sp|Q9FHL4|FTRA1_ARATH ----> Ferredoxin-thioredoxin reductase subunit A1, chloroplastic

Intron 1 GTATTATATA ... TTAACTCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	9.52	19	10.7	2
A2	14.29	24	15.7	4
A3	21.44	18.3	13	5
A4	12.2	36	11.3	5
A5	0	11	7.3	0
A6	21.47	173	63.7	47.3
A7	19.11	151	67.3	35.7
A8	24.61	145	66.7	47.3
A9	14.9	158	77.3	27.7
A10	12.93	123	69.7	18.3

>TRINITY_DN39769_c0_g1_i2 from sample A7 / Example spliced isoform

GGCGTTTGAAAATTGCAAAATAAAATAAGAAATCCTTACCAAGACAGTGAGTTGGCTCTTTCACCCTGTGACCCTAAGGTGTCACCAACTCCATTCGAATCTCCAACCTCCCAAACATGATCTTATCGAACGCTCAACATCATGCTCCACACCAACCAATGTTTCCTAAACATTTTAGGTGCGTTAAGTTTGATTTGATG
ACCAGAATTCTTCTAGCCCTCCAAGTTCAAAAAATATCTTGAGCAATCTATATCTACAGCCCACACACACTCCTCCAGTTGTGCAATCCAAAGAAACCTTTAATTAAAAATGGCATTTATTTGCGCTCCAAATCCACTGGTTTCAACTTGCAGATCCACATCTGTTTCATTGGGTTTTCGCACCAAGAAAATCCCCACAA
ACAGCGGACAAATCTGCCATCTGCCCATCTACACCATTTCCGTTTTCAGCCAGCAGAACAAATCGCTAACAGGCAGAAGAAGAGGAAGAGCCATGGTTACCTGCAAAGTGGCCTTAGAGGAGACAGACCAGTCCATTGAAGACATACAACTCAAAGCTAAAGTTGGCGACAGAGTCAAAGTGAGAGGACCCTTGAAGGTC
TATCACGTACCCAAAACGCCAGAGTTCGATCTTGGGGGCATGGAGGGCGTAGTCAACGACTACGTGGGTCTATGGAAAGGTTTTAAAAGCAATAACTCTCTTCTCATCAACTCTTAAGACATTTTTCAAAGAGGTCTTTCTCGCATTCTGCATTCCTTTGACAAGGCATATTTCCATAACTGGAGAAATTTGAATGGTGT
TGGATGATCCATCATTGCTATGGCCCTATAGGACTTTGGAGTTTACCTATCAACTCATATGCATTAGTAGGTTCCTTCAAAATGTGTGATAACTCCATATGTTGGATTGGATGGAATGCTTGATGGGCATTATCTTGTTGCCATGTCAATTCTTTCCTACATCTCTTGTTGATTGGCCATCTATGTTTTATTTTAAGCTT
TGTTATGTTTGAATTCACTTTCTAGGCCCTAGGCACATGCTCTCTCGGGAATGACATCTTATTTTGTACACACTCCAGGAGCTTATATATTTTAAAGTACTATTAAAATGCTCATTTCTTTAAAATTGATGTCTTGTGAAACAGATTGACGAAAATCAAGCATAATTGGCTTTGTTAACAATGTATTATATTTATAATTT
GTATTTTGGGATTTTATATTTTGCATAATAGGTGCAAATATCATTGATATATTGGAAATATCGCGAC

>TRINITY_DN39769_c0_g1_i3 from sample A7 / Example unspliced isoform:

GGCGTTTGAAAATTGCAAAATAAAATAAGAAATCCTTACCAAGACAGTGAGTTGGCTCTTTCACCCTGTGACCCTAAGGTGTCACCAACTCCATTCGAATCTCCAACCTCCCAAACATGATCTTATCGAACGCTCAACATCATGCTCCACACCAACCAATGTTTCCTAAACATTTTAGGTGCGTTAAGTTTGATTTGATG
ACCAGAATTCTTCTAGCCCTCCAAGTTCAAAAAATATCTTGAGCAATCTATATCTACAGCCCACACACACTCCTCCAGTTGTGCAATCCAAAGAAACCTTTAATTAAAAATGGCATTTATTTGCGCTCCAAATCCACTGGTTTCAACTTGCAGATCCACATCTGTTTCATTGGGTTTTCGCACCAAGAAAATCCCCCAAA
ACAGCGGACAAATCTGCCATCTGCCCATCTACACCATTTCCGTTTTCAGCCAGCAGAACAAATCGCTAACAGGCAGAAGAAGAGGAAGAGCCATGGTTACCTGCAAAGTGGCCTTAGAGGAGACAGACCAGTCCATTGAAGACATACAACTCAAAGCTAAAGTTGGCGACAGAGTCAAAGTGAGAGGACCCTTGAAGGTC
TATCACGTACCCAAAACGCCAGAGTTCGATCTTGGGGGCATGGAGGGCGTAGTCAACGACTACGTGGGTCTATGGAAAGgtattatataccgctaagtatattttgttcttaattacgtgcttttaactccagGTTTTAAAAGCAATAACTCTCTTCTCATCAACTCTTAAGACATTTTTCAAAGAGGTCTTTCTCGCAT
TCTGCATTCCTTTGACAAGGCATATTTCCATAACTGGAGAAATTTGAATGGTGTTGGATGATCCATCATTGCTATGGCCCTATAGGACTTTGGAGTTTACCTATCAACTCATATGCATTAGTAGGTTCCTTCAAAATGTGTGATAACTCCATATGTTGGATTGGATGGAATGCTTGATGGGCATTATCTTGTTGCCATGT
CAATTCTTTCCTACATCTCTTGTTGATTGGCCATCTATGTTTTATTTTAAGCTTTGTTATGTTTGAATTCACTTTCTAGGCCCTAGGCACATGCTCTCTCGGGAATGACATCTTATTTTGTACACACTCCAGGAGCTTATATATTTTAAAGTACTATTAAAATGCTCATTTCTTTAAAATTGATGTCTTGTGAAACAGAT
TGACGAAAATCAAGCATAATTGGCTTTGTTAACAATGTATTATATTTATAATTTGTATTTTGGGATTTTATATTTTGCATAATAGGTGCAAATATCATTGATATATTGGAAATATCGCGAC

Intron 2 GTGTTATAGT ... TTGATTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	26.32	14	0	5
A2	0	20	0	0
A3	15.79	16	0	3
A4	5.88	16	0	1
A5	15.38	11	0	2
A6	6.52	86	1	6
A7	0	84	0	0
A8	3.75	77	1	3
A9	6.9	108	0	8
A10	5.32	89	0	5

>TRINITY_DN36012_c0_g1_i4 from sample A6 / Example spliced isoform

CAAAACAGCGGACAAATCTGCCATCTGCCCATCTACACCATTTCCGTTTTCAGCCAGCAGAACAAATCGCTAACAGGCAGAAGAAGAGGAAGAGCCATGGTTACCTGCAAAGTGGCCTTAGAGGAGACAGACCAGTCCATTGAAGACATACAACTCAAAGCTAAAGTTGGCGACAGAGTCAAAGTGAGAGGACCCTTGAA
GGTCTATCACGTACCCAAAACGCCAGAGTTCGATCTTGGGGGCATGGAGGGCGTAGTCAACGACTACGTGGGTCTATGGAAAGGACTTGTTTCATCATCAGAAGGCAGAGTTGGTTTCTCAAACAAACTCCATACATCAGATAATATATATCGTACAGCAGGGATAATTCTTGCAGTTCCTTGTTCCCAACTTTCAAGAA
TACTATCTGCAAAATATTCTAGCTGATTTATTAGATTATTACGTTTTTGTTTCAATGATACTGTAGCTGTTTCAGAAGGATTATCGCTATCCATTGATCTTAAACTCCAAGCAATATGCAAATTCATGTTCAAATGTACAAGACGAATTACCTCATCATCCAAACTTCTGAAACCTTTTATAAGACCAAGCATGCCTGAG
GACGTAGTTTCTCTTGACCCAAACTTTGATAATTGCAGTTGATAAGGCCTTCTAAGATTTACTGTTAAG

>TRINITY_DN36012_c0_g1_i3 from sample A6 / Example unspliced isoform:

ACTACGTGGGTCTATGGAAAGgtgttatagtaacattgccattttccccagctttctgctattcctctgtgaaacatcttcaaaactaaagggaagtatgtatctttgaattgtttagtatgatcactgatgattgactgaagatctgccttgattatagGACTTGTTTCATCATCAGAAGGCAGAGTTGGTTTCTCAAA
CAAACTCCATACATCAGATAATATATATCGTACAGCAGGGATAATTCTTGCAGTTCCTTGTTCCCAACTTTCAAGAATACTATCTGCAAAATATTCTAGCTGATTTATTAGATTATTACGTTTTTGTTTCAATGATACTGTAGCTGTTTCAGAAGGATTATCGCTATCCATTGATCTTAAACTCCAAGCAATATGCAAAT
TCATGTTCAAATGTACAAGACGAATTACCTCATCATCCAAACTTCTGAAACCTTTTATAAGACCAAGCATGCCTGAGGACGTAGTTTCTCTTGACCCAAACTTTGATAATTGCAGTTGATAAGGCCTTCTAAGATTTACTGTTAAG