCATGTTTGGGTATAAAGTGGGTTATTTTGCGT
CTATTTAGGTGCTGGAAGAGC