sp|Q9FNG8|PP366_ARATH ----> Putative pentatricopeptide repeat-containing protein At5g06400, mitochondrial

Intron 1 GTACGAGTTT ... AAATCCACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	68.83	15	30.3	36
A2	63.08	12	28	13
A3	65.12	15	24	32
A4	43.66	20	15	16
A5	65.52	5	12	7
A6	46.22	35.5	29	32
A7	67	25	53.5	48
A8	56.43	29.3	25.8	50
A9	64.82	26.8	40.5	58
A10	57.89	32	51	37

>TRINITY_DN100538_c1_g4_i4 from sample A4 / Example spliced isoform

TTTTTGGGAACGGTGTTTATAAAGGTTTTGAGTTATTAAGAGTAATAGAATATCCATCTTTCATTGAATAAATACTATTCATTCCTATTTCATTGAATAACCTTAAGATTCATCCTTGACCTAATTTGCTCACATAAAACTCAACATAGAGAGCATAGTTTTCCTCTTTACGAGTATCTTTTTTCCATCTACAAAATCCT
TGGGATGAAATTTTGGAAGGACATCGAGATGGATTCATTGCACTAGCTAATATAATTATGATGTGAAGCATAGCATAACCCTATCATAGGAAAAGCCCTCTCCTGTAGCTTCAATCTTTTCGATTGCTTCCTACACCACTGAAAAATCCTAAACCAGAACTCCTTGCAATGCAGGTCGTGGCTTATGTGCCTCGATCAGG
ACTGGCCTTTGTCGGGCGAGTGTTTTCAGCAACCCAGCTGCGCCATCAAAACTGGAGCTCTGTAACATCGCAATGGCACCGCAATTCGGACTCCAGCGCCTTGAAAATCTTCCAAAACGATCGTAATAATGGTGTTGGTATTGGATCGAACAGTTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCACACTACAA
CCCGGGTTCAAACATAACATTCCAACTTATGATGCGCTTACCAGAAATATCGCCCGTTCTAAGGACTTCAACACTCTGCAGATGGTTTTCTCAGAGAGATTGGGTGCACACGTCGATGTTTCTGTGAGAACATTCAGGTTCGCCACCGACTGGCATGATGATCCCAACTTGCTCAATGAAGTCATACGAATCATCGAGAA
GATGCCATTTTCCACCAGAAAACGCTCTTACAATTTGCTGATTAGGGCTCTTTGTCCAAAGAATGTCAATGCAGCCTTAAGTGTATTGGAAAAGATGGTGATTGCTGATTGTGCTCCGGAAAGTATCACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATAAACAAATGGATAATCTACAGGAGATTTATGAAACGA
TGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGGGTAAACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGATTCAGGTAACTATGAATATTTGAT
TAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAGGAGATTTATGAAACGATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGG
GTAAACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGAGTCAGGTAACTATGAATATTTGATTAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAAGCTAAGCCCCAGCTCAGTATTATCATGCCCCCACCTGAAGATGGGGAGCTGTCAAACTTGGTCAATGTATACATTG
TTTTAGGGAATGCTCACTGGGGTTTGAACCTGGGTCAGTTGCATGGTTATGCACTGTCTCAACCACGAGACCACAATCCGATAGACATACACATTCATCATTGTTATCCTAATATATTCAGCCGAGTTTACTGGAAGCTTGTCAGGTCATTGCAGGTATGAACCAAAGGGTTCTCTCACCAAGTTAATTTTTGATGCATT
TAGACTGGTTACCGAATGCAAGTTGCATGAAGGCGTTTAGCCTAATGGTAATTTTCATTGAAGCTTGAAAGGAAATAGTTCCTTGATTTCACCTCAAGTGCATGAATACTTATGGTTAGCTGTTTCTGCATCATGCAAGTCATGCAGAAATGTGAACATACAGATATAGATGATTTGAATGCTGAACAAGACAAGTTTTG
TCCTGTTTTCAAATGTTTTATCTGACAACATATTATTGTGGCTATAATGCTGTCTCAAGAATTTCATCACGAAACATGTGAGAACTGAGAAGTAGAATAAGGGTGGTGGTGCTTAAAAAGGGGACGA

>TRINITY_DN100538_c1_g4_i1 from sample A4 / Example unspliced isoform:

TTTTTGGGAACGGTGTTTATAAAGGTTTTGAGTTATTAAGAGTAATAGAATATCCATCTTTCATTGAATAAATACTATTCATTCCTATTTCATTGAATAACCTTAAGATTCATCCTTGACCTAATTTGCTCACATAAAACTCAACATAGAGAGCATAGTTTTCCTCTTTACGAGTATCTTTTTTCCATCTACAAAATCCT
TGGGATGAAATTTTGGAAGGACATCGAGATGGATTCATTGCACTAGCTAATATAATTATGATGTGAAGCATAGCATAACCCTATCATAGGAAAAGCCCTCTCCTGTAGCTTCAATCTTTTCGATTGCTTCCTACACCACTGAAAAATCCTAAACCAGAACTCCTTGCAATGCAGGTCGTGGCTTATGTGCCTCGATCAGG
ACTGGCCTTTGTCGGGCGAGTGTTTTCAGCAACCCAGCTGCGCCATCAAAACTGGAGCTCTGTAACATCGCAATGGCACCGCAATTCGGACTCCAGCGCCTTGAAAATCTTCCAAAACGgtacgagttttctcccttttcatgaactcattttcggccataaattttactcaacgaatgcatctgccacggttcaaatct
ctgagaaaactcagtcagcatctgacaaggaggaaagccccgaatcgcaagccctgaacagcaaaaaacaggcagatagcttgcctaactcgaacaaatctaacaaaccaaacaaaccgaataaaccgaacaaacccttgcccaactggacgatgatgggacttaaacgagcaatatgtaaagttcttgaaaagggcggc
aacgatatggaagaaaccctaactaaattgggtttttggctaaatccacagATCGTAATAATGGTGTTGGTATTGGATCGAACAGTTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCACACTACAACCCGGGTTCAAACATAACATTCCAACTTATGATGCGCTTACCAGAAATATCGCCCGTTCTAAGGACTT
CAACACTCTGCAGATGGTTTTCTCAGAGAGATTGGGTGCACACGTCGATGTTTCTGTGAGAACATTCAGGTTCGCCACCGACTGGCATGATGATCCCAACTTGCTCAATGAAGTCATACGAATCATCGAGAAGATGCCATTTTCCACCAGAAAACGCTCTTACAATTTGCTGATTAGGGCTCTTTGTCCAAAGAATGTCA
ATGCAGCCTTAAGTGTATTGGAAAAGATGGTGATTGCTGATTGTGCTCCGGAAAGTATCACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATAAACAAATGGATAATCTACAGGAGATTTATGAAACGATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAA
CTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGGGTAAACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGATTCAGGTAACTATGAATATTTGATTAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAGGAGATTTATGAAAC
GATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGGGTAAACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGAGTCAGGTAACTATGAATATTTG
ATTAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAAGCTAAGCCCCAGCTCAGTATTATCATGCCCCCACCTGAAGATGGGGAGCTGTCAAACTTGGTCAATGTATACATTGTTTTAGGGAATGCTCACTGGGGTTTGAACCTGGGTCAGTTGCATGGTTATGCACTGTCTCAACCACGA
GACCACAATCCGATAGACATACACATTCATCATTGTTATCCTAATATATTCAGCCGAGTTTACTGGAAGCTTGTCAGGTCATTGCAGGTATGAACCAAAGGGTTCTCTCACCAAGTTAATTTTTGATGCATTTAGACTGGTTACCGAATGCAAGTTGCATGAAGGCGTTTAGCCTAATGGTAATTTTCATTGAAGCTTGA
AAGGAAATAGTTCCTTGATTTCACCTCAAGTGCATGAATACTTATGGTTAGCTGTTTCTGCATCATGCAAGTCATGCAGAAATGTGAACATACAGATATAGATGATTTGAATGCTGAACAAGACAAGTTTTGTCCTGTTTTCAAATGTTTTATCTGACAACATATTATTGTGGCTATAATGCTGTCTCAAGAATTTCATC
ACGAAACATGTGAGAACTGAGAAGTAGAATAAGGGTGGTGGTGCTTAAAAAGGGGACGA

Intron 2 GTTATGATGT ... TGCGATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	3	14
A2	70.37	4	7	12
A3	100	0	4	17
A4	66.67	3	2	10
A5	100	0	0	2
A6	77.78	2	2	12
A7	80.33	6	16	33
A8	79.66	6	12	35
A9	81.25	3	8	18
A10	77.08	11	21	53

>TRINITY_DN47424_c0_g1_i9 from sample A10 / Example spliced isoform

CGAGCATATGTAGCATAGGGCATAACCCACTATAACAAATAATAATAATAATAACCAGACAGTATCAATGAAGAGCATATGGGACAGCAATCAAACAGATCTGCCCAATAGACAATTAGCAACAGAGAAATATATCAGACTATCAACAGATAACTTGCTAATAGAGTCGTGTCTCGTGTACCTCGATCAGGACTGGCCTT
CATCAGGCGAGTGTTTTCGGCAACTCCGCTGCTGCATCAAAACTGGAGCTCTGTAACATCTCAATGGCATCGAAATTCGGGCTCCAGGGCCCTGAAAATCTTCCAAAACGGTAAGAGTTTTCTCCCTTTTAATGAATTCATTTTCAACCATAATTTTACTCAACAAATGCATCTGCCACAGTTCAAATCTCCGAGAAAAC
TCAATCAGCATCAGACGAGGAGGAAAGTCCTGAATCCCAAGCGCTGAACAGCGAAAAACAGGCAGATCGCTTGCCTTATTCGAACAAACCTAACAAATCCTTACCAAAAAAGGACTGGAATAGGGTTATTAAACGAGAAATATGCCAAGTTCTTGAAAAGGACAACAACGACATGGAAGAAACCCTAACTAAATTGGGTT
TTCAGTTATCTCGGCAGATAGTAATAATGGTATTGAATCAAACAAGTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCAAACTACAACCCGGGTTCAAACATGGCGCTGCAACTTATAATGCGCTTACCACGATTCTCGCCCGTTCCAGGGACTTGAACTCTATCCAGATGGTTTTCTCAGAGAGATTGGATGCA
CAAGTCGATGTTTCGGCGTCAACATTCAGTTTCGCCACCGCCTGGCATGATGATCCCGACTTGCTCAATGAAGTCATACGAATCATCGAGAAGATGCCATTTCCCAGCAGAGGACGCGCTTACAATTTCCTTATTAGGGTTCTTTGTAGACAGAATGCCAATGCAGCCTTAAGGGTATTGGAAAAGATGGTGATTGCTGG
TTGTGCTCCGAATATAAAAACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATATCCAAATGGATAAGGTACAGGAGATTTATGAGACGATGGAGATTTTCGGCTGCCCACCGGTAGCGTTCGTTTGTGGTGGTTTGGATGCAAAACCAAGGCCTTGCGGCCTCCTTACCGTGGTAGATGATCATTTGACTATTCTGA
ATGCCCAAATTCGTGTTATTAGGAGTGTGAATTATGATATTAAACAGGCACTGCAGCATCTGAGTGCCTTGGAGCAGACAACTCGTCTGGAGGCTCGTAACAGCAACATCAACCTCAGCGCGAAAGTGGATAGTCTCTCCGCTGGTCTGGACAGTGGTCCTTGTTCAAATTTGGAGGCCCAAATCAGGGCGGTTCGTGTC
ATTATAAAAAGAATTGAGGGCAAGGTCGAAAGTATGCGCAATGAGTTAATGGCATTGAAGATGGAGATGCTGAACCCAGGTGGAGAAGCTGGAAGCAAGGAAGCAGCGTTTCGGATTTAGCAAGCAAACACGGTGCTTTTGACTGTGTCTTTTTTGGGTTTCCTTTCTGTATAGACTGTGTCTTTTTTGGGTCACTCCGT
CTTTAAGAAGTTGTGTAATTTGCCTAAATTTATATGGGAGTTTCGGTCTGAACCCTCTTGCTAGGACATCGGCATTCTGTATAAGCATAAGTCTGTAGTATTTCTAGAAGCTCAAAGTGAACTCATTTCCCTCCTAGGTTTCTTTTTTGTCGAAGTAGATGTTGAATTGTAAAAGATGATAGTTAAGACATGGTAGCTCT
CCACTCTCAAGAAGCAGGCCTGCTCTGACATTGTGCAACTCTGTTTCTGCTATCTTTTTATATATAAAAAAAAATTCTTATCCGTTTTTGTTAAAAAAAAATGATTTGTGAAGACTTCAC

>TRINITY_DN47424_c0_g1_i6 from sample A10 / Example unspliced isoform:

CGAGCATATGTAGCATAGGGCATAACCCACTATAACAAATAATAATAATAATAACCAGACAGTATCAATGAAGAGCATATGGGACAGCAATCAAACAGATCTGCCCAATAGACAATTAGCAACAGAGAAATATATCAGACTATCAACAGATAACTTGCTAATAGAgttatgatgtgaatcttagcataaccctggcataa
gaaaaacccctgctcctctagtttccattttttcgattgctttcctacactactgaaaagtcctaaaccagaactctttgcgatgcagGTCGTGTCTCGTGTACCTCGATCAGGACTGGCCTTCATCAGGCGAGTGTTTTCGGCAACTCCGCTGCTGCATCAAAACTGGAGCTCTGTAACATCTCAATGGCATCGAAATT
CGGGCTCCAGGGCCCTGAAAATCTTCCAAAACGGTAAGAGTTTTCTCCCTTTTAATGAATTCATTTTCAACCATAATTTTACTCAACAAATGCATCTGCCACAGTTCAAATCTCCGAGAAAACTCAATCAGCATCAGACGAGGAGGAAAGTCCTGAATCCCAAGCGCTGAACAGCGAAAAACAGGCAGATCGCTTGCCTT
ATTCGAACAAACCTAACAAATCCTTACCAAAAAAGGACTGGAATAGGGTTATTAAACGAGAAATATGCCAAGTTCTTGAAAAGGACAACAACGACATGGAAGAAACCCTAACTAAATTGGGTTTTCAGTTATCTCGGCAGATAGTAATAATGGTATTGAATCAAACAAGTTCTCCAATCTTAGCTCGGAGGTTTTTTCAA
TGGGCCAAACTACAACCCGGGTTCAAACATGGCGCTGCAACTTATAATGCGCTTACCACGATTCTCGCCCGTTCCAGGGACTTGAACTCTATCCAGATGGTTTTCTCAGAGAGATTGGATGCACAAGTCGATGTTTCGGCGTCAACATTCAGTTTCGCCACCGCCTGGCATGATGATCCCGACTTGCTCAATGAAGTCAT
ACGAATCATCGAGAAGATGCCATTTCCCAGCAGAGGACGCGCTTACAATTTCCTTATTAGGGTTCTTTGTAGACAGAATGCCAATGCAGCCTTAAGGGTATTGGAAAAGATGGTGATTGCTGGTTGTGCTCCGAATATAAAAACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATATCCAAATGGATAAGGTACAGG
AGATTTATGAGACGATGGAGATTTTCGGCTGCCCACCGGTAGCGTTCGTTTGTGGTGGTTTGGATGCAAAACCAAGGCCTTGCGGCCTCCTTACCGTGGTAGATGATCATTTGACTATTCTGAATGCCCAAATTCGTGTTATTAGGAGTGTGAATTATGATATTAAACAGGCACTGCAGCATCTGAGTGCCTTGGAGCAG
ACAACTCGTCTGGAGGCTCGTAACAGCAACATCAACCTCAGCGCGAAAGTGGATAGTCTCTCCGCTGGTCTGGACAGTGGTCCTTGTTCAAATTTGGAGGCCCAAATCAGGGCGGTTCGTGTCATTATAAAAAGAATTGAGGGCAAGGTCGAAAGTATGCGCAATGAGTTAATGGCATTGAAGATGGAGATGCTGAACCC
AGGTGGAGAAGCTGGAAGCAAGGAAGCAGCGTTTCGGATTTAGCAAGCAAACACGGTGCTTTTGACTGTGTCTTTTTTGGGTTTCCTTTCTGTATAGACTGTGTCTTTTTTGGGTCACTCCGTCTTTAAGAAGTTGTGTAATTTGCCTAAATTTATATGGGAGTTTCGGTCTGAACCCTCTTGCTAGGACATCGGCATTC
TGTATAAGCATAAGTCTGTAGTATTTCTAGAAGCTCAAAGTGAACTCATTTCCCTCCTAGGTTTCTTTTTTGTCGAAGTAGATGTTGAATTGTAAAAGATGATAGTTAAGACATGGTAGCTCTCCACTCTCAAGAAGCAGGCCTGCTCTGACATTGTGCAACTCTGTTTCTGCTATCTTTTTATATATAAAAAAAAATTC
TTATCCGTTTTTGTTAAAAAAAAATGATTTGTGAAGACTTCAC

Intron 3 GTAAGAGTTT ... TCTGCCACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	82.76	5	22	26
A2	49.15	15	15	14
A3	68.51	9	21.2	18
A4	41.18	5	4	3
A5	48.39	8	4	11
A6	56.76	16	20	22
A7	68.32	16	37	32
A8	68.64	11	22.2	26
A9	65.6	13	23.6	26
A10	53.22	40	50	41

>TRINITY_DN40683_c2_g1_i1 from sample A9 / Example spliced isoform

TAATAATAACCAGACAGTATCAATGAAGAGCATATGGGACAGCAATCAAACAGATCTGCCCAATAGACAATTAGCAACAGAGAAATATATCAGACTATCAACAGATAACTTGCTAATAGAGTTATGATGTGAATCTTAGCATAACCCTGGCATAAGAAAAACCCCTGCTCCTCTAGTTTCCATTTTTTCGATTGCTTTCC
TACACTACTGAAAAGTCCTAAACCAGAACTCTTTGCGATGCAGGTCGTGTCTCGTGTACCTCGATCAGGACTGGCCTTCATCAGGCGAGTGTTTTCGGCAACTCCGCTGCTGCATCAAAACTGGAGCTCTGTAACATCTCAATGGCATCGAAATTCGGGCTCCAGGGCCCTGAAAATCTTCCAAAACGTTCAAATCTCCG
AGAAAACTCAATCAGCATCAGACGAGGAGGAAAGTCCTGAATCCCAAGCGCTGAACAGCGAAAAACAGGCAGATCGCTTGCCTTATTCGAACAAACCTAACAAATCCTTACCAAAAAAGGACTGGAATAGGGTTATTAAACGAGAAATATGCCAAGTTCTTGAAAAGGACAACAACGACATGGAAGAAACCCTAACTAAA
TTGGGGTTTCAGTTATCTCGGCAGATAGTAATAATGGTATTGAATCAAACAAGTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCAAACTACAACCCGGGTTCACACATAGCGCTGCAACTTATAATGCGCTTACCACGATTCTCGCCCGTTCTAGGGACTTGAATTCTATCCAGATGGTTTTCTCAGAGAGATT
GGATGCACAAGTCGATATTTCGGCGTCAACATTCAGTTTCGCCACCGCCTGGCATGATGATCCCGACTTGCTCAATGAAGTCACACGAATCATCGAGAAGATGCCATTTCCCAGTAGAGGACGCGCTTACAATTTCCTTATTAGGGTTCTTTGTAGACAGAATGCCAATGCAGCCTTAAGGGTATTGGAAAAGATGGTGA
TTGCTGGTTGTGCTCCGAATATAAAAACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATATCCAAATGGATAAGGTACAGGAGATTTATGAGACGATGGAGATTTTCGGCTGCCCACCGGTAGCGTTCGTTTGTGGTGGTTTGGATGCAAAACCAAGGCCTTGCGGCCTCCTTACCGTGGTAGATGATCATTTGACT
ATTCTGAATGCCCAAATTCGTGTTATTAGGAGTGTGAATTATGATATTAAACAGGCACTGCAGCATCTGAGTGCCTTGGAGCAGACAACTCGTCTGGAGGCTCGTAACAGCAACATCAACCTCAGCGCGAAAGTGGATAGTCTCTCCGCTGGTCTGGACAGTGGTCCTTGTTCAAATTTGGAGGCCCAAATCAGGGCGGT
TCGTGTCATTATAAAAAGAATTGAGGGCAAGGTCGAAAGTATGCGCAATGAGTTAATGGCATTGAAGATGGAGATGCTGAACCCAGGTGGAGAAGCTGGAAGCAAGGAAGCAGCGTTTCGGATTTAGCAAGCAAACACGGTGCTTTTGACTGTGTCTTTTTTGGGTTTCCTTTCTGTATAGACTGTGTCTTTTTTGGGTC
ACTCCGTCTTTAAGAAGTTGTGTAATTTGCCTAAATTTATATGGGAGTTTCGGTCTGAACCCTCTTGCTAGGACATCGGCATTCTGTATAAGCATAAGTCTGTAGTATTTCTAGAAGCTCAAAGTGAACTCATTTCCCTCCTAGGTTTCTTTTTTGTCGAAGTAGATGTTGAATTGTAAAAGATGATAGTTAAGACATGG
TAGCTCTCCACTCTCAAGAAGCAGGCCTGCTCTGACATTGTGCAACTCTGTTTCTGCTATCTTTTTATATATAAAAAAAAATTCTTATCCGC

>TRINITY_DN40683_c2_g1_i3 from sample A9 / Example unspliced isoform:

TAATAATAACCAGACAGTATCAATGAAGAGCATATGGGACAGCAATCAAACAGATCTGCCCAATAGACAATTAGCAACAGAGAAATATATCAGACTATCAACAGATAACTTGCTAATAGAGTTATGATGTGAATCTTAGCATAACCCTGGCATAAGAAAAACCCCTGCTCCTCTAGTTTCCATTTTTTCGATTGCTTTCC
TACACTACTGAAAAGTCCTAAACCAGAACTCTTTGCGATGCAGGTCGTGTCTCGTGTACCTCGATCAGGACTGGCCTTCATCAGGCGAGTGTTTTCGGCAACTCCGCTGCTGCATCAAAACTGGAGCTCTGTAACATCTCAATGGCATCGAAATTCGGGCTCCAGGGCCCTGAAAATCTTCCAAAACGgtaagagttttc
tcccttttaatgaattcattttcaaccataattttactcaacaaatgcatctgccacagTTCAAATCTCCGAGAAAACTCAATCAGCATCAGACGAGGAGGAAAGTCCTGAATCCCAAGCGCTGAACAGCGAAAAACAGGCAGATCGCTTGCCTTATTCGAACAAACCTAACAAATCCTTACCAAAAAAGGACTGGAATA
GGGTTATTAAACGAGAAATATGCCAAGTTCTTGAAAAGGACAACAACGACATGGAAGAAACCCTAACTAAATTGGGGTTTCAGTTATCTCGGCAGATAGTAATAATGGTATTGAATCAAACAAGTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCAAACTACAACCCGGGTTCACACATAGCGCTGCAACTTAT
AATGCGCTTACCACGATTCTCGCCCGTTCTAGGGACTTGAATTCTATCCAGATGGTTTTCTCAGAGAGATTGGATGCACAAGTCGATATTTCGGCGTCAACATTCAGTTTCGCCACCGCCTGGCATGATGATCCCGACTTGCTCAATGAAGTCACACGAATCATCGAGAAGATGCCATTTCCCAGTAGAGGACGCGCTTA
CAATTTCCTTATTAGGGTTCTTTGTAGACAGAATGCCAATGCAGCCTTAAGGGTATTGGAAAAGATGGTGATTGCTGGTTGTGCTCCGAATATAAAAACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATATCCAAATGGATAAGGTACAGGAGATTTATGAGACGATGGAGATTTTCGGCTGCCCACCGGTAGCGT
TCGTTTGTGGTGGTTTGGATGCAAAACCAAGGCCTTGCGGCCTCCTTACCGTGGTAGATGATCATTTGACTATTCTGAATGCCCAAATTCGTGTTATTAGGAGTGTGAATTATGATATTAAACAGGCACTGCAGCATCTGAGTGCCTTGGAGCAGACAACTCGTCTGGAGGCTCGTAACAGCAACATCAACCTCAGCGCG
AAAGTGGATAGTCTCTCCGCTGGTCTGGACAGTGGTCCTTGTTCAAATTTGGAGGCCCAAATCAGGGCGGTTCGTGTCATTATAAAAAGAATTGAGGGCAAGGTCGAAAGTATGCGCAATGAGTTAATGGCATTGAAGATGGAGATGCTGAACCCAGGTGGAGAAGCTGGAAGCAAGGAAGCAGCGTTTCGGATTTAGCA
AGCAAACACGGTGCTTTTGACTGTGTCTTTTTTGGGTTTCCTTTCTGTATAGACTGTGTCTTTTTTGGGTCACTCCGTCTTTAAGAAGTTGTGTAATTTGCCTAAATTTATATGGGAGTTTCGGTCTGAACCCTCTTGCTAGGACATCGGCATTCTGTATAAGCATAAGTCTGTAGTATTTCTAGAAGCTCAAAGTGAAC
TCATTTCCCTCCTAGGTTTCTTTTTTGTCGAAGTAGATGTTGAATTGTAAAAGATGATAGTTAAGACATGGTAGCTCTCCACTCTCAAGAAGCAGGCCTGCTCTGACATTGTGCAACTCTGTTTCTGCTATCTTTTTATATATAAAAAAAAATTCTTATCCGC

Intron 4 GTACGAGTTT ... AAATCCACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	68.75	15	30	36
A2	63.08	12	28	13
A3	65.12	15	24	32
A4	43.66	20	15	16
A5	65.52	5	12	7
A6	46.56	35	29	32
A7	67.11	25	54	48
A8	56.39	29	25	50
A9	65.33	26	40	58
A10	57.89	32	51	37

>TRINITY_DN119091_c0_g2_i2 from sample A1 / Example spliced isoform

CACCACTGAAAAATCCTAAACCAGAACTCCTTGCAATGCAGGTCGTGGCTTATGTGCCTCGATCAGGACTGGCCTTTGTCGGGCGAGTGTTTTCAGCAACCCAGCTGCGCCATCAAAACTGGAGCTCTGTAACATCGCAATGGCACCGCAATTCGGACTCCAGCGCCTTGAAAATCTTCCAAAACGATCGTAATAATGGT
GTTGGTATTGGATCGAACAGTTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCACACTACAACCCGGGTTCAAACATAACATTCCAACTTATGATGCGCTTACCAGAAATATCGCCCGTTCTAAGGACTTCAACACTCTGCAGATGGTTTTCTCAGAGAGATTGGGTGCACACGTCGATGTTTCTGTGAGAACAT
TCAGGTTCGCCACCGACTGGCATGATGATCCCAACTTGCTCAATGAAGTCATACGAATCATCGAGAAGATGCCATTTTCCACCAGAAAACGCTCTTACAATTTGCTGATTAGGGCTCTTTGTCCAAAGAATGTCAATGCAGCCTTAAGTGTATTGGAAAAGATGGTGATTGCTGATTGTGCTCCGGAAAGTATCACTTTT
CGTCCATTTATAAAGTTTTACCGCCGGCATAAACAAATGGATAATCTACAGGAGATTTATGAAACGATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGGGTA
AACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGATTCAGGTAACTATGAATATTTGATTAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAAGCTAAGCCCCAGCTCAGTATTATCATGCCCCCACCTGAAGATGGGGAGCTGTCAAACTTGGTCAATGTATACATTGTTT
TAGGGAATGCTCACTGGGGTTTGAACCTGGGTCAGTTGCATGGTTATGCACTGTCTCAACCACGAGACCACAATCCGATAGACATACACATTCATCATTGTTATCCTAATATATTCAGCCGAGTTTACTGGAAGCTTGTCAGGTCATTGCAGGTATGAACCAAAGGGTTCTCTCACCAAGTTAATTTTTGATGCATTTAG
ACTGGTTACCGAATGCAAGTTGCATGAAGGCGTTTAGCCTAATGGTAATTTTCATTGAAGCTTGAAAGGAAATAGTTCCTTGATTTCACCTCAAGTGCATGAATACTTATGGTTAGCTGTTTCTGCATCATGCAAGTCATGCAGAAATGTGAACATACAGATATAGATGATTTGAATGCTGAACAAGACAAGTTTTGTCC
TGTTTTCAAATGTTTTATCTGACAACATATTATTGTGGCTATAATGCTGTCTCAAGAATTTCATCACGAAACATGTGAGAACTGAGAAGTAGAACAAGGGTGGTGGTGCTTAAAAAGGGGACGATTCTTTTCAGTATTCATAGAATTGTGATTCAAACTTA

>TRINITY_DN119091_c0_g2_i1 from sample A1 / Example unspliced isoform:

CACCACTGAAAAATCCTAAACCAGAACTCCTTGCAATGCAGGTCGTGGCTTATGTGCCTCGATCAGGACTGGCCTTTGTCGGGCGAGTGTTTTCAGCAACCCAGCTGCGCCATCAAAACTGGAGCTCTGTAACATCGCAATGGCACCGCAATTCGGACTCCAGCGCCTTGAAAATCTTCCAAAACGgtacgagttttctc
ccttttcatgaactcattttcggccataaattttactcaacgaatgcatctgccacggttcaaatctctgagaaaactcagtcagcatctgacaaggaggaaagccccgaatcgcaagccctgaacagcaaaaaacaggcagatcgcttgcctaactcgaacaaatctaacaaatctaacaaaccaaacaaaccgaataa
accgaacaaacccttgcccaactggacgatgatgggacttaaacgagcaatatgtaaagttcttgaaaagggcggcaacgatatggaagaaaccctaactaaattgggtttttggctaaatccacagATCGTAATAATGGTGTTGGTATTGGATCGAACAGTTTCTCCAATCTTAGCTCGGAGGTTTTTTCAATGGGCCA
CACTACAACCCGGGTTCAAACATAACATTCCAACTTATGATGCGCTTACCAGAAATATCGCCCGTTCTAAGGACTTCAACACTCTGCAGATGGTTTTCTCAGAGAGATTGGGTGCACACGTCGATGTTTCTGTGAGAACATTCAGGTTCGCCACCGACTGGCATGATGATCCCAACTTGCTCAATGAAGTCATACGAATC
ATCGAGAAGATGCCATTTTCCACCAGAAAACGCTCTTACAATTTGCTGATTAGGGCTCTTTGTCCAAAGAATGTCAATGCAGCCTTAAGTGTATTGGAAAAGATGGTGATTGCTGATTGTGCTCCGGAAAGTATCACTTTTCGTCCATTTATAAAGTTTTACCGCCGGCATAAACAAATGGATAATCTACAGGAGATTTA
TGAAACGATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTCGGGTAAGGGTAAACTCTTTTTTCATCTGTGGGGAGCTATAAATTGCAATTTGGATTCAGGTAACTATGAA
TATTTGATTAGGGTTTGTATGAGGTCGGGCCTATGCAAGTGCTTTTGTTTTACCTGTGGGAGGAGATTTATGAAACGATGAAGATTTTCCGCTGCCCTCTGGTCTTTGAATAGGGATTTGGAACTTCCGGGTGACTAATTGTGCAACTAGGCTTTACATAAAAACCATGTTAGTGAGGCATATTCATCATTGATTTTTTC
GGGTAAGG