sp|Q946J8|LHP1_ARATH ----> Chromo domain-containing protein LHP1

Intron 1 GTACGATCAA ... TTGTGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50.43	58	59	24
A2	49.25	34	33	11
A3	53.85	54	63	26
A4	52.38	20	22	15
A5	51.43	17	18	4
A6	53.6	103	119	40
A7	51.58	230	245	45
A8	51.37	249	263	58
A9	52.09	206	224	33
A10	53.16	141	160	46

>TRINITY_DN47041_c5_g1_i3 from sample A7 / Example spliced isoform

CTTACTATTATTAGATCCACTTAAACAACAATCGTATTCCTAAAGCATGATATAGAAGGTTGTGAATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATTGCTAGATGTTACATTAA
AGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATGATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGAGAGGCCCAAGAGAGGGC
ACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCAGGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTGCAATATTTGGTTAAGTG
GCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAGTGCTGATGAAGGTGCAG
ATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCGCACATCCCAGAAAAAGAAGGA
AAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAGGGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTGGAGGAATCTAAACCAGA
TCAGGGGGCTGCAGTCAATGACTCGAGTAGACAAATTCAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAACAGGGAATTCAAGGGTGC
AAGAAGGGGACACTGTAGGAAACGGGGAAGAAGCTAAAAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATGTGTCTGTCCTTTTTAAA
GCACAGAGGGAGAAAATGTCATGACATCAACATTAATATTGTCATAGAAATATGATTCTTTGGTATCAGTGGCTGCTTGTCTCCAAAAGCCTAGGACAATGGTCCAACCAATCATGCAGTATCTATCAGGACTATATATGTATTATGCAGGGTTTTCATTTTATGTCTTTCTGCAGTGTGCCAACTTGCAAGCGTTGCCT
TCTATATCAGATACTGAAAGAGACATCATGACTCGTCAGAGAACCCAACAGTACTTGTTGGCATTCAATTCAAATTTTTCCTTTCGTGGCTACATATTTTTGGGATTCTGAGAGGCTGTTTTAATGCTTAGTCGGTAATTTTTGCACGCTGATCATTGTTTGAATCACTTTCTTATGCATGTTGTACAAGTCTGTGGTCT
TGCATTGACAACCTCTTTTTATCTGCCAACAATATCCTGCGAGACTATCTATTAAAAAATATGCTCCATACTGTTTCAACCACTGCCATACTGTAGGCCCAGTGCAGTAATTGCGAGGCCAATCTGTTGGGTAATACCTTTTATTTCTGTGAGCATTTTATGTATTTTTCCTATTCACTTCTTGGGAAATATGTTGTCTG
TTTTGTTTAATGATAATAATTGTATGGGAGGTTGGGGGTTTCAATTAATTCGTAACCTCTCTTGACTGGTTCTTTAGTTAGGTTTATTCTATCACCCTATGGCACTGTTTTAGACAACATTAGACATAGTGTTTTTCCTTTGACATAATCCAGATGACCTTGTTATTATCTAGTTATGCTAAA

>TRINITY_DN47041_c5_g1_i1 from sample A7 / Example unspliced isoform:

CTTACTATTATTAGATCCACTTAAACAACAATCGTATTCCTAAAGCATGATATAGAAGGTTGTGAATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATTGCTAGATGTTACATTAA
AGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATGATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGAGAGGCCCAAGAGAGGGC
ACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCAGGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTGCAATATTTGGTTAAGTG
GCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAGTGCTGATGAAGGTGCAG
ATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCGCACATCCCAGAAAAAGAAGGA
AAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAGGGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTGGAGGAATCTAAACCAGA
TCAGGGGGCTGCAGTCAATGACTCGAGTAGACAAATTCAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAACAGGGAATTCAAGGGTGC
AAGAAGGGGACACTGTAGGAAACGGGGAAGAAGCTAAAAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATGTGTCTGTCCTTTTTAAA
GCACAGAGgtacgatcaagaacagcctacactttacagaaatgtgttgaatatcacagttggaagaaaacctaggacattcgattaatttctttgttaaggttatatattagatgcaattttgtgtgtagGGAGAAAATGTCATGACATCAACATTAATATTGTCATAGAAATATGATTCTTTGGTATCAGTGGCTGCTT
GTCTCCAAAAGCCTAGGACAATGGTCCAACCAATCATGCAGTATCTATCAGGACTATATATGTATTATGCAGGGTTTTCATTTTATGTCTTTCTGCAGTGTGCCAACTTGCAAGCGTTGCCTTCTATATCAGATACTGAAAGAGACATCATGACTCGTCAGAGAACCCAACAGTACTTGTTGGCATTCAATTCAAATTTT
TCCTTTCGTGGCTACATATTTTTGGGATTCTGAGAGGCTGTTTTAATGCTTAGTCGGTAATTTTTGCACGCTGATCATTGTTTGAATCACTTTCTTATGCATGTTGTACAAGTCTGTGGTCTTGCATTGACAACCTCTTTTTATCTGCCAACAATATCCTGCGAGACTATCTATTAAAAAATATGCTCCATACTGTTTCA
ACCACTGCCATACTGTAGGCCCAGTGCAGTAATTGCGAGGCCAATCTGTTGGGTAATACCTTTTATTTCTGTGAGCATTTTATGTATTTTTCCTATTCACTTCTTGGGAAATATGTTGTCTGTTTTGTTTAATGATAATAATTGTATGGGAGGTTGGGGGTTTCAATTAATTCGTAACCTCTCTTGACTGGTTCTTTAGT
TAGGTTTATTCTATCACCCTATGGCACTGTTTTAGACAACATTAGACATAGTGTTTTTCCTTTGACATAATCCAGATGACCTTGTTATTATCTAGTTATGCTAAA

Intron 2 GTAAGACGAA ... ATATTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	15.25	50	9	9
A2	11.11	32	6	2
A3	12.5	49	5	9
A4	20.93	17	3	6
A5	16.67	10	2	2
A6	6.4	95	9	4
A7	4.79	149	7	8
A8	3.93	232	10	9
A9	3.62	133	7	3
A10	6.96	127	12	7

>TRINITY_DN98316_c0_g1_i4 from sample A4 / Example spliced isoform

CTAGCATGTTTAAAAAAAATACATAAAACATACATATTATTTATGGCCCTATTCCAAAGGAGGAAACCTATCTTGTGTAAATGTATATTATGCTGGGAAACTTATCTAGTGTAATTTATATTATGCAGCCTTCTGTTAAGCTCCTTGCAATGTTGGGGCCAGTCAAGCCCATTTTCCCAAACGCTACATCTATTGTTGGT
TGCTATCAAATTATTTTTGATGACATCATCCTTGTGAAAGAATACTTTTGCTATGAAATAAGCAAGTTGTTTAATCTGCATATTTAATATTGGCCAGGGAAACCTGGAGTGAGTAATAACTATCAGAGAACTTTGATATGAGAATATGAATGTACTTTTGGCCTTTGGCAATGAGAAGAGCATTTAAGAAGAAACAATGA
AGAAGAGAAAATTGGCTTTTACTGCTACATGGAGCTGATGGCCAAGAGGTGGTGGTCGACAACAAATTCTTGAGGGCAAATTACCCATTGTTGTTGATTGACTTTTATGAGCAACATCTTCGGTACAGCACTGCACAGTAGAGTTATACCATATACAAAGCAACCTGATCACAGCTTGAAAACAGAATTGTTTCATGAGT
ATGTTTTAGGAATTTTAGGTTCCTGCCTTCTTGTCATATCGTTTGTGTTATTTAAAGTAAGGTTCTCAGAATTTCTCAGTTCTTTCTCTAGAGAAGTGTGGGAGAAGTCAGTGTTATGTTCTGGAAAATCTGTGGTTACATTTTTACCATAAGCTGAAGCTGGTCACCGAATTATGATTTCAAACAATAAACAGGTCAGT
TCTATCATGTATTTACCTTGAATTTTCAAGGCGTTTGATGCATATAATGGAGTTATTGTCAATCAGGTTCAAGGGATAGGTAGATACAGATTTTTGTTCATTGTAATCTTATGGATATTGCACTGTAACTGAGGTGGATCCTAGATTCTTTTAATTTTCTGTGTATATGTGTTTTTGTATGCTAATGTATATTTTGCAGT
AGTCGGGACCATGGCCATGAAGCATTCTGTTTGGATAAGCATGGGAAGAGAACTTCACTTAAAAAATAAAATAGTTGTGGGG

>TRINITY_DN98316_c0_g1_i3 from sample A4 / Example unspliced isoform:

CTAGCATGTTTAAAAAAAATACATAAAACATACATATTATTTATGGCCCTATTCCAAAGGAGGAAACCTATCTTGTGTAAATGTATATTATGCTGGGAAACTTATCTAGTGTAATTTATATTATGCAGCCTTCTGTTAAGCTCCTTGCAATGTTGGGGCCAGTCAAGCCCATTTTCCCAAACGCTACATCTATTGTTGGT
TGCTATCAAATTATTTTTGATGACATCATCCTTGTGAAAGAATACTTTTGCTATGAAATAAGCAAGTTGTTTAATCTGCATATTTAATATTGGCCAGGGAAACCTGGAGTGAGTAATAACTATCAGAGAACTTTGATATGAGAATATGAATGTACTTTTGGCCTTTGGCAATGAGAAGAGCATTTAAGAAGAAACAATGA
AGAAGAGAAAATTGGCTTTTACTGCTACATGGgtaagacgaaaggatacacttgagtgtggaatatttatttctcacactaatcagcagttaacatacttgcagaagctttaattttttatggttacagaatatgcaaaagttcttgcaatgtaatttttaagatgtttagaatttatttcatagagtatgagtgttttc
aaattgttgttgaatgttatattgacagAGCTGATGGCCAAGAGGTGGTGGTCGACAACAAATTCTTGAGGGCAAATTACCCATTGTTGGTAAGTGATATTTTATTCTGTCCTTTTGTAACTATATATCTATTGGTTTATTATTGCCTGCGCTGACTTTTGCCTTGTTTCTTGGCCTATTCATTATCTTTGTACAATTTG
TTAATGTGTTTGTTTGGAACCATTGTACTTTTTATTTTTGTATTTATGGCATCTAATTTATCCCTTTACTGACCTTACAGTTGATTGACTTTTATGAGCAACATCTTCGGTACAGCACTGCACAGTAGAGTTATACCATATACAAAGCAACCTGATCACAGCTTGAAAACAGAATTGTTTCATGAGTATGTTTTAGGAAT
TTTAGGTTCCTGCCTTCTTGTCATATCGTTTGTGTTATTTAAAGTAAGGTTCTCAGAATTTCTCAGTTCTTTCTCTAGAGAAGTGTGGGAGAAGTCAGTGTTATGTTCTGGAAAATCTGTGGTTACATTTTTACCATAAGCTGAAGCTGGTCACCGAATTATGATTTCAAACAATAAACAGGTCAGTTCTATCATGTATT
TACCTTGAATTTTCAAGGCGTTTGATGCATATAATGGAGTTATTGTCAATCAGGTTCAAGGGATAGGTAGATACAGATTTTTGTTCATTGTAATCTTATGGATATTGCACTGTAACTGAGGTGGATCCTAGATTCTTTTAATTTTCTGTGTATATGTGTTTTTGTATGCTAATGTATATTTTGCAGTAGTCGGGACCATG
GCCATGAAGCATTCTGTTTGGATAAGCATGGGAAGAGAACTTCACTTAAAAAATAAAATAGTTGTGGGG

Intron 3 GTACGATCAA ... CTTTCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	54.13	50	59	8
A2	53.23	29	33	10
A3	56.76	48	63	19
A4	56.41	17	22	8
A5	51.43	17	18	13
A6	56.67	91	119	53
A7	53.61	212	245	33
A8	53.24	231	263	69
A9	54.5	187	224	35
A10	55.56	128	160	22

>TRINITY_DN47553_c3_g4_i3 from sample A10 / Example spliced isoform

CTTACTATTATTATATCCTTACTATTATTAGATCCACTTAAACAACAATCGTATTCCTAAAGCATGATATAGAAGGTTGTGAATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATT
GCTAGATGTTACATTAAAGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATGATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGA
GAGGCCCAAGAGAGGGCACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCAGGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTG
CAATATTTGGTTAAGTGGCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAG
TGCTGATGAAGGTGCAGATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCACACA
TCCCAGAAAAAGAAGGAAAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAGGGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTG
GAGGAATCTAAACCAGATCAGGGGGCTGCAGTCAATGACTCGAGTAGACAAATTCAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAAC
AGGGAATTCAAGGGTGCAAGAAGGGGACACTGTAGGAAACGGGGAAGAAGCTAAAAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATG
TGTCTGTCCTTTTTAAAGCACAGAGTGTGCCAACTTGCAAGCGTTGCCTTCTATATCAGATACTGAAAGAGACATCATGACTCGTCAGAGAACCCAACAGTACTTGTTGGCATTCAATTCAAATTTTTCCTTTCGTGGCTACATATTTTTGGGATTCTGAGAGGCTGTTTTAATGCTTAGTCGGTAATTTTTGCACGCTG
ATCATTGTTTGAATCACTTTCTTATGCATGTTGTACAAGTCTGTGGTCTTGCATTGACAACCTCTTTTTATCTGCCAACAATATCCTGCGAGACTATCTATTAAAAAATATGCTCCATACTGTTTCAACCACTGCCATACTGTAGGCCCAGTGCAGTAATTGCGAGGCCAATCTGTTGGGTAATACCTTTTATTTCTGTG
AGCATTTTATGTATTTTTCCTATTCACTTCTTGGGAAATATGTTGTCTGTTTTGTTTAATGATAATAATTGTATGGGAGGTTGGGG

>TRINITY_DN47553_c3_g4_i1 from sample A10 / Example unspliced isoform:

CTTACTATTATTATATCCTTACTATTATTAGATCCACTTAAACAACAATCGTATTCCTAAAGCATGATATAGAAGGTTGTGAATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATT
GCTAGATGTTACATTAAAGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATGATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGA
GAGGCCCAAGAGAGGGCACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCAGGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTG
CAATATTTGGTTAAGTGGCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAG
TGCTGATGAAGGTGCAGATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCACACA
TCCCAGAAAAAGAAGGAAAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAGGGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTG
GAGGAATCTAAACCAGATCAGGGGGCTGCAGTCAATGACTCGAGTAGACAAATTCAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAAC
AGGGAATTCAAGGGTGCAAGAAGGGGACACTGTAGGAAACGGGGAAGAAGCTAAAAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATG
TGTCTGTCCTTTTTAAAGCACAGAGgtacgatcaagaacagcctacactttacagaaatgtgttgaatatcacagttggaagaaaacctaggacattcgattaatttctttgttaaggttatatattagatgcaattttgtgtgtagggagaaaatgtcatgacatcaacattaatattgtcatagaaatatgattcttt
ggtatcagtggctgcttgtctccaaaagcctaggacaatggtccaaccaatcatgcagtatctatcaggactatatatgtattatgcagggttttcattttatgtctttctgcagTGTGCCAACTTGCAAGCGTTGCCTTCTATATCAGATACTGAAAGAGACATCATGACTCGTCAGAGAACCCAACAGTACTTGTTGG
CATTCAATTCAAATTTTTCCTTTCGTGGCTACATATTTTTGGGATTCTGAGAGGCTGTTTTAATGCTTAGTCGGTAATTTTTGCACGCTGATCATTGTTTGAATCACTTTCTTATGCATGTTGTACAAGTCTGTGGTCTTGCATTGACAACCTCTTTTTATCTGCCAACAATATCCTGCGAGACTATCTATTAAAAAATA
TGCTCCATACTGTTTCAACCACTGCCATACTGTAGGCCCAGTGCAGTAATTGCGAGGCCAATCTGTTGGGTAATACCTTTTATTTCTGTGAGCATTTTATGTATTTTTCCTATTCACTTCTTGGGAAATATGTTGTCTGTTTTGTTTAATGATAATAATTGTATGGGAGGTTGGGG

Intron 4 GTGAGTCCCA ... AATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.28	201	49	73
A2	22.26	131	23	52
A3	24.56	192	43	82
A4	27.92	71	14	41
A5	21.74	54	7	23
A6	22.69	92	19	35
A7	22.54	725	110	312
A8	23.76	486	92	211
A9	23.11	619	114	258
A10	24.28	758	143	343

>TRINITY_DN98316_c0_g1_i2 from sample A4 / Example spliced isoform

ATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATTGCTAGATGTTACATTAAAGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATG
ATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGAGAGGCCCAAGAGAGGGCACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCA
GGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTGCAATATTTGGTTAAGTGGCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATA
TTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAGTGCTGATGAAGGTGCAGATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGAT
AACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCGCACATCCCAGAAAAAGAAGGAAAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAGGGAAAAGAAACAGAAGAGCAGAATGGGA
GTAGGGGTGTAGGGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTGGAGGAATCTAAACCAGATCAGGGGGCTGCAGTCAATGACTCG
AGTAGACAAATTCAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAACAGGGAATTCAAGGGTGCAAGAAGGGGACACTGTAGGAAACGG
GGAAGAAGCTAAAAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATGTGTCTGTCCTTTTTAAAGCACAGAGAGCTGATGGCCAAGAGG
TGGTGGTCGACAACAAATTCTTGAGGGCAAATTACCCATTGTTGTTGATTGACTTTTATGAGCAACATCTTCGGTACAGCACTGCACAGTAGAGTTATACCATATACAAAGCAACCTGATCACAGCTTGAAAACAGAATTGTTTCATGAGTATGTTTTAGGAATTTTAGGTTCCTGCCTTCTTGTCATATCGTTTGTGTT
ATTTAAAGTAAGGTTCTCAGAATTTCTCAGTTCTTTCTCTAGAGAAGTGTGGGAGAAGTCAGTGTTATGTTCTGGAAAATCTGTGGTTACATTTTTACCATAAGCTGAAGCTGGTCACCGAATTATGATTTCAAACAATAAACAGGTCAGTTCTATCATGTATTTACCTTGAATTTTCAAGGCGTTTGATGCATATAATG
GAGTTATTGTCAATCAGGTTCAAGGGATAGGTAGATACAGATTTTTGTTCATTGTAATCTTATGGATATTGCACTGTAACTGAGGTGGATCCTAGATTCTTTTAATTTTCTGTGTATATGTGTTTTTGTATGCTAATGTATATTTTGCAGTAGTCGGGACCATGGCCATGAAGCATTCTGTTTGGATAAGCATGGGAAGA
GAACTTCACTTAAAAAATAAAATAGTTGTGGGG

>TRINITY_DN98316_c0_g1_i1 from sample A4 / Example unspliced isoform:

ATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATTGCTAGATGTTACATTAAAGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGGTTTGGTTTGGCAAGGTTGAGCGGCAATG
ATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGAGAGGCCCAAGAGAGGGCACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGGAGGAACAGGAACACGAAGAAGAGCAGCA
GGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTGCAATATTTGGTTAAGTGgtgagtcccaggtgttattcatacacatggcgtaactccatttaaaaatcgacttcattgacata
ttaaaataattttgcagGCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCTTACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAG
TGCTGATGAAGGTGCAGATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAAACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCGCACA
TCCCAGAAAAAGAAGGAAAAGAAACAGAAGAGCAGAA

Intron 5 GTAAGTGATA ... GACCTTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20.85	107.2	11.2	28
A2	22.9	58	5.7	17.1
A3	28.05	111.5	14.4	43
A4	29.77	40.8	4.2	17
A5	24.03	41.2	2.3	13
A6	19.4	307.4	5	72.1
A7	18.86	412.2	12.9	93
A8	18.91	585.9	16.5	133.6
A9	19.35	399.7	10.8	93
A10	17.9	320.3	10.5	68

>TRINITY_DN114518_c0_g1_i3 from sample A1 / Example spliced isoform

TCCTAAAGCATGATATAGAAGGTTGTGAATTTGTGTGAGGTTGTGTTGTCACCGAAATCCTATCAAGCCTCCTTTGAACGCGACGAGGGCATTCGATGGAAGAAGGGATACTGAAGTGGAATTGAAATGAATTTCTGTCGCTAATTGCTAGATGTTACATTAAAGAAAGCTTTCTTCGAGGGATTCTGGAATGGAATAGG
TTTGGTTTGGCAAGGTTGAGCGGCAATGATCATGGAGGATGGTAGATGGTAAATGGTAGGCGGAGGAGTCTGGAAGAGTAGGAGGAGGAGCGTGGGCAGCGGCAGCGGCAACTCAATGAAGTCGAGCAGCAAGAAGAGGGTTAAGAGAGGCCCAAGAGAGGGCACAGAGGAGGACGAAGAAACCAAAGAAAGCGAAGGGG
AGGAACAGGAACACGAAGAAGAGCAGCAGGAAGAAGAAGACGAAGAAGATCAAGGAGAGGAGGAATCCGAGAATGGACAAGTGCTTGGAGAGGGGTTTTATGAAGTCGAAGATATCAGAAAGAAAAGAATTCGCAAGGGGGAGGTGCAATATTTGGTTAAGTGGCGGGGATGGCCAGAGACTGCAAATACATGGGAGCCT
TACGAGAATGTTAAATCGTGTGCTGATATTGTTCAAGCATTCGAAGAGAGCTATGGCGGTAGGATTTCAAAGCCTGGAAGGAAGGCGAGGCGCAAATCCGGATTTCCACTCTCTCATCAAAAGAGAAAGCGCGTCTCTTTGTCCAGTGCTGATGAAGGTGCAGATGCAGAGGTCGAGGCCGAGGCTGAGCCCGAGGCTAA
ACGGGCCAAAACTTCTTATTCTTCGGATAACCAAATTCCTGGTAAGTCAGAGGTGGAGGTAGAGCCTCAACAACTGCATGGTACTGGCATCGGCACGGAGTCTGAGCAATGCCACCCAGAGAAAGAGGACGGAGCCCAGCCACACATCCCAGAAAAAGAAGGAAAAGAAACAGAAGAGCAGAATGGGAGTAGGGGTGTAG
GGAAGAGTGTAGAAGAAGAAGTAGAGAACAAAACGGAAAATCAAAATCCAAAGCAAGATGAGCCCACTTCAGAAAATGATGCTAAAAATGGGGTTTCTCCCTCTCTCGATGACACCAGATTCGTTGAAGAAAAGGAAATGGCTGTGGAGGAATCTAAACCAGATCAGGGGGCTGCAGTCAATGACTCGAGTAGACAAATT
CAGACTACCCAATTTACTGGAGCCAAGAAGAGGAAATCTGGATTTGTAAGGCGCGTGAAGCAAGCTTTGGATTCACGAGAGCATGAACTAAAGCAGAGAGAGGAAAATAGCAATATCCAGCGGGCACATGAAATGTTATCCGGAACAGGGAATTCAAGGGTGCAAGAAGGGGACACTGTAGGAAACGGGGAAGAAGCTAA
AAGTCAGAAGCCTTTGGTTGCAGGGCTTCATTCCAATACAAACAATAAATCGTCAAATTCTCCTGACAGCTTGCTTACTTCAGCGATCACCCAAATACTGAAGGCAATCAGCTACAACAATTCCACCTCAAACAACAAACAAGATGTGTCTGTCCTTTTTAAAGCACAGAGAGCTGATGGCCAAGAGGTGGTGGTCGACA
ACAAATTCTTGAGGGCAAATTACCCATTGTTGTTGATTGACTTTTATGAGCAACATCTTCGGTACAGCACTGCACAGTAGAGTTATACCATATACAAAGCAACCTGATCACAGCTTGAAAACAGAATTGTTTCATGAGTATGTTTTAGGAATTTTAGGTTCCTGCCTTCTTGTCATATCGTTTGTGTTATTTAAAGTAAG
GTTCTCAGAATTTCTCAGTTCTTTCTCTAGAGAAGTGTGGGAGAAGTCAGTGTTATGTTCTGGAAAATCTGTGGTTACATTTTTACCATAAGCTGAAGCTGGTCACCGAATTATGATTTCAAACAATAAACAGGTCAGTTCTATCATGTATTTACCTTGAATTTTCAAGGCGTTTGATGCATATAATGGAGTTATTGTCA
ATCAGGTTCAAGGGATAGGTAGATACAGATTTTTGTTCATTGTAATCTTATGGATATTGCACTGTAACTGAGGTGGATCCTAGATTCTTTTAATTTTCTGTGTATATGTGTTTTTGTATGCTAATGTATATTTTGCAGTAGTCGGGACCATGGCCATGAAGCATTCTGTTTGGATAAGCATGGGAAGAGAACTTCACTTA
AAAAATAAAATAGTTGTGGGGCAAATGTTGAAAATCTTTTATTGCATTGTATCAGATCAGTTAATTATGATTGATATATTTGCAACATAGAACTAGTCCCTTTTTTTACGTTTAATGTCAACTTTTAGATAGTTTTTGTTCTCTAACTGTGAGATTGTTATCACAGTTATTTGTCCCATAGAGCTAGTCTCTTTTTTACA
TTTAATGTCAACATTTTAGATAGTTTTTGTTCTTGAACTGTGAAACCTTGAGATTGTTATCAAGCTTATTTGTCCCAAAGTGAAGAAAATGTCAACATTTTAGATAGTTTTTGTTCTTGAACTGTGAAACCTTGAGATTGTTATCAAGCTTATTTGTCCCAAAGTGAAGAAAATGGCCACTTGCAAGGGGTAGTAAAGTA
TCACAGTTGAAATGGTTTGCTGTTGATTTTTGCTGTTGAATCATATACAAGGAGCTTACTGTAGTTCAAGACAAAATCAAGATGGGAAGGTTGGCAACGTAACAATTACTAATATTTTTAGTTCAAGACTTAAACTCATGATGGAAGGTTGGCCACGTAAGGATTAGTTCATAAAGACAATAGTTGGTGGATGAAAGGGA
TCTGGTACCACACTGTGATAACAATAGTTCTATTGACCGTGACTCATGGAATTGAGAATGAAATTCTGCTTCTAAATTTGAATAGAAGCTCGGCCCCTGGAATAATTATTAGAATTACATGCAATCCTGGCCTTAGTTTTGGATCACCATACTTCTGTTTCCATATTCATTGATAAAGAGGAATAGGGTGGGTAGAAACC
CATCTCATCTCCATGCATTCCCATGATCCGGTGTGCTGCAGGTAGATGATTGGTAGCTGTCTGTGAGGACTGGAATCAAACGATCAACCTTGTGGTTCAATAGAACCCGTCTCAAGTTGCACTCGGCCAACACCGTTCGAGCATTCTCCATGATTTGATCAACAATGTTAAATAAGACCAAAAAATCAATAATAAGATAG
ACACACAGAGACCTATTATTCTCTTTCTCTTCACTTTCATGGAAATTCTAACATCTATCGTATACAAGCAACATACTACTCAACAGTTCCAAGCTCAAGATTTATATCAATTACAGTATGTCGTTAACACTCGTCAAATTTAACCTTCACGAAATCTATAGTAGAAATACCATTTGAAGTCAAGTTCATAATAGTTACTA
TTGATATATCAGGGGTAATGGTTAGATTGCATATGAAAGGCAATTGATATTTCATATACATAACACATCAACACTATCAGGCGTGATCGTAGTAATCCCAGTTGAAATGGTTTGCTATTGATTTTGGCAGTTGAATCATACACAAGGAGCTTACCC

>TRINITY_DN114518_c0_g1_i2 from sample A1 / Example unspliced isoform:

ATGAGACAAAAATCCTAGGGGACCTAGTGCATGTCCATATGACTCAATACTGATGGCTAGCATGTTTAAAAAAAATACATAAAACATACATATTATTTATGGCCCTATTCCAAAGGAGGAAACCTATCTTGTGTAAATGTATATTATGCTGGGAAACTTATCTAGTGTAATTTATATTATGCAGCCTTCTGTTAAGCTCC
TTGCAATGTTGGGGCCAGTCAAGCCCATTTTCCCAAACGCTACATCTATTGTTGGTTGCTATCAAATTATTTTTGATGACATCATCCTTGTGAAAGAATACTTTTGCTATGAAATAAGCAAGTTGTTTAATCTGCATATTTAATATTGGCCAGGGAAACCTGGAGTGAGTAATAACTATCAGAGAACTTTGATATGAGAA
TATGAATGTACTTTTGGCCTTTGGCAATGAGAAGAGCATTTAAGAAGAAACAATGAAGAAGAGAAAATTGGCTTTTACTGCTACATGGGTAAGACGAAAGGATACACTTGAGTGTGGAATATTTATTTCTCACACTAATCAGCAGTTAACATACTTGCAGAAGCTTTAATTTTTTATGGTTACAGAATATGCAAAAGTTC
TTGCAATGTAATTTTTAAGATGTTTAGAATTTATTTCATAGAGTATGAGTGTTTTCAAATTGTTGTTGAATGTTATATTGACAGAGCTGATGGCCAAGAGGTGGTGGTCGACAACAAATTCTTGAGGGCAAATTACCCATTGTTGgtaagtgatattttattctgtccttttgtaactatatatctattggtttattatt
gcctgcgctgacttttgccttgtttcttggcctattcattatctttgtacaatttgttaatgtgtttgtttggaaccattgtactttttatttttgtatttatggcatctaatttatccctttactgaccttacagTTGATTGACTTTTATGAGCAACATCTTCGGTACAGCACTGCACAGTAGAGTTATACCATATACA
AAGCAACCTGATCACAGCTTGAAAACAGAATTGTTTCATGAGTATGTTTTAGGAATTTTAGGTTCCTGCCTTCTTGTCATATCGTTTGTGTTATTTAAAGTAAGGTTCTCAGAATTTCTCAGTTCTTTCTCTAGAGAAGTGTGGGAGAAGTCAGTGTTATGTTCTGGAAAATCTGTGGTTACATTTTTACCATAAGCTGA
AGCTGGTCACCGAATTATGATTTCAAACAATAAACAGGTCAGTTCTATCATGTATTTACCTTGAATTTTCAAGGCGTTTGATGCATATAATGGAGTTATTGTCAATCAGGTTCAAGGGATAGGTAGATACAGATTTTTGTTCATTGTAATCTTATGGATATTGCACTGTAACTGAGGTGGATCCTAGATTCTTTTAATTT
TCTGTGTATATGTGTTTTTGTATGCTAATGTATATTTTGCAGTAGTCGGGACCATGGCCATGAAGCATTCTGTTTGGATAAGCATGGGAAGAGAACTTCACTTAAAAAATAAAATAGTTGTGGGGCAAATGTTGAAAATCTTTTATTGCATTGTATCAGATCAGTTAATTATGATTGATATATTTGCAACATAGAACTAG
TCCCTTTTTTTACGTTTAATGTCAACTTTTAGATAGTTTTTGTTCTCTAACTGTGAGATTGTTATCACAGTTATTTGTCCCATAGAGCTAGTCTCTTTTTTACATTTAATGTCAACATTTTAGATAGTTTTTGTTCTTGAACTGTGAAACCTTGAGATTGTTATCAAGCTTATTTGTCCCAAAGTGAAGAAAATGTCAAC
ATTTTAGATAGTTTTTGTTCTTGAACTGTGAAACCTTGAGATTGTTATCAAGCTTATTTGTCCCAAAGTGAAGAAAATGGCCACTTGCAAGGGGTAGTAAAGTATCACAGTTGAAATGGTTTGCTGTTGATTTTTGCTGTTGAATCATATACAAGGAGCTTACTGTAGTTCAAGACAAAATCAAGATGGGAAGGTTGGCA
ACGTAACAATTACTAATATTTTTAGTTCAAGACTTAAACTCATGATGGAAGGTTGGCCACGTAAGGATTAGTTCATAAAGACAATAGTTGGTGGATGAAAGGGATCTGGTACCACACTGTGATAACAATAGTTCTATTGACCGTGACTCATGGAATTGAGAATGAAATTCTGCTTCTAAATTTGAATAGAAGCTCGGCCC
CTGGAATAATTATTAGAATTACATGCAATCCTGGCCTTAGTTTTGGATCACCATACTTCTGTTTCCATATTCATTGATAAAGAGGAATAGGGTGGGTAGAAACCCATCTCATCTCCATGCATTCCCATGATCCGGTGTGCTGCAGGTAGATGATTGGTAGCTGTCTGTGAGGACTGGAATCAAACGATCAACCTTGTGGT
TCAATAGAACCCGTCTCAAGTTGCACTCGGCCAACACCGTTCGAGCATTCTCCATGATTTGATCAACAATGTTAAATAAGACCAAAAAATCAATAATAAGATAGACACACAGAGACCTATTATTCTCTTTCTCTTCACTTTCATGGAAATTCTAACATCTATCGTATACAAGCAACATACTACTCAACAGTTCCAAGCTC
AAGATTTATATCAATTACAGTATGTCGTTAACACTCGTCAAATTTAACCTTCACGAAATCTATAGTAGAAATACCATTTGAAGTCAAGTTCATAATAGTTACTATTGATATATCAGGGGTAATGGTTAGATTGCATATGAAAGGCAATTGATATTTCATATACATAACACATCAACACTATCAGGCGTGATCGTAGTAAT
CCCAGTTGAAATGGTTTGCTATTGATTTTGGCAGTTGAATCATACACAAGGAGCTTACCC