sp|P31726|CYT1_MAIZE ----> Cystatin-1

Intron 1 GTATGGATGT ... TCTTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	37.63	24	14	15
A2	29.48	15	7	5.6
A3	35.5	14	8.6	6.9
A4	31.21	14	1	11.7
A5	18.37	32	7	7.4
A6	27.79	30	15	8.1
A7	30.94	25	12	10.4
A8	28.78	12	4	5.7
A9	23.92	20.6	8.6	4.4
A10	41.65	11	7	8.7

>TRINITY_DN124761_c1_g1_i11 from sample A1 / Example spliced isoform

TCACGTACTTATGGAACGCATGGCCTGCTTAGGAGTTTTCAATTACATAAAACAGCCAGAGGGTGGATTACATATTTGTCAATCATACTAGTTCTCATTTTATAGAATTTGAATACTAGAATCAACAACAGTAAAATTGTCTGCATATTTCAAAATGCCATCAACGATTGTTGGTTCCAACTCGTTGGAAGGATTCTATG
TAGAAAATGCATCACTGAGAATGCCTACGAGAAAATCAGATGTCGCAAACGAAAATGGGTCGTCCCTAAACCTCGGGCAAGCCGTAGAACCAGAGGATCAATGCAATTATTCTCTGCAGAAGTCTGCCCACAAAATGGACAACGATCCTTGGTACCAAGTGGGATTGCTGCTGGTCACGAGCTTCAACTGTGTTTACATT
TTGGGGTTTTCCAACCTCATTCTGGTTCCTCTAGGACTGGTCTGGGGGTTAATCAGCATGATTGTTATAGGCGCTTTCTCGCTATATGCCAATCTGCTGCTCTCAAATTTATACATCATAGATGGCCAGCGCTTCATCAGATATAGGGATTTAATTGGCTACGCATTTGGTAAGTAATACTTTCATACAAAAGAAGATAA
TTAAAGGCGCGTTTTTTTCTTTTCGGGTCAATTTTTGTGCGGCTACGTTGTAGCCAATGTTTGTTGATTTAGTTAGTGGAAAGATACAGTGAGATTAGCTGCAAAGAGGGTCTATCATGATTTTATTGTTTGACAATATTGCATAAGCAATTTGTGGCTTAGTGCATTGCAGGAAGGAAAATGTATTATTTATCCCGGGC
TCTACAATTTGTTCATTTCATACTCTGCAACATGGGATTCCTCCTGCTTTCAGGAAAGGCTTTGGAGGATATCTTTGTGGATCACAACAGGATGGTCACGCTGAAACTCCCAGAATTCATTATGATTTCAGGAGTAACATATTTCATTTTTGCCTTCTCGGTACCGCATTTGTCAGCAATGGGCATATGGTCTGGAATTT
CAGCATTCCTAACGTTTGTCTATGTTGCGATAGCAATGATAATATCAATCAGAGATGGCAATTCTAGGTCGAAGGAGTACCATGTCCCTGGAACGGAGCAACAAAAAGTTTTCAATGCATTAGGAGCAATCGCAGCCATTGCCTTTGCAAATAACTCTGGCATGTTACCTGAAATTCAGGCTACATTGAAGCACCCTGCT
ATCAAAAACATGCACAAAGCGCTTTACTTACAATATTCCTTCGGAATGGCGATATACTACACGGTTACAGTTATTGGATACTGGGCATACGGGTCATCTGTCTCAGAATATCTCCTCGATGATCTGAGCGGGCCAAAGTGGGCGAAAATTCTGGCAAACACAGCTGCATTTTTGCAGACTATTGTATCACAACATGTATA
TAATTTCTTCCATTTCATTAGACACAAGAGAACATAGATTTAGACTAATCCTAGAATTAGGCCTTCACCCAAACTTCCATTCCAGGGAAAGTGGTTGTGTAGCACACAAACCTTCACCTCCTCACCTCACCTGTGTGAAGAATCATAAATATTCACCCCACCATTCATCCTCCCTCATATCCCCATACACAAACCTTCAG
CCCTAAAGGGTGG

>TRINITY_DN124761_c1_g1_i3 from sample A1 / Example unspliced isoform:

TCACGTACTTATGGAACGCATGGCCTGCTTAGGAGTTTTCAATTACATAAAACAGCCAGAGGGTGGATTACATATTTGTCAATCATACTAGTTCTCATTTTATAGAATTTGAATACTAGAATCAACAACAGTAAAATTGTCTGCATATTTCAAAATGCCATCAACGATTGTTGGTTCCAACTCGTTGGAAGGATTCTATG
TAGAAAATGCATCACTGAGAATGCCTACGAGAAAATCAGATGTCGCAAACGAAAATGGGTCGTCCCTAAACCTCGGGCAAGCCGTAGAACCAGAGGATCAATGCAATTATTCTCTGCAGAAGTCTGCCCACAAAATGGACAACGATCCTTGGTACCAAGTGGGATTGCTGCTGGTCACGAGCTTCAACTGTGTTTACATT
TTGGGGTTTTCCAACCTCATTCTGGTTCCTCTAGGACTGGTCTGGGGGTTAATCAGCATGATTGTTATAGGCGCTTTCTCGCTATATGCCAATCTGCTGCTCTCAAATTTATACATCATAGATGGCCAGCGCTTCATCAGATATAGGGATTTAATTGGCTACGCATTTGGTAAGTAATACTTTCATACAAAAGAAGATAA
TTAAAGGCGCGTTTTTTTCTTTTCGGGTCAATTTTTGTGCGGCTACGTTGTAGCCAATGTTTGTTGATTTAGTTAGTGGAAAGATACAGTGAGATTAGCTGCAAAGAGGGTCTATCATGATTTTATTGTTTGACAATATTGCATAAGCAATTTGTGGCTTAGTGCATTGCAGGAAGGAAAATGTATTATTATCCCGGGCT
CTACAATTTGTTCATTTCATACTCTGCAACATGGGATTCCTCCTGCTTTCAGGAAAGTTTTTGAAGGTGATTTTGCTAGTTATCATTTAGCATTTAGAATTCATCAGTCACAGACTAGAAAAAAATGAATACTTTTGCAAATTGTTTTGAAAATAAGGCCGTTTAGGAAACTGTATTTATCACATTTAAGTCTATAACCT
CAAAGGAAAACGGTCATTACCAGAAAACTATCAAAGCTCTGAATGCTTATGGATAACGTTATCTGCTCTCAGTCATCTTTGGTCTTAATCTGTAAAAACATAGTGGGGTCCGGTTGAACTTTCTACTCCAGTAGGCCAAGCTGGGATCCGCCTATATATATTACTGATGCTGCAATGAGTTTACATAGCAAATCACATTG
GAAACATTGTTTCTTTTCTTTATTTTTGTTTGAAATATTGTTGAATTTGAATTTTTTATTTATTTTTCCTCTGATTGTTTTGTGATACCGGTATGGAGAACTATACGACAGCTTACAGTGTTTTTCTTAGAACTTGTAAAAAATATAATCTTTATTGTGCAAAAAACCACACAGATGAGCTTGATTAAAAATGGACAAAA
GCCCACCCAAATGCTTGAAAATTTGAGGCTTTCACAACCCCGACCCCACCGCAAAACACTCTCGACACCTGCCCATGTTAAACCAAGCCCTGCTCATATTATAAATGAATCCAGCCGTGGTTTTCTCAAGGCTTGTCATTTATATGAGGTTGGGATGGGGGATGGGATCTACCTGAACTTATCTTAGGCTTTAAGAAAAA
AGAAACAAAGGATTCAAGGGAAGTCTGTACATTTCTCCATGATTTTTGGGCTTGAAAGACTTGTGGGTGCTTCTCAATTATTTCCTTTCATGATGACACAGGATATCTTTGTGGATCACAACAGGATGGTCACGCTGAAACTCCCAGAATTCATTATGATTTCAGGAGTAACATATTTCATTTTTGCCTTCTCGGTACCG
CATTTGTCAGCAATGGGCATATGGTCTGGAATTTCAGCATTCCTAACGTTTGTCTATGTTGCGATAGCAATGATAATATCAATCAGAGATGgtatggatgttctgcattgaaatctctctgctgcaaaggttcttaatggtcatttatcaagaattcccaaaaggtaatattacaagctttcttttgcagGCAATTCTAG
GTCGAAGGAGTACCATGTCCCTGGAACGGAGCAACAAAAAGTTTTCAATGCATTAGGAGCAATCGCAGCCATTGCCTTTGCAAATAACTCTGGCATGTTACCTGAAATTCAGGTGATGAGCACCTGATTTTTCTCAAAGTTCCTAGTCTCTTTTTAATTTAATAAAAAAACACTAATCTAACTCAGCG

Intron 2 GTAATATTTC ... TCTGTGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	38.46	8	5	0
A2	18.75	13	3	1
A3	21.05	15	4	1
A4	22.22	7	2	0
A5	30.77	9	4	0
A6	26.51	61	22	2
A7	19.51	33	8	1
A8	21.05	60	16	1
A9	18.87	43	10	2
A10	32.26	21	10	0

>TRINITY_DN44664_c1_g1_i11 from sample A10 / Example spliced isoform

CTTTAGCTGTTAGAGATCAATCAGTGATTTCTCCTTCTCGGACTTCAACTGTTTTTGTTTTTTTAGCTTTTCTATATATATTTATATCACGTACTTATGGAACGCATGGCCTGCTTAGGAGTTTTCAATTACATAAAACAGCCAGAGGGTGGATTACATATTTGTCAATCATACTAGTTCTCATTTTATAGAATTTGAAT
ACTAGAATCAACAACAGTAAAATTGTCTGCATATTTCAAAATGCCATCAACGATTGTTGGTTCCAACTCGTTGGAAGGATTCTATGTAGAAAATGCATCACTGAGAATGCCTACGAGAAAATCAGATGTCGCAAACGAAAATGGGTCGTCCCTAAACCTCGGGCAAGCCGTAGAACCAGAGGATCAATGCAATTATTCTC
TGCAGAAGTCTGCCCACAAAATGGACAACGATCCTTGGTACCAAGTGGGATTGCTGCTGGTCACGAGCTTCAACTGTGTTTACATTTTGGGGTTTTCCAACCTCATTCTGGTTCCTCTAGGACTGGTCTGGGGGTTAATCAGCATGATTGTTATAGGCGCTTTCTCGCTATATGCCAATCTGCTGCTCTCAAATTTATAC
ATCATAGATGGCCAGCGCTTCATCAGATATAGGGATTTAATTGGCTACGCATTTGGAAGGAAAATGTATTATTTATCCTGGGCTCTACAATTTGTTCATTTCATACTCTGCAACATGGGATTCCTCCTGCTTTCAGGAAAGGCTTTGGAGGATATCTTTGTGGATCACAACAGGATGGTCACGCTGAAACTCCCAGAATT
CATTATGATTTCAGGAGTAACATATTTCATTTTTGCTTTCTCGGTACCGCATTTGTCAGCAATGGGCATATGGTCTGGAATTTCAGCATTCCTAACGTTTGTCTATGTTGCGATAGCAATGATAATATCAATCAGAGATGGTATGGATGTTCTGCATTGAAATCTCTCTGCTGCAAAGGTTCTTAATGGTCATTTATCAA
GAATTCCCAAAAGGTAATATTACAAGCTTTCTTTTGCAGGCAATTCTAGGTCGAAGGAGTACCATGTCCCTGGAACGGAGCAGCAAAAAGTTTTCAATGCATTAGGAGCAATCGCAGCCATTGCCTTTGCAAATAACTCTGGCATGTTACCTGAAATTCAGGCTACATTGAAGCACCCTGCTATCAAAAACATGCACAAA
GCGCTTTACTTACAATATTCCTTCGGAATGGCGATATACTACACGGTTACAGTTATTGGATACTGGGCATACGGGTCATCTGTCTCAGAATATCTCCTCGATGATCTGAGCGGGCCAAAGTGGGCGAAAATTCTGGCAAACACAGCTGCATTTTTGCAGACTATTGTATCACAACATATATTCTGTGTTCCTGTGCATGA
GGCTCTTGACACCAAATTTTGTCGCCTGGATGAACATGAAAATTCCTTATATAACCTTACAACTCGATTCATCCTGCGGGCGCTATTTTTTGCAATCAGCACACTGTCTGCTGCCATGTTTCCCTTCATAGGAGACTTTGTAACCCTGGTGGGCTCATTGTCTCTCATTCCATTAACGTTCGTGTTTCCATCCCTGGTAT
TCCTTAAGGTGAATCGACATAGTAGCAGTGTATGGGAGAAATCATGGCATATGTTCACTGTTGTTTTATTTGTTCTTGTAACCTTGGCGACCACTGCATCGGCTTTTCGTTTGATAATAACAAACGCTAAAACGTACCGTTTATTTGCAAACGCTTGAAAATATAACATAGCAGGAAATTTGGATTTCCTCCAATCTCGC
TGTGATGAAGCAATCTCTTCCGGTTGCAGCCCGAACCTAAAAATGTTGTGTATATTATCATATTTCATGGCGAGATACATGTGAATGGAGTATTTGTCAGGTTGTCAC

>TRINITY_DN44664_c1_g1_i13 from sample A10 / Example unspliced isoform:

GTTGCAGATATTCTGTGTTTCTTATCCAACTATTCATACATCACCTAGAAGGTTTTTTTTATGCTCATTTGATGAAAGATCCTGTATTTTTTGGTTGCAGATATTCTGTGTTCCTGTGCATGAGGCTCTTGACACCAAATTTTGTCGCCTGGATGAACATGAAAATTCCTTATATAACCTTACAACTCGATTCATCCTGC
GGGCGCTATTTTTTGCAATCAGCACACTGTCTGCTGCCATGTTTCCCTTCATAGGAGACTTTGTAACCCTGGTGGGCTCATTGTCTCTCATTCCATTAACGTTCGTGTTTCCATCCCTGGTATTCCTTAAGgtaatatttcttatgattatcaatacttctccctcccttcatatatttcttttgccggaaattgggacc
taattgaacagctgcttccatgtctgtggcagGTGAATCGACATAGTAGCAG

Intron 3 GTTAGTTTCG ... AGGGTTTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	49.67	43.6	43	13
A2	48.17	25.9	24	10
A3	51.39	35	37	8.1
A4	55.23	27.6	34	15
A5	52.38	30	33	5
A6	49.63	255.7	252	70
A7	49.13	234	226	38.1
A8	48.78	257.3	245	58.3
A9	49.14	271.1	262	56.4
A10	47.93	201	185	32.7

>TRINITY_DN124761_c1_g1_i2 from sample A1 / Example spliced isoform

ATGAAAATGTCGATGAAAATGCCGACGAGATGCAGCCGAACAATGGCGGTGTTGATACTGTTGTTCTTGGGATGCCTCTGCATGTCGGATGCTTCTGCTCGCGTTGGGGGCATCCGCGACATACCGGATGTAGAGCACAAGCAAGATATTCAAGATCTCGGACAGTTTGCCGTCAATGAATACAACGCGCAACAGAATGT
CGGTATTTCGTTTTCCAAGGTGTTAAAAGCCCAGGAGCAAGTGGTCTCAGGCCTGCTGTACTTCCTCACAATAGAGACCAAAGCCGGCGGTAAAACCAAGCTGTATGCGGCCAAACTATGGGTGAAGCCATGGGAGAAATTCAAGCAGCTGCAAGAGTTCAAGCCTGTGCAGACTATGCATTAATGACGGATTCGGAGAA
AAATATTGCAAATGCTCGGATCGGATGGTGTAGATTCAATGCTTAGGAACCTGAATGCCTGTTTAGCAATGCTGTTTAGCAATGTTGCTCACAAGCTTGAAGGTCGTCATGGCATTTACCATCTAGGGCTGGTTTTTGGCTTTGTATGTCTGTAACTGATGGTAATGGTGAAATCAAATGTTCGTTAGTATCCATGGATG
ACCCAAAAGAACTCTACATGTGATTTCGGCAAAATGATAAAGTGGAAAGTAGTGATAATATTTAATATTCAATTTATATAACTAGTAAATATTCCTCTGGCCGAAATATAAATTTGATTTGATTTTATGTAATTAGTTTATTGTTTTAATATTTAATATTCAGTTTAAATAACTAGTAAATATTCCTCTGGCCGAAATAT
AAATTTGATTTGATTTTATGTAATTAGTTTATTGTTTATTTATTTTTATTTAGGTGAAAATCTTCTTGATATCTATGTCAATATGCATTCTCTGCACACAAATTAAGGCACACAAATATAGGGGCGAGTCGGGCGACAAG

>TRINITY_DN124761_c1_g1_i12 from sample A1 / Example unspliced isoform:

ATGAAAATGTCGATGAAAATGCCGACGAGATGCAGCCGAACAATGGCGGTGTTGATACTGTTGTTCTTGGGATGCCTCTGCATGTCGGATGCTTCTGCTCGCGTTGGGGGCATCCGCGACATACCGGATGTAGAGCACAAGCAAGATATTCAAGATCTCGGACAGTTTGCCGTCAATGAATACAACGCGCAACAGAATGT
CGGTATTTCGTTTTCCAAGGTGTTAAAAGCCCAGGAGCAAGTGGTCTCAGGCCTGCTGTACTTCCTCACAATAGAGACCAAAGCCGGCGGTAAAACCAAGCTGTATGCGGCCAAACTATGGGTGAAGCCATGGGAGAAATTCAAGCAGCTGCAAGAGTTCAAGCCTGTGCAGACTATGCATTAATGACGgttagtttcgt
cttcttctgtctttttcttttctttttcccttttctgaaggtagggtttcagGATTCGGAGAAAAATATTGCAAATGCTCGGATCGGATGGTGTAGATTCAATGCTTAGGAACCTGAATGCCTGTTTAGCAATGCTGTTTAGCAATGTTGCTCACAAGCTTGAAGGTCGTCATGGCATTTACCATCTAGGGCTGGTTTTT
GGCTTTGTATGTCTGTAACTGATGGTAATGGTGAAATCAAATGTTCGTTAGTATCCATGGATGACCCAAAAGAACTCTACATGTGATTTCGGCAAAATGATAAAGTGGAAAGTAGTGATAATATTTAATATTCAATTTATATAACTAGTAAATATTCCTCTGGCCGAAATATAAATTTGATTTGATTTTATGTAATTAGT
TTATTGTTTTAATATTTAATATTCAGTTTAAATAACTAGTAAATATTCCTCTGGCCGAAATATAAATTTGATTTGATTTTATGTAATTAGTTTATTGTTTATTTATTTTTATTTAGGTGAAAATCTTCTTGATATCTATGTCAATATGCATTCTCTGCACACAAATTAAGGCACACAAATATAGGGGCGAGTCGGGCGAC
AAG

Intron 4 GTAAGTAATA ... TGCATTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52.79	24	35	18.7
A2	44.22	29	27	19
A3	35.28	33	26	10.3
A4	48.08	27	25	25
A5	55.67	13	23	9.7
A6	30.22	25	15	6.7
A7	27.21	20	8	7.3
A8	47.78	4	4	3.3
A9	22.59	26	12	3.3
A10	34.87	11	10	2

>TRINITY_DN124761_c1_g1_i5 from sample A1 / Example spliced isoform

TCACGTACTTATGGAACGCATGGCCTGCTTAGGAGTTTTCAATTACATAAAACAGCCAGAGGGTGGATTACATATTTGTCAATCATACTAGTTCTCATTTTATAGAATTTGAATACTAGAATCAACAACAGTAAAATTGTCTGCATATTTCAAAATGCCATCAACGATTGTTGGTTCCAACTCGTTGGAAGGATTCTATG
TAGAAAATGCATCACTGAGAATGCCTACGAGAAAATCAGATGTCGCAAACGAAAATGGGTCGTCCCTAAACCTCGGGCAAGCCGTAGAACCAGAGGATCAATGCAATTATTCTCTGCAGAAGTCTGCCCACAAAATGGACAACGATCCTTGGTACCAAGTGGGATTGCTGCTGGTCACGAGCTTCAACTGTGTTTACATT
TTGGGGTTTTCCAACCTCATTCTGGTTCCTCTAGGACTGGTCTGGGGGTTAATCAGCATGATTGTTATAGGCGCTTTCTCGCTATATGCCAATCTGCTGCTCTCAAATTTATACATCATAGATGGCCAGCGCTTCATCAGATATAGGGATTTAATTGGCTACGCATTTGGAAGGAAAATGTATTATTTATCCCGGGCTCT
ACAATTTGTTCATTTCATACTCTGCAACATGGGATTCCTCCTGCTTTCAGGAAAGGCTTTGGAGGATATCTTTGTGGATCACAACAGGATGGTCACGCTGAAACTCCCAGAATTCATTATGATTTCAGGAGTAACATATTTCATTTTTGCCTTCTCGGTACCGCATTTGTCAGCAATGGGCATATGGTCTGGAATTTCAG
CATTCCTAACGTTTGTCTATGTTGCGATAGCAATGATAATATCAATCAGAGATGGCAATTCTAGGTCGAAGGAGTACCATGTCCCTGGAACGGAGCAACAAAAAGTTTTCAATGCATTAGGAGCAATCGCAGCCATTGCCTTTGCAAATAACTCTGGCATGTTACCTGAAATTCAGGCTACATTGAAGCACCCTGCTATC
AAAAACATGCACAAAGCGCTTTACTTACAATATTCCTTCGGAATGGCGATATACTACACGGTTACAGTTATTGGATACTGGGCATACGGGTCATCTGTCTCAGAATATCTCCTCGATGATCTGAGCGGGCCAAAGTGGGCGAAAATTCTGGCAAACACAGCTGCATTTTTGCAGACTATTGTATCACAACATATATTCTG
TGTTCCTGTGCATGAGGCTCTTGACACCAAATTTTGTCGCCTGGATGAACATGAAAATTCCTTATATAACCTTACAACTCGATTCATCCTGCGGGCGCTATTTTTTGCAATCAGCACACTGTC

>TRINITY_DN124761_c1_g1_i11 from sample A1 / Example unspliced isoform:

TCACGTACTTATGGAACGCATGGCCTGCTTAGGAGTTTTCAATTACATAAAACAGCCAGAGGGTGGATTACATATTTGTCAATCATACTAGTTCTCATTTTATAGAATTTGAATACTAGAATCAACAACAGTAAAATTGTCTGCATATTTCAAAATGCCATCAACGATTGTTGGTTCCAACTCGTTGGAAGGATTCTATG
TAGAAAATGCATCACTGAGAATGCCTACGAGAAAATCAGATGTCGCAAACGAAAATGGGTCGTCCCTAAACCTCGGGCAAGCCGTAGAACCAGAGGATCAATGCAATTATTCTCTGCAGAAGTCTGCCCACAAAATGGACAACGATCCTTGGTACCAAGTGGGATTGCTGCTGGTCACGAGCTTCAACTGTGTTTACATT
TTGGGGTTTTCCAACCTCATTCTGGTTCCTCTAGGACTGGTCTGGGGGTTAATCAGCATGATTGTTATAGGCGCTTTCTCGCTATATGCCAATCTGCTGCTCTCAAATTTATACATCATAGATGGCCAGCGCTTCATCAGATATAGGGATTTAATTGGCTACGCATTTGgtaagtaatactttcatacaaaagaagataa
ttaaaggcgcgtttttttcttttcgggtcaatttttgtgcggctacgttgtagccaatgtttgttgatttagttagtggaaagatacagtgagattagctgcaaagagggtctatcatgattttattgtttgacaatattgcataagcaatttgtggcttagtgcattgcagGAAGGAAAATGTATTATTTATCCCGGGC
TCTACAATTTGTTCATTTCATACTCTGCAACATGGGATTCCTCCTGCTTTCAGGAAAGGCTTTGGAGGATATCTTTGTGGATCACAACAGGATGGTCACGCTGAAACTCCCAGAATTCATTATGATTTCAGGAGTAACATATTTCATTTTTGCCTTCTCGGTACCGCATTTGTCAGCAATGGGCATATGGTCTGGAATTT
CAGCATTCCTAACGTTTGTCTATGTTGCGATAGCAATGATAATATCAATCAGAGATGGCAATTCTAGGTCGAAGGAGTACCATGTCCCTGGAACGGAGCAACAAAAAGTTTTCAATGCATTAGGAGCAATCGCAGCCATTGCCTTTGCAAATAACTCTGGCATGTTACCTGAAATTCAGGCTACATTGAAGCACCCTGCT
ATCAAAAACATGCACAAAGCGCTTTACTTACAATATTCCTTCGGAATGGCGATATACTACACGGTTACAGTTATTGGATACTGGGCATACGGGTCATCTGTCTCAGAATATCTCCTCGATGATCTGAGCGGGCCAAAGTGGGCGAAAATTCTGGCAAACACAGCTGCATTTTTGCAGACTATTGTATCACAACATGTATA
TAATTTCTTCCATTTCATTAGACACAAGAGAACATAGATTTAGACTAATCCTAGAATTAGGCCTTCACCCAAACTTCCATTCCAGGGAAAGTGGTTGTGTAGCACACAAACCTTCACCTCCTCACCTCACCTGTGTGAAGAATCATAAATATTCACCCCACCATTCATCCTCCCTCATATCCCCATACACAAACCTTCAG
CCCTAAAGGGTGG

Intron 5 GTCTGTCTGT ... CTTTCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	15.47	235	6	43
A2	14.11	274	0	45
A3	12.75	260	0	38
A4	17.24	216	0	45
A5	12.12	116	0	16
A6	13.92	1669	0	270
A7	13.14	1758	0	266
A8	16.21	1422	1	275
A9	15.77	1645	0	308
A10	11.83	1297	0	174

>TRINITY_DN124761_c1_g1_i4 from sample A1 / Example spliced isoform

ATGAAAATGTCGATGAAAATGCCGACGAGATGCAGCCGAACAATGGCGGTGTTGATACTGTTGTTCTTGGGATGCCTCTGCATGTCGGATGCTTCTGCTCGCGTTGGGGGCATCCGCGACATACCGGATGTAGAGCACAAGCAAGATATTCAAGATCTCGGACAGTTTGCCGTCAATGAATACAACGCGCAACAGAATGT
CGGTATTTCGTTTTCCAAGGTGTTAAAAGCCCAGGAGCAAGTGGTCTCAGGCCTGCTGTACTTCCTCACAATAGAGACCAAAGCCGGCGGTAAAACCAAGCTGTATGCGGCCAAACTATGGGTGAAGCCATGGGAGAAATTCAAGCAGCTGCAAGAGTTCAAGCCTGTGCAGACTATGCATTAATGACGTGTGCAGGTGG
TAATGGGTGATGGAACACTGCATCCTGTTGTTTGATTTTGCTTCTCCAGTTCTGGTTCACGAGGGTTGATGTGATGCCCAGGGTGTACTTAGTAGATTAAGCATGATAGGATGTTTTGATATTAGATTTGGTATTAATGGTAAGACAGAGTTTGTTCTCAATTGGACCTGATGGTTTGTAAAGTTGGCATTAAATGGACT
GTCCAGTGTCAGATGGGGTTCTAATCAGCTATTAAATGCTTTTTGGACTTAAAAAAAA

>TRINITY_DN124761_c1_g1_i6 from sample A1 / Example unspliced isoform:

TGAATACAACGCGCAACAGgtctgtctgtgtataaatacaatctctggtttagattccgccattgctgtaatgcacttgacattgtggtttttctttgctttctgcagAATGTCGGTATTTCGTTTTCCAAGGTGTTAAAAGCCCAGGAGCAAGTGGTCTCAGGCCTGCTGTACTTCCTCACAATAGAGACCAAAGCCGG
CGGTAAAACCAAGCTGTATGCGGCCAAACTATGGGTGAAGCCATGGGAGAAATTCAAGCAGCTGCAAGAGTTCAAGCCTGTGCAGACTATGCATTAATGACGTGTGCAGGTGGTAATGGGTGATGGAACACTGCATCCTGTTGTTTGATTTTGCTTCTCCAGTTCTGGTTCACGAGGGTTGATGTGATGCCCAGGGTGTA
CTTAGTAGATTAAGCATGATAGGATGTTTTGATATTAGATTTGGTATTAATGGTAAGACAGAGTTTGTTCTCAATTGGACCTGATGGTTTGTAAAGTTGGCATTAAATGGACTGTCCAGTGTCAGATGGGGTTCTAATCAGCTATTAAATGCTTTTTGGACTTAAAAAAAA