sp|O64886|COX10_ARATH ----> Protoheme IX farnesyltransferase, mitochondrial

Intron 1 GTCAGCTATC ... TGTTTCTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.44	55	3.5	44
A2	45.07	40.2	2.8	33
A3	33.75	53	3.3	27
A4	29.89	61	4.4	26
A5	42.31	30	4.1	22
A6	41.97	112	4.8	81
A7	40.22	157.5	9.3	106
A8	34.34	65	2.1	34
A9	37.14	160.8	8.5	95
A10	45.04	155	14.6	127

>TRINITY_DN125511_c11_g1_i3 from sample A1 / Example spliced isoform

ATTAGCCTACGCTGTTCGATGATGTTAACCAATGTTAACATGGTATTACGCTGTTTGATGTAATAGGGATGCGGCGCAGCCAGAAGTCTGGACAGGGAGACTAATACACAAAGACAACATTACAGGTCTTCGAGTGTTTTTCTTCGGAATTCGAACGCCATGGCAACGATACTGAGAAGGTCTTCAAATAAATCTGCATA
TTTTGCTCTTCTGAAAGGGTTTTCGATTACATCGACCTCTCGTTGCCTCCCATTGAATGAAAATGGGAATGGGAGGGTTCGTCATCTGTTTTCTACCCGGCGGAATTTCGATCTGGATACAAGTATGGGGAATTCCTCTTTGTTCGATTCTTCTGCGAGAGCTCTCGAACATTCTTTGAAGGGGTTTGGAGGAGGCATGC
GAAATGTGACTTCTGCTTCTGCTTCTGCTTCTGCAACACTGGGTGACAACTCCGTAGTGATGCAATCAAAGGGAATGGTGGAGTCTATACGACATCATGGACAGTGCTTCTGGGAGCTATCCAAAGCCCGATTAAGCATGCTTGTGGTGGCAACTTCTGGAGCAGGGTTTGTTCTTGGTAGCGGTGCAAGTGTTGATTTG
GCTGCACTTTCCTGGACTTGCACTGGTACAATGTTGGTTGCTGCTTCTGCCAACTCCTTCAATCAGGTTTGGTTTTTGACTGAAGACAGTTGCATTCTTTAAGGCTTGTCCCTCAAGGCCTACATGCTTGATTGGTATGTGTTGTTATTGAAGTCTTTTCTTTCTTGACAAAGTACAAATACTTTACCATACGTCGTAGA
TAATAATTTAAATATTTAATTATTTTAGGCAAGGATTGTTGTTGTTGTAGCTACGTGAGGTATCCTCACTAGCTAAAGCCGACCTACAAAAGAAATAAATAAAATCAAATGTATTTTATTATACAAAAAGTGAAGTTGGCCC

>TRINITY_DN125511_c11_g1_i6 from sample A1 / Example unspliced isoform:

ATTAGCCTACGCTGTTCGATGATGTTAACCAATGTTAACATGGTATTACGCTGTTTGATGTAATAGGGATGCGGCGCAGCCAGAAGTCTGGACAGGGAGACTAATACACAAAGACAACATTACAGgtcagctatcctattattccttcctccgatccctgtgagtcgtctgttgatatagtctgggatttattgttcgca
tttgtttctcagGTCTTCGAGTGTTTTTCTTCGGAATTCGAACGCCATGGCAACGATACTGAGAAGGTCTTCAAATAAATCTGCATATTTTGCTCTTCTGAAAGGGTTTTCGATTACATCGACCTCTCGTTGCCTCCCATTGAATGAAAATGGGAATGGGAGGGTTCGTCATCTGTTTTCTACCCGGCGGAATTTCGATC
TGGATACAAGTATGGGGAATTCCTCTTTGTTCGATTCTTCTGCGAGAGCTCTCGAACATTCTTTGAAGGGGTTTGGAGGAGGCATGCGAAATGTGACTTCTGCTTCTGCTTCTGCTTCTGCAACACTGGGTGACAACTCCGTAGTGATGCAATCAAAGGGAATGGTGGAGTCTATACGACATCATGGACAGTGCTTCTGG
GAGCTATCCAAAGCCCGATTAAGCATGCTTGTGGTGGCAACTTCTGGAGCAGGGTTTGTTCTTGGTAGCGGTGCAAGTGTTGATTTGGCTGCACTTTCCTGGACTTGCACTGGTACAATGTTGGTTGCTGCTTCTGCCAACTCCTTCAATCAGATTTTTGAAGTTAACAACGATGCCAAGATGAAACGTACAATGAGAAG
GCCTTTACCTGGAGGACGACTAAGCATACCTAGTGCAGTTACATGGGCTATGTGTATGGGCTTTACTGGCAGTGTTCTTTTGGCATTGAAGGCTAATGTTCTTGCGGCTGGGCTTGCAACATCAAATCTTGCTTTGTATGCACTTATTTATACTCCATTAAAGCAGATTCACCCAATAAATACCTGGGTTGGAGCTCTTG
TTGGTGCAATTCCTCCATTGATTGGGTGGGCGGCTGCTACTGGACAAGTTACATTAGAAGGGCTGGTTCTTCCGGCGGTTCTTTATTTTTGGCAAATCCCACATTTCATGGCCCTTGCATATTTATGCCGGAATGATTATGCTGCTGGAGGATTCAAAATGCTCTCACTACTGGATGCCACAGGGGAGAAAACATCACTT
GTGGCTCTTCGAAACTGCATTTACCTTCTTCCAGTGGGCTTTGTTGCATATGACTGGAATATCACATCAGCATGGTTCGGGCTAGAGACAGCATTGCTAACTTCAGGCATGGGTGCAGCTGCATTGTTATTTTATTTCCACCGAAATACCAAAAATGCTCGGAGGCTTTTCCATGGTAGTCTTTTGTATCTTCCATTATT
GATGATTGGAATGCTTTTTCACCGCTTTCCCCACGTGCAACTTGATGGGGCTACAACTAATCTGGGTGAAAGTGACAACATGGCCTTGGAAAATACTGAATTCACTGATAGTGAAAGAAGTAAAGGCAGAGATATATTGAGCAAATATCCTCTTGGTAGTTCATCGCGACCACCTGTTGCTTATGCTTCTGCAGCACCAT
TTCCGTTCTTACCTGTACCTGTATTTTCCTCAGCTGATTGATAAGCTATAGCTGTTGGTTTTGAATATGAAACATAAAGGAGATTTCTTTGTGAGTTTCCATCGAGTTTGCCAAGGTATCCACTCATTCTCAGTGCAGCGTGTTAGGTTTTTGTCAACTTGGAAATATGTAAATTGCAGGGTACATGGAAAATATTTTTA
TTGAGATACTTTCTGAAGTTCCTCAGATAAAGAGGCGATAATAATAGATTCATAACCTATATTGAATGTCTTGAGTTTGTACTGGAACCTTTGTGTAAGAATCTGTTAAAGTATTAGCCCTCGATTTTTAACCAAG

Intron 2 GTATGTGCAT ... CTTCGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.08	35	6	15
A2	24.39	31	10	10
A3	28.16	37	14	15
A4	20	16	6	2
A5	23.29	28	6	11
A6	23.15	156	35	59
A7	20.88	161	29	56
A8	20.25	193	37	61
A9	19.9	157	31	47
A10	22.31	148	36	49

>TRINITY_DN106066_c1_g1_i1 from sample A3 / Example spliced isoform

ATTACAGGTCAGCTATCCTATTATTCCTTCCTCCGATCCCTGTGAGTCGTCTGTTGATATAGTCTGGGATTTATTGTTCGCATTTGTTTCTCAGGTCTTCGAGTGTTTTTCTTCGGAATTCGAACGCCATGGCAACGATACTGAGAAGGTCTTCAAATAAATCTGCATATTTTGCTCTTCTGAAAGGGTTTTCGATTACA
TCGACCTCTCGTTGCCTCCCATTGAATGAAAATGGGAATGGGAGGGTTCGTCATCTGTTTTCTACCCGGCGGAATTTCGATCTGGATACAAGTATGGGGAATTCCTCTTTGTTCGATTCTTCTGCGAGAGCTCTCGAACATTCTTTGAAGGGGTTTGGAGGAGGCATGCGAAATGTGACTTCTGCTTCTGCTTCTGCTTC
TGCAACACTGGGTGACAACTCCGTAGTGATGCAATCAAAGGGAATGGTGGAGTCTATACGACATCATGGACAGTGCTTCTGGGAGCTATCCAAAGCCCGATTAAGCATGCTTGTGGTGGCAACTTCTGGAGCAGGGTTTGTTCTTGGTAGCGGTGCAAGTGTTGATTTGGCTGCACTTTCCTGGACTTGCACTGGTACAA
TGTTGGTTGCTGCTTCTGCCAACTCCTTCAATCAGATTTTTGAAGTTAACAACGATGCCAAGATGAAACGTACAATGAGAAGGCCTTTACCTGGAGGACGACTAAGCATACCTAGTGCAGTTACATGGGCTATGTGTATGGGCTTTACTGGCAGTGTTCTGTTGGCATTGAAGGCTAATGTTCTTGCGGCTGGGCTTGCA
ACATCAAATCTTGCTTTGTATGCACTTATTTATACTCCATTAAAGCAGATTCACCCAATAAATACCTGGGTTGGAGCTCTTGTTGGTGCAATTCCTCCATTGATTGGGTGGGCGGCTGCTACTGGACAAGTTACATTAGAAGGGCTGGTTCTTCCGGCGGTTCTTTATTTTTGGCAAATCCCACATTTCATGGCCCTTGC
ATATTTATGCCGGAATGATTATGCTGCTGGAGGATTCAAAATGCTCTCACTACTGGATGCCACAGGGGAGAAAACATCACTTGTGGCTCTTCGAAACTGCATTTACCTTCTTCCAGTGGGCTTTGTTGCATATGACTGGAATATCACATCAGCATGGTTCGGGCTAGAGACAGCATTGCTAACTTCAGGCATGGGTGCAG
CTGCATTGTTATTTTATTTCCACCGAAATACCAAAAATGCTCGGAGGCTTTTCCATGGTAGTCTTTTGTATCTTCCATTATTGATGATTGGAATGCTTTTTCACCGCTTTCCCCACGTGCAACTTGATGGGGCTACAACTAATCTGGGTGAAAGTGACAACATGGCCTTGGAAAATACTGAATTCACTGATAGTGAAAGA
AGTAAAGGCAGAGATATATTGAGCAAATATCCTCTTGGTAGTTCATCGCGACCACCTGTTGCTTATGCTTCTGCAGCACCATTTCCGTTCTTACCTGTACCTGTATTTTCCTCAGCTGATTGATAAGCTATAGCTGTTGGTTTTGAATATGAAACATAAAGGAGATTTCTTTGTGAGTTTCCATCGAGTTTGCCAAGGTA
TCCACTCATTCTCAGTGCAGCGTGTTAGGTTTTTGTCAACTTGGAAATATGTAAATTGCAGGGTACATGGAAAATATTTTTATTGAGATACTTTCTGAAGTTCCTCAGATAAAGAGGCGATAATAATAGATTCATAACCTATATTGAATGTCTTGAGTTTGTACTGGAACCTTTGTGTAAGAATCTGTTAAAGTATTAGC
CCT

>TRINITY_DN106066_c1_g1_i5 from sample A3 / Example unspliced isoform:

ATTTTTGAAGTTAACAACGATGCCAAGATGAAACGTACAATGAGAAGGCCTTTACCTGGAGGACGACTAAGCATACCTAGTGCAGTTACATGGGCTATGTGTATGGGCTTTACTGGCAGTGTTCTGTTGGCATTGAAGGCTAATGTTCTTGCGGCTGGGCTTGCAACATCAAATCTTGCTTTGTATGCACTTATTTATAC
TCCATTAAAGCAGATTCACCCAATAAATACCTGGGTTGGAGCTCTTGTTGGTGCAATTCCTCCATTGATTGGGTGGGCGGCTGCTACTGGACAAGTTACATTAGAAGGGCTGGTTCTTCCGGCGGTTCTTTATTTTTGGCAAATCCCACATTTCATGGCCCTTGCATATTTATGCCGGAATGATTATGCTGCTGGAGGgt
atgtgcattagttgctagtctctgtaagttagttttgtgtagtactagtaattgcttcacttttgctcatggcgggttgattttgagacattctttgcttctacttcgtgcagATTCAAAATGCTCTCACTACTGGATGCCACAGGGGAGAAAACATCACTTGTGGCTCTTCGAAACTGCATTTACCTTCTTCCAGTGGG
CTTTGTTGCATATGACTGGAATATCACATCAGCATGGTTCGGGCTAGAGACAGCATTGCTAACTTCAGGCATGGGTGCAGCTGCATTGTTATTTTATTTCCACCGAAATACCAAAAATGCTCGGAGGCTTTTCCATGGTAGTCTTTTGTATCTTCCATTATTGATGATTGGAATGCTTTTTCACCGCTTTCCCCACGTGC
AACTTGATGGGGCTACAACTAATCTGGGTGAAAGTGACAACATGGCCTTGGAAAATACTGAATTCACTGATAGTGAAAGAAGTAAAGGCAGAGATATATTGAGCAAATATCCTCTTGGTAGTTCATCGCGACCACCTGTTGCTTATGCTTCTGCAGCACCATTTCCGTTCTTACCTGTACCTGTATTTTCCTCAGCTGAT
TGATAAGCTATAGCTGTTGGTTTTGAATATGAAACATAAAGGAGATTTCTTTGTGAGTTTCCATCGAGTTTGCCAAGGTATCCACTCATTCTCAGTGCAGCGTGTTAGGTTTTTGTCAACTTGGAAATATGTAAATTGCAGGGTACATGGAAAATATTTTTATTGAGATACTTTCTGAAGTTCCTCAGATAAAGAGGCGA
TAATAATAGATTCATAACCTATATTGAATGTCTTGAGTTTGTACTGGAACCTTTGTGTAAGAATCTGTTAAAGTATTAGCCCT