sp|P82538|PPL1_ARATH ----> PsbP-like protein 1, chloroplastic

Intron 1 GTGCATTCTC ... GTTTACGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.22	7	2	2
A2	27.78	13	8	2
A3	20	16	6	2
A4	21.74	18	7	3
A5	33.33	8	7	1
A6	17.46	52	11	11
A7	15.71	59	9	13
A8	8.86	36	4	3
A9	25.15	61	24	17
A10	23.08	45	14	13

>TRINITY_DN102200_c0_g1_i4 from sample A2 / Example spliced isoform

GGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAACATTGCAAAATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGT
TGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCACTGACAGCAAGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTTACCCTTTTGGGT
GGCAGGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGCAGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAG
CGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATGGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATTATTCGATGTATG
AAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTGCCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCC
TAATTATGTATCATTTATT

>TRINITY_DN102200_c0_g1_i3 from sample A2 / Example unspliced isoform:

GGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAACATTGCAAAATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGgtgcattctctatatgagcctacccacatactatttcatccaaaacaaaacggaat
gtcctacattgattgctacaatacattggggattcacctcaacagaagcgtctgtgggcagtggccatatcccgtgtatatgtgtagcgatttctacttcatgtcctgaatcctcctttgtttacgtagGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGTTGTGAGGGCTTCTGC
ACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCACTGACAGCAAGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTTACCCTTTTGGGTGGCAGGAAGTTGCGG
TTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGCAGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAGCGCACAGCTGAGGGC
AAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATGGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATTATTCGATGTATGAAATCACTCTCCTTC
AGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTGCCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCCTAATTATGTATCATT
TATT

Intron 2 GCCTCATCAT ... CTGCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	14.29	12	3	1
A2	33.33	3	2	1
A3	22.58	12	1	6
A4	23.08	5	3	0
A5	20	4	1	1
A6	23.81	40	13	12
A7	17.5	33	3	11
A8	21.33	59	19	13
A9	17.02	39	7	9
A10	25	24	6	10

>TRINITY_DN43876_c0_g2_i3 from sample A6 / Example spliced isoform

CAAAGATGATCTTGATCGTTAGATAAACATGATAAAAAATCATGGGGAAAGCCAAGGAAAACGAAAGGATAAGGTGACGATATTGCATCGAAGTCTCATGAGCGGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAACATTGCAAA
ATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGTTGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCACTGACAGCA
AGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTTACCCTTTTGGGTGGCAGGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGC
AGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAGCGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATG


GGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATTATTCGATGTATGAAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTGCCGATATA
GAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCCTAATTATGTATCATTTATTCACGAAGATAAATAATTTTTTGGAAATCTTATGGACTCTTGAGTACGAGTACCTCGCGAATGGTCTTGATATGTAATT
TGTAGATCTTTCAATTGCTGACATGTTTTTGAAAGCGTTCAACAAATCATTGCTATGCATATCCATGAAATGTTTGAAGGATGGGAACCCAGCCAATTTAAAATTTGGCCTTTAAACGGCAATCCCACCTCAACCGGTTCTTTATAATGATGTTAGAGGTACAACTCTACCTGGGAGCAAAATTCGAGTAACTGTTACGA
GAATGCTATTTGTTTCCATTTCATTATGTTACTAGTCTTTTTGCCAA

>TRINITY_DN43876_c0_g2_i4 from sample A6 / Example unspliced isoform:

CAAAGATGATCTTGATCGTTAGATAAACATGATAAAAAATCATGGGGAAAGCCAAGGAAAACGAAAGGATAAGGTGACGATATTGCATCGAAGTCTCATGAGCGGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAACATTGCAAA
ATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGTTGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCACTGACAGCA
AGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTTACCCTTTTGGGTGGCAGGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGC
AGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAGCGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATG


gcctcatcatcatgttttgcatgaaactgcttgcagGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATTATTCGATGTATGAAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTA
TTTCCGACAGTCTTGAAGTCAAATACTGCCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCCTAATTATGTATCATTTATTCACGAAGATAAATAATTTTTTGGAAATCTTATGGACTCTTGA
GTACGAGTACCTCGCGAATGGTCTTGATATGTAATTTGTAGATCTTTCAATTGCTGACATGTTTTTGAAAGCGTTCAACAAATCATTGCTATGCATATCCATGAAATGTTTGAAGGATGGGAACCCAGCCAATTTAAAATTTGGCCTTTAAACGGCAATCCCACCTCAACCGGTTCTTTATAATGATGTTAGAGGTACAA
CTCTACCTGGGAGCAAAATTCGAGTAACTGTTACGAGAATGCTATTTGTTTCCATTTCATTATGTTACTAGTCTTTTTGCCAA

Intron 3 GTACACAGCA ... GTATCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25	9	4	3
A2	28.57	15	0	6
A3	40	15	0	10
A4	25.93	20	0	7
A5	30	7	0	3
A6	39.91	43.7	2	29
A7	35.21	46	0	25
A8	40.68	35	0	24
A9	28.99	49	1	20
A10	30.77	36	9	16

>TRINITY_DN43876_c0_g2_i1 from sample A6 / Example spliced isoform

CAAAGATGATCTTGATCGTTAGATAAACATGATAAAAAATCATGGGGAAAGCCAAGGAAAACGAAAGGATAAGGTGACGATATTGCATCGAAGTCTCATGAGCGGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAACATTGCAAA
ATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGTTGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGGAATTCAATGTTCTGGCTGATTCCCTTTCCAAAGAGGCA

>TRINITY_DN43876_c0_g2_i5 from sample A6 / Example unspliced isoform:

CAAAGATGATCTTGATCGTTAGATAAACATGATAAAAAATCATGGGGAAAGCCAAGGAAAACGAAAGGATAAGGTGACGATATTGCATCGAAGTCTCATGAGCGGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGgtacacagcagtgcttttcagg
cggttgaagatgatgagattgccctacaattgaggggtaccgtcctagaattgaaggataacgtcctctttgtttgtgtatctgcagGCAACAATGGCAACATTGCAAAATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATT
TATCCCCTCAGTTGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCACTGACAGCAAGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTT
ACCCTTTTGGGTGGCAGGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGCAGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTA
AATGTGCAAGAGCGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATGGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATT
ATTCGATGTATGAAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTGCCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTAT
TGTTTTAACTCCTAATTATGTATCATTTATTCACGAAGATAAATAATTTTTTGGAAATCTTATGGACTCTTGAGTACGAGTACCTCGCGAATGGTCTTGATATGTAATTTGTAGATCTTTCAATTGCTGACATGTTTTTGAAAGCGTTCAACAAATCATTGCTATGCATATCCATGAAATGTTTGAAGGATGGGAACCCA
GCCAATTTAAAATTTGGCCTTTAAACGGCAATCCCACCTCAACCGGTTCTTTATAATGATGTTAGAGGTACAACTCTACCTGGGAGCAAAATTCGAGTAACTGTTACGAGAATGCTATTTGTTTCCATTTCATTATGTTACTAGTCTTTTTGCCAA

Intron 4 GTAGGTGCTG ... AAAATTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	27.5	8	1	3
A2	32.73	18.5	0	9
A3	37.38	18.5	0	11
A4	31.13	15.5	0	7
A5	18.34	4.5	0	1
A6	25.49	27	0	9
A7	27.23	51	0	19
A8	28.89	37	0	15
A9	31.46	41.5	0	19
A10	18.1	37	0	8

>TRINITY_DN104167_c0_g1_i1 from sample A1 / Example spliced isoform

GTTGATGTCAAAGATGATCTTGATCGTTAGATAAACATGATAAAAAATCATGGGGAAAGCCAAGGAAAACGAAAGGATAAGGTGACGATATTGCATCGAAGTCTCATGAGCGGATAGGCAGCTTCAGTTGCTTGTGGTGTTACCTAGTGCCTTGGTCGGACATTGCATTCGGAGAGATTTGCGCAGGCAACAATGGCAAC
ATTGCAAAATGCAACTGTCCTTCATAGAACATGGTCTTCCCTCACTCCTTGCCAGGTTCTTTTGTTCAGCCAGAGTTCTGGAGTTGCTAACAGAAGATTTATCCCCTCAGTTGTGAGGGCTTCTGCACAAGGAGACAATGTTTACCTTGCCAAACAAGGTACGACTCCACGGAGAGAGGTCTTGGCAGCAGTTGGGGCAC
TGACAGCAAGTGTTTTTTTCACAAATACTGTTTGGGCAGCACAGGCACCAAAAGGTTTCCAGGCTTTCTTGGACAAATTTGATGGATATTCATTCCTTTACCCTTTTGGGTGGCAGGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACA
AGTAAAGCAGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTCTTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAGCGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTAT
TGGAAATGGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGCTACGCACTATTGTAGATTCATTTTCATTATTCGATGTATGAAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTG
CCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATTGAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCCTAATTATGTATCATTTATTCACGAAG

>TRINITY_DN104167_c0_g1_i4 from sample A1 / Example unspliced isoform:

ACCCTTTTGGGTGGCAGgtaggtgctgcggtaaatttgtgattgattgctttgcagtttcaatgaaatgaggcaaaagtatggtggtatgcctaatcttctagaattcaaaggtttcaattaataatgtcatttgattaggtttccgagaacctagtttcttacgaaacagtttgagaatctttaaatttaatctcaaat
tcctactgatgaggagcaaacaatgatagacttttaaaatttcagGAAGTTGCGGTTAGCGGCCAGGATAAAGCCTACAAAGATGTGATTGAACCCTTAGAAAGTGTTAGCATCACTATTGTACCAACAAGTAAAGCAGATATTCATGAACTTGGACCACCGGAGCAGGTTGCCGAGACTTTAGTTAGAAAGGTTTTGTC
TTCTCCATCTCAAAAAACAAGGCTGTTAAATGTGCAAGAGCGCACAGCTGAGGGCAAGATCTATTACACTTTTGAGTTTGTCGCCCAGGCCCCAAACTACATACGACATGCCCTGGGAACTGTTGCTATTGGAAATGGGAAATTTTACACACTCACAACTGGTGCAAATGAACGGCGTTGGAGTAAAATAGAAGAAAAGC
TACGCACTATTGTAGATTCATTTTCATTATTCGATGTATGAAATCACTCTCCTTCAGCACCAGAGGCATTGTAATGCATGTCATATGCTATTGCAAGGGTATTTCCGACAGTCTTGAAGTCAAATACTGCCGATATAGAGCTTGTAGTAAGCAAAACTTTACTGGGAGCTTTTTCTTGATCCCTGTAAAAGGGTCTGATT
GAGACAAGGATATGGCAGAAGTAGTTATTGTTTTAACTCCTAATTATGTATCATTTATTCACGAAG