sp|P23444|H1_MAIZE ----> Histone H1

Intron 1 GTAATTGTAA ... TTTCATATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	71.43	2	7	3
A2	100	0	3	2
A3	100	0	4	8
A4	55.98	4	2	7
A5	83.33	1	5	5
A6	68.84	29.8	58	69
A7	76.5	8.5	24	30
A8	65.42	28.5	53	53
A9	63.31	31.8	53	55.3
A10	74.82	15.8	43	49

>TRINITY_DN44799_c1_g2_i3 from sample A6 / Example spliced isoform

AAAAGAAGCCGAGGGCTTCCAGGGGATCGAAACCGCCACCTTCTCATCCGACATATCTCCAGATGATCACAGAAGCGATTACATCTTTGAAGGAGAGAACGGGGTCCAGTCAGTATGCCATAGCAGCCTATATCGGCAGCAAGTATCAATCACAACTCCCTGCGAATTTCAAGAAGCTGCTAACGGTTCGGCTAAGAAAT
CTTGCCCAATCTGGCCAGCTCACCAAGGTCAAGAACTCCTTCAAGCTTTCTGAGGAGCTGAAGAAATCTGTGAAGCCCAAGGCCGCCAAGCCTATGAAGCTCAATGCCCCTGCCAAAAGGCTCGCAGCTAAGCCCAAGGCCGCCGAGCCTATGAAGCTCAATGCCCCTGCCAAAAGGCTCGCAACTAAGCCCAAGGCAGC
GCCTGCACCCAAGAAGGTTTCCAAGCCCGTTAAATCATCCGCCAAAGTAACCAAGTCTCCTAAGGTCGCAAAGCCGAAGCCTGCAGCGGCAGCTAAGAAGGTGGAGAAGGTAGCAGCGCCTGCTAAAAAGGCAGCGCCTGCTAAAAGGGCGGCATCTGCCAAGAAGCCTGTCCCTGCTAAGAAGTCTGTCAAGACTGTAA
AGAGGGCTAGCCCTCCCAAGACCAAGAAAGCGGCGCCGAAGCCCAAGAAAGCGGCGCCTGCTGCTAAGAAGGCTAAGAAATGAGATCGAGAAGCTAAATCTGTACATGAACAGGCGCAGGCACATAGGATAGGCTAGATTCAAGAGCACAGGGCGTGGGGTCGATT

>TRINITY_DN44799_c1_g2_i7 from sample A6 / Example unspliced isoform:

AAAAGAAGCCGAGGGCTTCCAGGGGATCGAAACCGCCACCTTCTCATCCGACATATCTCCAGATGATCACAGAAGCGATTACATCTTTGAAGGAGAGAACGGGGTCCAGTCAGTATGCCATAGCAGCCTATATCGGCAGCAAGTATCAATCACAACTCCCTGCGAATTTCAAGAAGCTGCTAACGGTTCGGCTAAGAAAT
CTTGCCCAATCTGGCCAGCTCACCAAGGTCAAGAACTCCTTCAAGCTTTCTGAGGAGCTGAAGAAATCTGTGAAGCCCAAGGCCGCCAAGCCTATGAAGCTCAATGCCCCTGCCAAAAGGCTCGCAGCTAAGCCCAAGGCCGCCGAGCCTATGAAGCTCAATGCCCCTGCCAAAAGGCTCGCAACTAAGCCCAAGGCAGC
GCCTGCACCCAAGAAGGTTTCCAAGCCCGTTAAATCATCCGCCAAAGTAACCAAGTCTCCTAAGGTCGCAAAGCCGAAGCCTGCAGCGGCAGCTAAGAAGGTGGAGAAGGTAGCAGCGCCTGCTAAAAAGGCAGCGCCTGCTAAAAGGGCGGCATCTGCCAAGAAGCCTGTCCCTGCTAAGAAGTCTGTCAAGACTGTAA
AGAGGGCTAGCCCTCCCAAGACCAAGAAAGCGGCGCCGAAGCCCAAGAAAGCGGCGCCTGCTGCTAAGAAGGCTAAGAAATGAGATCGAGAAGCTAAATCTgtaattgtaaactatcgtgatgcttttacagttattgttacatagtactgagatgcttttacagtttagtatttgtattgagtggaaatttttttcata
tagGTACATGAACAGGCGCAGGCACATAGGATAGGCTAGATTCAAGAGCACAGGGCGTGGGGTCGATTTGGGTGGGGATGGCCACAGCCACCCAGCCTACAGCAGGAGCCCCTTGCTATACATGTTAGTATGTGGGAGATGCTGAATTAGTTTAGGATTATAGCTTCTTAATGATGAGATTGTAAATTTATAGAATTTGG
ATTAATGATTAGATTGCAAATTTGTAGAATTTGGATTATTTTGGATTTAAACTAATTCTATGCTGGTTATTATTATAAACTGGATTAATGGTTTTGTATAAGTTGATGGTTCTATATATTTTCTGGATTGAGATACATTTGAACATGATATTTTTTTGTTTTTGGATGCACAGACATCAGTGGAGCTGAAATCTTTTTTT
TGTAATAGTTGGC

Intron 2 GTAATTGTAA ... TTTAGTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	78.75	2	7	7
A2	80	0.5	2	1
A3	87.5	0.5	3	3
A4	60.72	3.5	3	7
A5	87.5	0.5	3	3
A6	69.03	27.5	58	64
A7	78.72	7.5	29	26
A8	66	25	47	50
A9	60.3	27.5	43	40
A10	63.35	16	27	28

>TRINITY_DN44799_c1_g2_i6 from sample A6 / Example spliced isoform

TAAGAAGTCTGTCAAGACTGTAAAGAGGGCTAGCCCTCCCAAGACCAAGAAAGCGGCGCCGAAGCCCAAGAAAGCGGCGCCTGCTGCTAAGAAGGCTAAGAAATGAGATCGGGAGGCTAAATCTGTACATGAACAGGCGCAGGCACACAGGGTCGATTCGGGTGGGGATGGCCACAGCCACCCAGCCTACAGCAGGAGCC
CCTTGCTATACATGTTAGTATGTGGGAGATGCTGAATTAGTTTAGGATTATAGCTTCTTAATGATGAGATTGTAAATTTATAGAATTTGGATTAATGATTAGATTGCAAATTTGTAGAATTTGGATTATTTTGGATTTAAACTAATTCTATGCTGGTGGTTATTATTATAAACTGGATTAATGGTTTTGTATAAGTTGAT
GGTTCTATATATTTTCTGGATTGAGATACATTTGAACATGATATTTTTTTGTTTTTGGATGCACAGACATCAGTGGAGCTGAAATCTTTTTTTTGTAATAGTTGGC

>TRINITY_DN44799_c1_g2_i8 from sample A6 / Example unspliced isoform:

TAAGAAGTCTGTCAAGACTGTAAAGAGGGCTAGCCCTCCCAAGACCAAGAAAGCGGCGCCGAAGCCCAAGAAAGCGGCGCCTGCTGCTAAGAAGGCTAAGAAATGAGATCGGGAGGCTAAATCTgtaattgtaaactattgtgatatatgtatacttggttattgttacatagtactgagatgcttttacagtttagtat
agGTACATGAACAGGCGCAGGCACATAGGATAGGCTAGATTCAAGAGCACAGGGCGTGGGGTCGATTCGGGTGGGGATGGCCACAGCCACCCAGCCTACAGCAGGAGCCCCTTGCTATACATGTTAGTATGTGGGAGATGCTGAATTAGTTTAGGATTATAGCTTCTTAATGATGAGATTGTAAATTTATAGAATTTGGA
TTAATGATTAGATTGCAAATTTGTAGAATTTGGATTATTTTGGATTTAAACTAATTCTATGCTGGTTATTATTATAAACTGGATTAATGGTTTTGTATAAGTTGATGGTTCTATATATTTTCTGGATTGAGATACATTTGAACATGATATTTTTTTGTTTTTGGATGCACAGACATCAGTGGAGCTGAAATCTTTTTTTT
GTAATAGTTGGC