sp|Q38967|AAP2_ARATH ----> Amino acid permease 2

Intron 1 GTGAGTATCC ... CTTTTGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	-1	0	0	0
A2	-1	0	0	0
A3	11.76	15	1	2
A4	0	6	0	0
A5	0	2	0	0
A6	13.04	20	1.8	3
A7	0	6.4	0	0
A8	16.67	30	1	6
A9	11.11	16	0.6	2
A10	13.28	19.6	0.6	3

>TRINITY_DN39082_c0_g1_i1 from sample A6 / Example spliced isoform

CGTTACAAAGGTCGACAACAAACCCTAAGGCTCAACGCTATTCAGGGCGTCAGGGCGTCGAGGGTTTTTTTTAGAAGTTCAATTCTTTTACCATTGTCGTTTTCAGAAAAAAAATTAACATCCAGGTGCCGCCTAACTCTGTGAAAAGGTGCATTATATATAATAAGATGTGGCGGATTTTGTTTAGAAGCTCACTACGT
TGGCTACCCCAAATAGACAGGTTAGGTTCAAGTCGCTTGGCATGTTCGCTTTGATTTGTTCTCCCTATTCCTGGGTTGGTTAGTCTCGACGCAGACAAAAGAAAGCAAGTGGAACGTTGCATCCAGTGTTTACGTGTTGAAGAGAGATATACAGGACTCTTGTTCCATTTATGGCCTAAGGAAGGAAGATTATCTTGTTA
CAAGTTTAGTTTTGCATTGTTATTTTTTTTTCCTGTCAATGTTTTGTTTTGTTATTCATAATTGATATACAAAAGATCAATATCCAAATTTGACAAAGCTAATACATAAGTTCTTCCACGTTTATAACTGTGATAAAAAGAATGGTTGAATTTTCTGAACTTATCTAAAAAATAAGTACTATCTGAGCAACATATTTGTG
GTTATATACATACTTTTCAAGTGGTGTATGGACTGCATCCTCCCACGTAATAACAACAGTAATTGGATCCGGCGTGCTATCATTGGCATGGAGTATGTCTCAGCTGGGTTGGATAGTAGGGCCACTGGTTCTGTTGGGATTTTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATC
CTGTTACTGGGAGGCGCAACTATACCTATACAGATGCAGTCACAGCCATTCTCGGTGGGAAAAAGGTTTTGATATGTGGGATTGTACAGTATCTGAATCTGTTGGGAACATCCATTGGATATACCATCACTGCTTCTATAAGCATGGTGGCAATAGGTCGATCAGACTGTTTTCACGAGAAAGGGAAAGAATCGCCTTGC
CATATACCAAACAATCTGTATGTGGCGATTTTTGGAGCAGCCCAAGTGTTGCTCTCACAGATTCCCAATTTCAGCAAAATTTGGTGGTTGTCAACAGTTGCAGCTGTAATGTTTCCCACATATTCATTCATTGGACTCGATCTAGGAATCGGCATGGCTAGAGGTCTAAATCCTTTCCTTCACCAAATATATATATATTG
AATGTTCATTTTTATTATGATAAAGTCTGTTCTTGTTGTTAGCAGAGAAAGGGCATTCTCATGGCAGCTTAGGAGGAGCAAGGATTTCGTCTGTCTACAAATCAGTTGATAAAACCTGGAACTTTCATGGCAAGATAAGGTATGGC

>TRINITY_DN39082_c0_g1_i8 from sample A6 / Example unspliced isoform:

ACTATACCTATACAGATGCAGTCACAGCCATTCTCGGTGGGAAAAAGGTTTTGATATGTGGGATTGTACAGTATCTGAATCTGTTGGGAACATCCATTGGATATACCATCACTGCTTCTATAAGCATGGTgtgagtatcctcctttctgtatatccatcactgcttctataattagggttttgctgtaaaatatatttcc
tagagacatacaatatacaatatcttgatttcacattgcttttggcagGGCAATAGGTCGATCAGACTGTTTTCACGAGAAAGGGAAAGAATCGCCTTGCCATATACCAAACAATCTGTATGTGGCGATTTTTGGAGCAGCCCAAGTGTTGCTCTCACAGATTCCCAATTTCAGCAAAATTTGGTGGTTGTCAACAGTTG
CAGCTGTAATGTTTCCCACATATTCATTCATTGGACTCGATCTAGGAATCGGCATGGCTAGAGGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGACAAGCCATGACCAACATGAGTAAGTTTTTCTTCTAACATAGCGGTGCTACATATATCCATGTTTTGAATATTATGC
TTCTCCGCAGAAAGCAATAAAATTTTAAATTGATTTTATGTTATAATGCCATATTTGATGCGTACCAGGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTA

Intron 2 GTGGGAAAAA ... ATGGCTAGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	100	0	0	1
A2	50	4	4	4
A3	100	0	8	5
A4	66.67	1	2	2
A5	75	1	2	4
A6	76.92	3	6	14
A7	60	2	2	4
A8	89.47	2	13	21
A9	68.42	3	4	9
A10	57.14	6	9	7

>TRINITY_DN41162_c0_g1_i8 from sample A7 / Example spliced isoform

GGCAGGGCCACTGGTTCTGTTGGGATTTTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATCCTGTTACTGGGAGGCGCATACCTATACAGATGCAGTCACAGCCATTCTCGGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGACAA
GCCATGACCAACATGAGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTATCCCAATTTACCTTTTTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCTTTAGATG
GAAGAATCATTCCAAGGTAAATACATGTGGGGCCTTCAAGCCATGGGTTCTAAGAGGTGCCATCACACCAAATATTAACATGTTGTTTTAGAATTATGCCATTATTCAGATGGAGTTGTTCAAGTAAAATAAGTATGTTATAATAGC

>TRINITY_DN41162_c0_g1_i1 from sample A7 / Example unspliced isoform:

TGTGGAACATGGGTGAATTACTTCTTTCTCTGAATATTCAAAAGTACTTCCTTCTCTGTGGGCGAAGTACTCCAACCGCCATGGCAACGGTGCATTTATCTCATTCAAACCTTAGCTGCTGCTTTTCATTTCACCGTTACAAAGGTCGATAACAAACCCCAAGTCTCAACGCTATTCAGGGCGTCGAGGGTTTTTTTAGA
AGTTCAATTTTTTTTACCATTGTCGTTTTCAGAAAAAAAATTAACATCCAGGTGCCGCCTAACTCTGTGAAAAGGTGCATTATATATAATAAGATGTGGCGGATTTTGTTTAGAAGCTCACTACGTTGGCTACCCCAAATAGACAGGTTAGGTTCAAGTCGCTTGGCATGTTCGCTTTGATTTGTTCTCCTATTCCTGGG
TTGGTTAGTCTCGACGCAGACAAAAGAAAGCAAGTGGAACGTTGCATCCAGTGTTTACGTGTTGAAAAGAGATATACAGGTGGTGTATGGACTGCATCCTCCCACGTAATAACAACAGTAATTGGATCCGGCGTGCTATCATTGGCATGGAGTATGTCTCAGCTGGGTTGGATGGCAGGGCCACTGGTTCTGTTGGGATT
TTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATCCTGTTACTGGGAGGCGCATACCTATACAGATGCAGTCACAGCCATTCTCGgtgggaaaaaggttttgatatgtgggattgtacagtatctgaatctgttgggaacatccattggatataccatcactgcttctataagcat
ggtggcaataggtcgatcagactgttttcacgagaaagggaaagaatcgccttgccatataccaaacaatctgtatgtggcgatttttggagcagcccaagtgttgctctcacagattcccaatttcagcaaaatttggtggttgtcaacagttgcagctgtaatgtttcccacatattcattcattggactcgatctag
gaatcggcatggctagagGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGACAAGCCATGACCAACATGAGTAAGTTTTTCTTCTAACATAGCGGTGCTACATATATCCATGTTTTGAATATTATGCTTCTCCGCAGAAAGCAATAAAATTTTAAATTGATTTTATGTTATA
ATGCCATATTTGATGCGTACCAGGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTATCCCAATTTACCTTTTTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCT
TTAGATGGAAGAATCATTCCAAGGTAAATACATGTGGGGCCTTCAAGCCATGGGTTCTAAGAGGTGCCATCACACCAAATATTAACATGTTGTTTTAGAATTATGCCATTATTCAGATGGAGTTGTTCAAGTAAAATAAGTATGTTATAATAGC

Intron 3 GTTTAGTTTT ... ACTTTTCAAG

Found issues: Low number of reads

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	75	1	2	4
A2	-1	0	0	0
A3	-1	0	0	0
A4	100	0	2	0
A5	100	0	0	1
A6	50	4	4	4
A7	76.47	2	8	5
A8	33.33	9	2	7
A9	60	2	3	3
A10	63.64	2	5	2

>TRINITY_DN41324_c0_g1_i6 from sample A9 / Example spliced isoform

CCGTTACAAAGGTCGATAACAAACCCCAAGTCTCAACGCTATTCAGGGCGTCGAGGGTTTTTTTAGAAGTTCAATTTTTTTTACCATTGTCGTTTTCAGAAAAAAAATTAACATCCAGGTGCCGCCTAACTCTGTGAAAAGGTGCATTATATATAATAAGATGTGGCGGATTTTGTTTAGAAGCTCACTACGTTGGCTAC
CCCAAATAGACAGGTTAGGTTCAAGTCGCTTGGCATGTTCGCTTTGATTTGTTCTCCCTATTCCTGGGTTGGTTAGTCTCGACGCAGACAAAAGAAAGCAAGTGGAACGTTGCATCCAGTGTTTACGTGTTGAAGAGAGATATACAGGACTCTTGTTCCATTTATGGCCTAAGGAAGGAAGATTATCTTGTTACAATGGT
GTATGGACTGCATCCTCCCACGTAATAACAACAGTAATTGGATCCGGCGTGCTATCATTGGCATGGAGTATGTCTCAGCTGGGTTGGATAGTAGGGCCACTGGTTCTGTTGGGATTTTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATCCTGTTACTGGGAGGCGCAACTATAC
CTATACAGAAGCAGTCACAGCCATTCTCGGTGGGAAAAAGGTTTTGATATGTGGGATTGTACAGTATCTGAATCTGTTGGGAACATCCATTGGATATACCATCACTGCTTCTATAAGCATGGTGGCAATAGGTCGATCAGACTGTTTTCACGAGAAAGGGAAAGAATCGCCTTGCCATATACCAAACAATCTGTATGTGG
CGATTTTTGGAGCAGCCCAAGTGTTGCTCTCACAGATTCCCAATTTCAGCAAAATTTGGTGGTTGTCAACAGTTGCAGCTGTAATGTTTCCCACATATTCATTCATTGGACTCGATCTAGGAATCGGCATGGCTAGAGGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGAC
AAGCCATGACCAACATGAGTAAGTTTTTCTTCTAACATAGCGGTGCTACATATATCCATGTTTTGAATATTATGCTTCTCCGCAGAAAGCAATAAAATTTTAAATTGATTTTATGTTATAATGCCATATTTGATGCGTACCAGGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTATCCCAATTTACCTTT
TTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCTTTAGATGGAAGAATCATTCCAAG

>TRINITY_DN41324_c0_g1_i8 from sample A9 / Example unspliced isoform:

CCGTTACAAAGGTCGATAACAAACCCCAAGTCTCAACGCTATTCAGGGCGTCGAGGGTTTTTTTAGAAGTTCAATTTTTTTTACCATTGTCGTTTTCAGAAAAAAAATTAACATCCAGGTGCCGCCTAACTCTGTGAAAAGGTGCATTATATATAATAAGATGTGGCGGATTTTGTTTAGAAGCTCACTACGTTGGCTAC
CCCAAATAGACAGGTTAGGTTCAAGTCGCTTGGCATGTTCGCTTTGATTTGTTCTCCCTATTCCTGGGTTGGTTAGTCTCGACGCAGACAAAAGAAAGCAAGTGGAACGTTGCATCCAGTGTTTACGTGTTGAAGAGAGATATACAGGACTCTTGTTCCATTTATGGCCTAAGGAAGGAAGATTATCTTGTTACAAgttt
agttttgcattgttatttttttttcctgtcaatgttttgttttgttattcataattgatatacaaaagatcaatatccaaatttgacaaagctaatacataagttcttccacgtttataactgtgataaaaagaatggttgaattttctgaacttatctaaaaaataagtactatctgagcaacatatttgtggttatat
acatacttttcaagTGGTGTATGGACTGCATCCTCCCACGTAATAACAACAGTAATTGGATCCGGCGTGCTATCATTGGCATGGAGTATGTCTCAGCTGGGTTGGATAGTAGGGCCACTGGTTCTGTTGGGATTTTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATCCTGTTAC
TGGGAGGCGCAACTATACCTATACAGAAGCAGTCACAGCCATTCTCGGTGGGAAAAAGGTTTTGATATGTGGGATTGTACAGTATCTGAATCTGTTGGGAACATCCATTGGATATACCATCACTGCTTCTATAAGCATGGTGGCAATAGGTCGATCAGACTGTTTTCACGAGAAAGGGAAAGAATCGCCTTGCCATATAC
CAAACAATCTGTATGTGGCGATTTTTGGAGCAGCCCAAGTGTTGCTCTCACAGATTCCCAATTTCAGCAAAATTTGGTGGTTGTCAACAGTTGCAGCTGTAATGTTTCCCACATATTCATTCATTGGACTCGATCTAGGAATCGGCATGGCTAGAGGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACT
ATCATTTCAAGTTGGGACAAGCCATGACCAACATGAGTAAGTTTTTCTTCTAACATAGCGGTGCTACATATATCCATGTTTTGAATATTATGCTTCTCCGCAGAAAGCAATAAAATTTTAAATTGATTTTATGTTATAATGCCATATTTGATGCGTACCAGGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTT
TTATCCCAATTTACCTTTTTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCTTTAGATGGAAGAATCATTCCAAG

Intron 4 GTAAGTTTTT ... TGCGTACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	-1	0	0	0
A2	100	0	4	1
A3	100	0	3	0
A4	-1	0	0	0
A5	100	0	1	0
A6	100	0	15	2
A7	64.71	6	11	11
A8	100	0	22	12
A9	72.73	3	9	7
A10	75	3	12	6

>TRINITY_DN41162_c0_g1_i8 from sample A7 / Example spliced isoform

GGCAGGGCCACTGGTTCTGTTGGGATTTTCCTTTGTCACCTATTACACCTCTATGTTGCTGGCTGATACATATCAGTCGCCTGATCCTGTTACTGGGAGGCGCATACCTATACAGATGCAGTCACAGCCATTCTCGGCAAATTGAAAAAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGACAA
GCCATGACCAACATGAGGGCGTAAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTATCCCAATTTACCTTTTTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCTTTAGATG
GAAGAATCATTCCAAGGTAAATACATGTGGGGCCTTCAAGCCATGGGTTCTAAGAGGTGCCATCACACCAAATATTAACATGTTGTTTTAGAATTATGCCATTATTCAGATGGAGTTGTTCAAGTAAAATAAGTATGTTATAATAGC

>TRINITY_DN41162_c0_g1_i4 from sample A7 / Example unspliced isoform:

TGTGGAACATGGGTGAATTACTTCTTTCTCTGAATATTCAAAAGTACTTCCTTCTCTGTGGGCGAAGTACTCCAACCGCCATGGCAACGGTGCATTTATCTCATTCAAACCTTAGCTGCTGCTTTTCATTTCACCGTTACAAAGGTCGATAACAAACCCCAAGTCTCAACGCTATTCAGGGCGTCGAGGGTTTTTTTAGA
AGTTCAATTTTTTTTACCATTGTCGTTTTCAGAAAAAAAATTAACATCCAGGTGCCGCCTAACTCTGTGAAAAGGTGCATTATATATAATAAGATGTGGCGGATTTTGTTTAGAAGCTCACTACGTTGGCTACCCCAAATAGACAGGTTAGGTTCAAGTCGCTTGGCATGTTCGCTTTGATTTGTTCTCCCTATTCCTGG
GTTGGTTAGTCTCGACGCAGACAAAAGAAAGCAAGTGGAACGTTGCATCCAGTGTTTACGTGTTGAAGAGAGATATACAGGTGGGAAAAAGGTTTTGATATGTGGGATTGTACAGTATCTGAATCTGTTGGGAACATCCATTGGATATACCATCACTGCTTCTATAAGCATGGTGGCAATAGGTCGATCAGACTGTTTTC
ACGAGAAAGGGAAAGAATCGCCTTGCCATATACCAAACAATCTGTATGTGGCGATTTTTGGAGCAGCCCAAGTGTTGCTCTCACAGATTCCCAATTTCAGCAAAATTTGGTGGTTGTCAACAGTTGCAGCTGTAATGTTTCCCACATATTCATTCATTGGACTCGATCTAGGAATCGGCATGGCTAGAGGCAAATTGAAA
AAGCTACTGGTCCTTGTGGGATTAACCGTGACTATCATTTCAAGTTGGGACAAGCCATGACCAACATGAgtaagtttttcttctaacatagcggtgctacatatatccatgttttgaatattatgcttctccgcagaaagcaataaaattttaaattgattttatgttataatgccatatttgatgcgtaccagGGGCGT

AAAGATTGCAAACAAAGTGTTGTTTCAAGTTTTTTATCCCAATTTACCTTTTTTATTATATTTGAGTATGAACAAATTCTTAGGAAAACTTAATATTTATACTACTTTCAACAAAAACAAGCTCTTGTGCAATTTAGTCATTTAGATAACGCCTCTTCTACGAGATCTGCTTTAGATGGAAGAATCATTCCAAGGTAAAT
ACATGTGGGGCCTTCAAGCCATGGGTTCTAAGAGGTGCCATCACACCAAATATTAACATGTTGTTTTAGAATTATGCCATTATTCAGATGGAGTTGTTCAAGTAAAATAAGTATGTTATAATAGC