sp|I3XHK1|FANCM_ARATH ----> DEAD-box ATP-dependent RNA helicase FANCM

Intron 1 GTAAGCTGAT ... AATCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	51.08	57.3	3	57
A2	51.36	47.3	9	46.3
A3	56.96	50.3	5	55.7
A4	58.2	31.3	2	34.3
A5	61.75	21.3	5	26.3
A6	49.74	43.3	2	42.7
A7	51.38	162.7	27	162.7
A8	48.04	174.7	10	167.7
A9	51.21	158	6	158
A10	47.34	144	6	141

>TRINITY_DN43367_c2_g1_i2 from sample A7 / Example spliced isoform

AGGAAGCAGAATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGGTTTTGAAGGATGGACTCCAAGCTGTGCATGTTCCTTATGCATGTTCAAATAAGATCATTCCTTAATGCTTGGGTGTTGAAACTTGTGTCATATGACTTGCACAT
TTCTTGTTGCCGTATAAGAAATTTTATTAATCAGCTGGTTAAGTTTAAGCAACTGGAAAAAGAAAATGTTAGACCGCGTATCACAGATGTGGGTGGGCATCCAAATAACAAGAGAAATAGAACAGGCTCAAATGACTCAGATTTGGGTGGGCAGCCAGACAACAAGAGAAATAGAACAGACTCAAATGGCTCATCTGAAA
AAATTGGAGATCAAGCCACAAGGTGTACCTTTATAAATCATTCCAGGTTTCCTAAAGATCAGCAGCCTGACGTTAGTCTCTTGGAGAATACTTGCCAGGCTCCTTCAGTAAAGGCATGGGTGAATGGCATTAAGACAAACAATGCATCTTGTGAGAATGGTTGCAGAACTGATGCTAATGTGCAAGAGAACAAACATCTT
CAGAAGGCAAAGTTACCTGTCAAAGATAGGATCCGTCTCCTTGTGGGTTATGATGATTTAATTAGTGATGGTATACAAGATCATGATTTCAAGGAAGAGAATGGTGGGCATATCCAGGATGCTATATGAGGAGCAGGATTGATAGTCATATGCAATCTTACTATTTTCTGGGCTCATACATTCTCAAGCTGTGCAAATAC
TCTGTTAGGGTTAGGAATAAGTAGCCTTTGATGAGATCTACTTTTTTCTGGCAGCATATGAGAAATGATATGGAGTTACTAAAAAAATCGTTGTATTCTTTCAGAACTGTACAGTGGCCATCATATTTTTCTTTGTCAAATGAAATAGATTTCGATCGATCCTATTCTCTTCTGGTTTGGGGGATTGGCTTAAAATCAGA
AATGATGGTTAAGGTTTGGTGCACTACTTATTCAACAAACTACCCTTCAGTGTTATTTGATAACTAGCAGCACACAGATAAAAGCTATAGCTGATAAGCATTCTCAAAATGCCATCAATAGACTAGAAACATAAACAGAACATGTAGATTTTGCTCTTGCATCAATTGGAAGATGACACTAATAAAACAGTTGAATATGG
AGTTGTCTAAAAATTTGACGATTTGGCCCGGATGTGTGGGGTTTTCACCTAAATCCGATGTTTTTTATTTTGCAAAATCTGAATTTAAGTGTGTTTTAATGGTGATTTTGATGGTAGAAACGGATTCAACACCATAAAAAAATCCCGGGGCACCCAAAATTTCAGAGTTTGAAAGTTGTAACCAGGATTTTAAAAGAAAT
TCTCTCGCATTTTTTCAAAATCGTGCCGGAAAAATCAAATTTTTCCGTTTGAAATTGTAGATCTTTTAGACTACGTGGTTGAATATCCCTTTGTACCTGGGAAGTTGGATACTTTATCAGGGTCTGCAACAGATTTTTGATTTTTCATTAATTAATTGTGTATCTAGCCAGTTTTTTGCATATTAAATGATATATATTTA
TTGTTTTGTGG

>TRINITY_DN43367_c2_g1_i6 from sample A7 / Example unspliced isoform:

AGGAAGCAGAATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGTAGTCTACAGGTTTGTTTAGACTGATAAAGAAAGCTTTTGGTTATATCCCTTCATTAGATATGTGTTGTGATCTTATTGTTTCATTATAATTGGGTTCATCACAATGAAAGCCTT
TGTGTTTAGGTGTTTCAAAAGTTCGTGAAATTATTTCTATATAATTTTAGGAAATTTTCTACTTCATGAGCTGGTTATCCTTGAATATTTCTCTGAAGTATGTTTGTTTCACAGGTTTTGAAGGATGGACTCCAAGCTGTGCATGTTCCTTATGCATGTTCAAATAAGATCATTCCTTAATGCTTGGGTGTTGAAACTTG
TGTCATATGACTTGCACATTTCTTGTTGCCGTATAAGAAATTTTATTAATCAGCTGGTTAAGTTTgtaagctgatttttttttcttcagtttttaatagttatggaaatatttctatgttcttgaatggataattgtttaatcttgcagAAGCAACTGGAAAAAGAAAATGTTAGACCGCGTATCACAGATGTGGGTGGG
CATCCAAATAACAAGAGAAATAGAACAGGCTCAAATGACTCAGATTTGGGTGGGCAGCCAGACAACAAGAGAAATAGAACAGACTCAAATGGCTCATCTGAAAAAATTGGAGATCAAGCCACAAGGTGTACCTTTATAAATCATTCCAGGTTTCCTAAAGATCAGCAGCCTGACGTTAGTCTCTTGGAGAATACTTGCCA
GGCTCCTTCAGTAAAGGCATGGGTGAATGGCATTAAGACAAACAATGCATCTTGTGAGAATGGTTGCAGAACTGATGCTAATGTGCAAGAGAACAAACATCTTCAGAAGGCAAAGTTACCTGTCAAAGATAGGATCCGTCTCCTTGTGGGTTATGATGATTTAATTAGTGATGGTATACAAGATCATGATTTCAAGGAAG
AGAATGGTGGGCATATCCAGGATGCTATATGAGGAGCAGGATTGATAGTCATATGCAATCTTACTATTTTCTGGGCTCATACATTCTCAAGCTGTGCAAATACTCTGTTAGGGTTAGGAATAAGTAGCCTTTGATGAGATCTACTTTTTTCTGGCAGCATATGAGAAATGATATGGAGTTACTAAAAAAATCGTTGTATT
CTTTCAGAACTGTACAGTGGCCATCATATTTTTCTTTGTCAAATGAAATAGATTTCGATCGATCCTATTCTCTTCTGGTTTGGGGGATTGGCTTAAAATCAGAAATGATGGTTAAGGTTTGGTGCACTACTTATTCAACAAACTACCCTTCAGTGTTATTTGATAACTAGCAGCACACAGATAAAAGCTATAGCTGATAA
GCATTCTCAAAATGCCATCAATAGACTAGAAACATAAACAGAACATGTAGATTTTGCTCTTGCATCAATTGGAAGATGACACTAATAAAACAGTTGAATATGGAGTTGTCTAAAAATTTGACGATTTGGCCCGGATGTGTGGGGTTTTCACCTAAATCCGATGTTTTTTATTTTGCAAAATCTGAATTTAAGTGTGTTTT
AATGGTGATTTTGATGGTAGAAACGGATTCAACACCATAAAAAAATCCCGGGGCACCCAAAATTTCAGAGTTTGAAAGTTGTAACCAGGATTTTAAAAGAAATTCTCTCGCATTTTTTCAAAATCGTGCCGGAAAAATCAAATTTTTCCGTTTGAAATTGTAGATCTTTTAGACTACGTGGTTGAATATCCCTTTGTACC
TGGGAAGTTGGATACTTTATCAGGGTCTGCAACAGATTTTTGATTTTTCATTAATTAATTGTGTATCTAGCCAGTTTTTTGCATATTAAATGATATATATTTATTGTTTTGTGG

Intron 2 GTATAAGAAA ... AATCTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50.33	75	3	76
A2	53.33	49	10	56
A3	54.2	60	6	71
A4	53.93	41	4	48
A5	53.97	29	4	34
A6	54.21	49	4	58
A7	54.55	180	18	216
A8	51.13	217	17	227
A9	53.61	180	7	208
A10	50.78	190	7	196

>TRINITY_DN125675_c4_g1_i5 from sample A1 / Example spliced isoform

CAACATTCAAAGATCTCGGCCCAGCTATTCATTGATGAGGAAGCAGAATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGGTTTTGAAGGATGGACTCCAAGCTGTGCATGTTCCTTATGCATGTTCAAATAAGATCATTCCTTAATG
CTTGGGTGTTGAAACTTGTGTCATATGACTTGCACATTTCTTGTTGCCAAGCAACTGGAAAAAGAAAATGTTAGACCGCGTATCACAGATGTGGGTGGGCATCCAAATAACAAGAGAAATAGAACAGGCTCAAATGACTCAGATTTGGGTGGGCAGCCCAACAACAAGAGAAATAGAACGGACTCAAATGGTTCATCTGA
AAAAATTGGAGATCGAGCCACAAGGTGTACCTTTATAAATCATTCCAGGTTTCCTAAAGATCAGCAGCCTGACGTTAGTCTCTTGGAGAATACTTGCCAGGCTCCTTCAGTAAAGGCATGGGTGAATGGCATTAAGACAAACAATGCATCTTGTGAGAATGGTTGCAGAACTGATGCTAATGTGCAAGAGAACAAACATC
TTCAGAAGGCAAAGTTACCTGTCAAAGATAGGATCCGTCTCCTTGTGGGTTATGATGATTTAATTAGTGATGGTATACAAGATCATGATTTCAAGGAAGAGAATGGTGGGCATATCCAGGATGCTATATGAGGAGCAGGATTGATAGTCATATGCAATCTTACTATTTTCTGGGCTCATACATTCTCAAGCTGTGCAAAT
ACTCTGTTAGGGTTAGGAATAAGTAGCCTTTGATGAGATCTACTTTTTTCTGGCAGCATATGAGAAATGATATGGAGTTACTAAAAAAATCGTTGTATTCTTTCAGAACTGTACAGTGGCCATCATATTTTTCTTTGTCAAATGAAATAGATTTCGATCGATCCTATTCTCTTCTGGTTTGGGGGATTGGCTTAAAATCA
GAAATGATGGTTAAGGTTTGGTGCACTACTTATTCAACAAACTACCCTTCAGTGTTATTTGATAACTAGCAGCACACAGATAAAAGCTATAGCTGATAAGCATTCTCAAAATGCCATCAATAGACTAGAAACATAAACAGAACATGTAGATTTTGCTCTTGCATCAATTGGAAGATGACACTAATAAAACAGTTGAATAT
GGAGTTGTCTAAAAATTTGACGATTTGGCCCGGATGTGTGGGGTTTTCACCTAAATCCGATGTTTTTTATTTTGCAAAATCTGAATTTAAGTGTGTTTTAATGGTGATTTTGATGGTAGAAACGGATTCAACACCATAAAAAAATCCCGGGG

>TRINITY_DN125675_c4_g1_i4 from sample A1 / Example unspliced isoform:

CAACATTCAAAGATCTCGGCCCAGCTATTCATTGATGAGGAAGCAGAATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGGTTTTGAAGGATGGACTCCAAGCTGTGCATGTTCCTTATGCATGTTCAAATAAGATCATTCCTTAATG
CTTGGGTGTTGAAACTTGTGTCATATGACTTGCACATTTCTTGTTGCCgtataagaaattttattaatcagctggttaagtttgtaagctgattttttttttcttcagtttttaatagttatggaaatatttctatgttcttgaatggataattgtttaatcttgcagAAGCAACTGGAAAAAGAAAATGTTAGACCGCG
TATCACAGATGTGGGTGGGCATCCAAATAACAAGAGAAATAGAACAGGCTCAAATGACTCAGATTTGGGTGGGCAGCCCAACAACAAGAGAAATAGAACGGACTCAAATGGTTCATCTGAAAAAATTGGAGATCGAGCCACAAGGTGTACCTTTATAAATCATTCCAGGTTTCCTAAAGATCAGCAGCCTGACGTTAGTC
TCTTGGAGAATACTTGCCAGGCTCCTTCAGTAAAGGCATGGGTGAATGGCATTAAGACAAACAATGCATCTTGTGAGAATGGTTGCAGAACTGATGCTAATGTGCAAGAGAACAAACATCTTCAGAAGGCAAAGTTACCTGTCAAAGATAGGATCCGTCTCCTTGTGGGTTATGATGATTTAATTAGTGATGGTATACAA
GATCATGATTTCAAGGAAGAGAATGGTGGGCATATCCAGGATGCTATATGAGGAGCAGGATTGATAGTCATATGCAATCTTACTATTTTCTGGGCTCATACATTCTCAAGCTGTGCAAATACTCTGTTAGGGTTAGGAATAAGTAGCCTTTGATGAGATCTACTTTTTTCTGGCAGCATATGAGAAATGATATGGAGTTA
CTAAAAAAATCGTTGTATTCTTTCAGAACTGTACAGTGGCCATCATATTTTTCTTTGTCAAATGAAATAGATTTCGATCGATCCTATTCTCTTCTGGTTTGGGGGATTGGCTTAAAATCAGAAATGATGGTTAAGGTTTGGTGCACTACTTATTCAACAAACTACCCTTCAGTGTTATTTGATAACTAGCAGCACACAGA
TAAAAGCTATAGCTGATAAGCATTCTCAAAATGCCATCAATAGACTAGAAACATAAACAGAACATGTAGATTTTGCTCTTGCATCAATTGGAAGATGACACTAATAAAACAGTTGAATATGGAGTTGTCTAAAAATTTGACGATTTGGCCCGGATGTGTGGGGTTTTCACCTAAATCCGATGTTTTTTATTTTGCAAAAT
CTGAATTTAAGTGTGTTTTAATGGTGATTTTGATGGTAGAAACGGATTCAACACCATAAAAAAATCCCGGGG

Intron 3 GTTTGTTTAG ... GTCTTGACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	30.25	168.3	60.7	85.3
A2	17.55	126	22.7	31
A3	20.77	156.3	35.7	46.3
A4	26.17	113.3	34.3	46
A5	18.14	67.7	8	22
A6	20.83	55	14	15
A7	19.97	199.7	56.7	43
A8	21.67	159	32	56
A9	17.52	177.3	28.3	47
A10	22.79	194.7	54	61

>TRINITY_DN106400_c0_g1_i1 from sample A3 / Example spliced isoform

TAAGATAATGACTTTGATGCCCGACTCCTTGTTTCTTTAAATGTGTTGCGATTGAGTTGTGAACACTCCTGCTTTATTAAATACCCAGGAAATTTATATTTGGCTACAAGTTCAAATATGATTAGAAGAAATGTTGATTTGATCATTCTATATTTATTTCTCATTGGTAGCAAAATGTATTTCTTTGAGGTTAATGAACA
TGATACTGACATTAATGAAGGAGAATCGCAATCAGATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGGAGGTCCTTATTCACACAGCCGCCATTAGATGAAGAGTTGAATCCCTGGCTCATTTTTGTCGGCCACAGGCATTTACTGG
AAGTGAAAGTCCAGATCCTTCAGAAAGTATTACTGCTTCTGTAGATAACAATATTGGATCTATCATCTGATACAAAATCTTTGGCTACATCGTCT

>TRINITY_DN106400_c0_g1_i2 from sample A3 / Example unspliced isoform:

TAAGATAATGACTTTGATGCCCGACTCCTTGTTTCTTTAAATGTGTTGCGATTGAGTTGTGAACACTCCTGCTTTATTAAATACCCAGGAAATTTATATTTGGCTACAAGTTCAAATATGATTAGAAGAAATGTTGATTTGATCATTCTATATTTATTTCTCATTGGTAGCAAAATGTATTTCTTTGAGGTTGATGAACA
TGATACTGACATTAATGGAGGAGAATCGCAATCAGATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGgtttgtttagactgataaagaaagcttttggttcatagttttatgtaaacttgttgctgccttctactttttcagctaca
catttctttaagcgtgactaatggacttcattgattttaaatttttgctgtgatctgtcttgacagGAGGTCCTTATTCACACAGCCGCCATTAGATGAAGAGTTGAATCCCTGGCTCATTTTTGTCGGCCACAGGCATTTACTGGAAGTGAAAGTCCAGATCCTTCAGAAAGTATTACTGCTTCTGTAGATAACAATAT
TGGATCTATCATCTGATACAAAATCTTTGGCTACATCGTCT

Intron 4 GTTAGCTATT ... TTGGTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	49.58	30	23	36
A2	60	15	13	32
A3	39.73	22	11	18
A4	53.19	11	5	20
A5	28	9	3	4
A6	26.67	11	0	8
A7	56.6	23	25	35
A8	54.76	19	22	24
A9	18.64	24	2	9
A10	40.82	29	9	31

>TRINITY_DN42352_c2_g1_i7 from sample A10 / Example spliced isoform

CAGATACTTTATGCAAGAAAGAAGAAACATGACATTACCAATGATAGTATACAAAGGAAATCAAAGCTCTCAAAAGCAAAACAACATTCAAAGATCTCTGCCCAGCTATTCATTGATGAGGAAGCAGACAAAATGTATTTCTTTGAGGTCGATGAACATGATACGGACATTAATGAAGGAGAATCGCAATCAGATAGCTT
TATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAGGAGGTCCTTATTCACACAGCCGCCATTAGATGAAGAGTTGAATCCCTGGCTCATTTTTGTCGGCCACAGGCATTTACTGGAAGTGAAAGTCCAGATCCTTCAGAAAGTATTACTGCTTCTGT
AGATAACAATATTGGATCTATCATCTGATACAAAATCTTTGGCTACATCGTCTACACCAACTCTGATTAGGAATACAGATAATAAAACCTCCAGCTCTATGGGACTATACAATGCTGTTGACGATTCAAGAGTAGTTGAACTCAAGCCTAGCTCAAGTGAGGAAAAACACAGTAAAAAAAGAAAACTAAGTTTTCAGCCA
GTTGATTTTACTGGAAAGTCAAATGTTTTTGAGAGCCAAGTACCACCATTTTTAGTGGAAAACTTGAGAGAGAC

>TRINITY_DN42352_c2_g1_i4 from sample A10 / Example unspliced isoform:

CAGATACTTTATGCAAGAAAGAAGAAACATGACATTACCAATGATAGTATACAAAGGAAATCAAAGCTCTCAAAAGgttagctattttcagcttgctattattttcttatttatcttctgtctcgatatagaggtgagaactgaatgaagtagtgtaattttctatttttggactaaaggtttggtttttggttgcagCA
AAACAACATTCAAAGATCTCTGCCCAGCTATTCATTGATGAGGAAGCAGACAAAATGTATTTCTTTGAGGTCGATGAACATGATACGGACATTAATGAAGGAGAATCGCAATCAGATAGCTTTATAGACGATAGGGTAGAACCAACAGCAGCATCTACTCAATCTGAAGGCGATCAGGTTGACATAATGGCAGTCTACAG
GAGGTCCTTATTCACACAGCCGCCATTAGATGAAGAGTTGAATCCCTGGCTCATTTTTGTCGGCCACAGGCATTTACTGGAAGTGAAAGTCCAGATCCTTCAGAAAGTATTACTGCTTCTGTAGATAACAATATTGGATCTATCATCTGATACAAAATCTTTGGCTACATCGTCTACACCAACTCTGATTAGGAATACAG
ATAATAAAACCTCCAGCTCTATGGGACTATACAATGCTGTTGACGATTCAAGAGTAGTTGAACTCAAGCCTAGCTCAAGTGAGGAAAAACACAGTAAAAAAAGAAAACTAAGTTTTCAGCCAGTTGATTTTACTGGAAAGTCAAATGTTTTTGAGAGCCAAGTACCACCATTTTTAGTGGAAAACTTGAGAGAGAC