sp|O22609|DEGP1_ARATH ----> Protease Do-like 1, chloroplastic

Intron 1 GTAAGTAGAT ... GTTGCGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	59.09	9	6	20
A2	53.62	16	10	27
A3	54.17	11	11	15
A4	63.64	8	6	22
A5	40	3	1	3
A6	34.88	28	11	19
A7	52.69	22	26	23
A8	54.1	14	13	20
A9	57.89	20	22	33
A10	41.46	24	16	18

>TRINITY_DN40101_c0_g1_i6 from sample A10 / Example spliced isoform

CCCAATTAGCAATAGAATACGGATTCAATTTTCCTTTATCTCCCATGATGCTTATGAAATGTGAGGACCAAACCAAAGCCGAAGTTCCTATTCTGACCAGATTGCAGTGTATTACACGTTTCAAATCTCCCCAAAAACGACAAAAAGAGCAAAGCATTATTGAAGAACAAGTTATCCTACTGCATTTGATGGTTTTGAAA
ATTGATGATGCCAATGCCTATGTGGTAACCCCACGCAAAAAGCTACAAACGGATGAGTTAACTACTGTCAATCTCTTCAGAGACAATACTCCATCAGTAGTTTATATCACCAATCTTGCTGTCAGGCAAGATGCATTTACATTGGATGTTTTACAGGTTCCTCAAGGTTCTGGATCTGGATTTATTTGGGATAATAAAGG
ATATATTGTGACAAACTACCATGTCATTCGAGGTGCCTCCGATTTAAGGGTGACACTTGGTGACCAATCAGTATATGAAGCAAAGGTGATTGGATATGATCAAGATAAAGATGTTGCAGTTTTAAGCATTGATGCCCCAAAAGACAAATTGAGGCCTGTACCTGTTGGAAACTCAAGAGACCTTTTGGTAGGCCAGAAAG
TGTACGCCATTGGAAATCCTTTTGGCCTTGACCACACTTTGACAACTGGTGTTATCAGTGGACTTGGACGGGAGATTAATTCAGCTGCAACTGGCCGTCCAATACAAGATGTAATACAAACAGATGCAGCCATAAATCCTGGGAATAGTGGAGGTCCTTTACTAGACAGTTCTGGATTTTTGATAGGCATAAACACTGCT
ATCTACTCTCCCTCAGGAGCATCAGCTGGAGTTGGCTTTTCCATTCCAGTAGATACTGTAAGTAGCATTGTCGATCAGTTGGTTAAGTATGGAAAAATTACACGACCTGTACTAGGCATCAGGTTTGCACCAGATCAATCGGTTGAGCAATTAGGTGTTACTGGAGTGCTTGTGCTAGATGCCTCTCCAGATGGGCCAGC
CGACAAAGCAGGTCTACGGCCAACTAAACGAGATGCTTATGGTCGCCTTATTTTGGGGGATATCATTACAACTGTAAACGGTCAGAAAGTTAGCAATGGGAGTGATCTCTATAAAATTCTTGACCGTTGTAAAGTAGGAGATAAGGTCATGGTCGAGGTTTTACGTGGAGATCAGAAGGAAAATGTCTTGGTGACTCTTG
AACCAAAATCTTAGAGACATATAGGCGAAGATGTTAAACTGAAGTTACGCTGTGTAAAATAGAACATATTCCAATATTATTTGTGTATTCTTATTTAAAAATGTGTATAGTAAGCTTCAAAATTGTAATACAATTTCTATCCCATCTGTTAATAATTACAAATTCAATGCTGTGTTTCTCAAGAGCTTTCTCTACTAGAT
TCTCTCTACTGGGAGGTGGATTTCATGAGCTATATATAATATATTTTGTAATAATGGAAGGCATGGTAGAATTCTTACTTAGGTGCATAAAATAGAGTTTTACTAATCAAACGTTTGAACAAATTTGATTTTGACTTTGTATCAACTTTTACAAGTCAGAACATCTATGGCTGTGTTAAATTGCATTATATTGTCAAATA
TAA

>TRINITY_DN40101_c0_g1_i5 from sample A10 / Example unspliced isoform:

CCCAATTAGCAATAGAATACGGATTCAATTTTCCTTTATCTCCCATGATGCTTATGAAATGTGAGGACCAAACCAAAGCCGAAGTTCCTATTCTGACCAGATTGCAGTGTATTACACGTTTCAAATCTCCCCAAAAACGACAAAAAGAGCAAAGCATTATTGAAGAACAAGTTATCCTACTGCATTTGATGGTTTgtaag
tagattatttaaggattttccgaatattaatccatgtagaccaatctcccacttctttctcactagtgggaataactcgagtccgtcatgccaatggctctagttgcccaactgaaatttccaattaagtttctacaatttcctccacaacctcaatcccaaatcccttctaacggtagacccaattgcataataactgc
tccaaaccttctgctgaacaacagactgttagccattcagagagaacccaatgctcaatctattgataaagtgatactgccaaacgttcgagtcctgatattgcaaagatgtttctctgttgttcagaagttattcaattgcccagagaaaaattacattcaatcgaatttttggttatggtttgcttctttgtcagtaa
tgatttctgttgcgacagTGAAAATTGATGATGCCAATGCCTATGTGGTAACCCCACGCAAAAAGCTACAAACGGATGAGTTAACTACTGTCAATCTCTTCAGAGACAATACTCCATCAGTAGTTTATATCACCAATCTTGCTGTCAGGCAAGATGCATTTACATTGGATGTTTTACAGGTTCCTCAAGGTTCTGGATCT
GGATTTATTTGGGATAATAAAGGATATATTGTGACAAACTACCATGTCATTCGAGGTGCCTCCGATTTAAGGGTGACACTTGGTGACCAATCAGTATATGAAGCAAAGGTGATTGGATATGATCAAGATAAAGATGTTGCAGTTTTAAGCATTGATGCCCCAAAAGACAAATTGAGGCCTGTACCTGTTGGAAACTCAAG
AGACCTTTTGGTAGGCCAGAAAGTGTACGCCATTGGAAATCCTTTTGGCCTTGACCACACTTTGACAACTGGTGTTATCAGTGGACTTGGACGGGAGATTAATTCAGCTGCAACTGGCCGTCCAATACAAGATGTAATACAAACAGATGCAGCCATAAATCCTGGGAATAGTGGAGGTCCTTTACTAGACAGTTCTGGAT
TTTTGATAGGCATAAACACTGCTATCTACTCTCCCTCAGGAGCATCAGCTGGAGTTGGCTTTTCCATTCCAGTAGATACTGTAAGTAGCATTGTCGATCAGTTGGTTAAGTATGGAAAAATTACACGACCTGTACTAGGCATCAGGTTTGCACCAGATCAATCGGTTGAGCAATTAGGTGTTACTGGAGTGCTTGTGCTA
GATGCCTCTCCAGATGGGCCAGCCGACAAAGCAGGTCTACGGCCAACTAAACGAGATGCTTATGGTCGCCTTATTTTGGGGGATATCATTACAACTGTAAACGGTCAGAAAGTTAGCAATGGGAGTGATCTCTATAAAATTCTTGACCGTTGTAAAGTAGGAGATAAGGTCATGGTCGAGGTTTTACGTGGAGATCAGAA
GGAAAATGTCTTGGTGACTCTTGAACCAAAATCTTAGAGACATATAGGCGAAGATGTTAAACTGAAGTTACGCTGTGTAAAATAGAACATATTCCAATATTATTTGTGTATTCTTATTTAAAAATGTGTATAGTAAGCTTCAAAATTGTAATACAATTTCTATCCCATCTGTTAATAATTACAAATTCAATGCTGTGTTT
CTCAAGAGCTTTCTCTACTAGATTCTCTCTACTGGGAGGTGGATTTCATGAGCTATATATAATATATTTTGTAATAATGGAAGGCATGGTAGAATTCTTACTTAGGTGCATAAAATAGAGTTTTACTAATCAAACGTTTGAACAAATTTGATTTTGACTTTGTATCAACTTTTACAAGTCAGAACATCTATGGCTGTGTT
AAATTGCATTATATTGTCAAATATAA

Intron 2 GTTTGTAAGT ... GTTGCGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	58.14	9	5	20
A2	55.22	15	10	27
A3	54.17	11	11	15
A4	63.64	8	6	22
A5	45.45	3	2	3
A6	33.33	28	9	19
A7	52.69	22	26	23
A8	51.72	14	10	20
A9	58.7	19	21	33
A10	42.5	23	16	18

>TRINITY_DN85743_c1_g1_i1 from sample A4 / Example spliced isoform

ACGGATTCAATTTTCCTTTATCTCCCATTATGCTTATGAAATGTGAGGACCAAACCAAAGCCGAAGTTCCTATTCTGACCAGATTGCAGTGTATTACACGTTTCAAATCTCCCCAAAAACGACAAAAAGAGCAAAGCATTATTGAAGAACAAGTTATCCTACTGCATTTGATGTGAAAATTGATGATGCCAATGCCTATG
TGGTAACCCCACGCAAAAAGCTACAAACGGATGAGTTAACTACTGTCAATCTCTTCAGAGACAATACTCCATCAGTAGTTTATATCACCAATCTTGCTGTCAGGCAAGATGCATTTACATTGGATGTTTTACAGGTTCCTCAAGGTTCTGGATCTGGATTTATTTGGGATAATAAAGGATATATTGTGACAAACTACCAT
GTCATTCGAGGTGCCTCCGATTTAAGGGTGACACTTGGTGACCAATCAGTATATGAAGCAAAGGTGATTGGATATGATCAAGATAAAGATGTTGCAGTTTTAAGCATTGATGCCCCAAAAGACAAATTGAGGCCTGTACCTGTTGGAAACTCAAGAGACCTTTTGGTAGGCCAGAAAGTGTACGCCATTGGAAATCCTTT
TGGCCTTGACCACACTTTGACAACTGGTGTTATCAGTGGACTTGGACGGGAGATTAATTCAGCTGCAACTGGCCGTCCAATACAAGATGTAATACAAACAGATGCAGCCATAAATCCTGGGAATAGTGGAGGTCCTTTACTAGACAGTTCTGGATTTTTGATAGGCATAAACACTGCTATCTACTCTCCCTCAGGAGCAT
CAGCTGGAGTTGGCTTTTCCATTCCAGTAGATACTGTAAGTAGCATTGTCGATCAGTTGGTTAAGTATGGAAAAATTACACGACCTGTACTAGGCATCAGGTTTGCACCAGATCAATCGGTTGAGCAATTAGGTGTTACTGGAGTGCTTGTGCTAGATGCCTCTCCAGATGGGCCAGCCGACAAAGCAGGTCTACGGCCA
ACTAAACGAGATGCTTATGGTCGCCTTATTTTGGGGGATATCATTACAACTGTAAACGGTCAGAAAGTTAGCAATGGGAGTGATCTCTATAAAATTCTTGACCGTTGTAAAGTAGGAGATAAGGTCATGGTCGAGGTTTTACGTGGAGATCAGAAGGAAAATGTCTTGGTGACTCTTGAACCAAAATCTTAGATACATAT
AGGCGAAGATGTTAAACTGAAGTTACGCTGTGTAAAATAGAACATATTCCAATATTATTTGTGTATTCTTATTTAAAAATGTGTATAGTAAGCTTCAAAATTGTAATACAATTTCTATCCCAT

>TRINITY_DN85743_c1_g1_i3 from sample A4 / Example unspliced isoform:

ACGGATTCAATTTTCCTTTATCTCCCATTATGCTTATGAAATGTGAGGACCAAACCAAAGCCGAAGTTCCTATTCTGACCAGATTGCAGTGTATTACACGTTTCAAATCTCCCCAAAAACGACAAAAAGAGCAAAGCATTATTGAAGAACAAGTTATCCTACTGCATTTGATGgtttgtaagtagattatttaaggattt
tccgaatattaatccatgtagaccaatctcccacttctttctcactagtgggaataactcgagtccgtcatgccaatggctctagttgcccaactgaaatttccaattaagtttctacaatttcctccacaacctcaatcccaaatcccttctaacggtagacccaattgcataataactgctccaaaccttctgctgaa
caacagactgttagccattcagagagaacccaatgctcaatctattgataaagtgatactgccaaacgttcgagtcctgatattgcaaagatgtttctctgttgttcagaagttattcaattgcccagagaaaaattacattcaatcgaatttttggttatggtttgcttctttgtcagtaatgatttctgttgcgacag


TGAAAATTGATGATGCCAATGCCTATGTGGTAACCCCACGCAAAAAGCTACAAACGGATGAGTTAACTACTGTCAATCTCTTCAGAGACAATACTCCATCAGTAGTTTATATCACCAATCTTGCTGTCAGGCAAGATGCATTTACATTGGATGTTTTACAGGTTCCTCAAGGTTCTGGATCTGGATTTATTTGGGATAAT
AAAGGATATATTGTGACAAACTACCATGTCATTCGAGGTGCCTCCGATTTAAGGGTGACACTTGGTGACCAATCAGTATATGAAGCAAAGGTGATTGGATATGATCAAGATAAAGATGTTGCAGTTTTAAGCATTGATGCCCCAAAAGACAAATTGAGGCCTGTACCTGTTGGAAACTCAAGAGACCTTTTGGTAGGCCA
GAAAGTGTACGCCATTGGAAATCCTTTTGGCCTTGACCACACTTTGACAACTGGTGTTATCAGTGGACTTGGACGGGAGATTAATTCAGCTGCAACTGGCCGTCCAATACAAGATGTAATACAAACAGATGCAGCCATAAATCCTGGGAATAGTGGAGGTCCTTTACTAGACAGTTCTGGATTTTTGATAGGCATAAACA
CTGCTATCTACTCTCCCTCAGGAGCATCAGCTGGAGTTGGCTTTTCCATTCCAGTAGATACTGTAAGTAGCATTGTCGATCAGTTGGTTAAGTATGGAAAAATTACACGACCTGTACTAGGCATCAGGTTTGCACCAGATCAATCGGTTGAGCAATTAGGTGTTACTGGAGTGCTTGTGCTAGATGCCTCTCCAGATGGG
CCAGCCGACAAAGCAGGTCTACGGCCAACTAAACGAGATGCTTATGGTCGCCTTATTTTGGGGGATATCATTACAACTGTAAACGGTCAGAAAGTTAGCAATGGGAGTGATCTCTATAAAATTCTTGACCGTTGTAAAGTAGGAGATAAGGTCATGGTCGAGGTTTTACGTGGAGATCAGAAGGAAAATGTCTTGGTGAC
TCTTGAACCAAAATCTTAGATACATATAGGCGAAGATGTTAAACTGAAGTTACGCTGTGTAAAATAGAACATATTCCAATATTATTTGTGTATTCTTATTTAAAAATGTGTATAGTAAGCTTCAAAATTGTAATACAATTTCTATCCCAT