sp|Q9FKM7|IAA33_ARATH ----> Auxin-responsive protein IAA33

Intron 1 GTAAGTCTGC ... ATTGAATCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	25.19	98	20	46
A2	27.39	57	25	18
A3	27.36	77	12	46
A4	25.27	34	19	4
A5	23.46	31	6	13
A6	29.41	288	84	156
A7	28.63	405	113	212
A8	27.09	592	160	280
A9	28.16	435	132	209
A10	29.11	330	100	171

>TRINITY_DN105414_c0_g1_i1 from sample A1 / Example spliced isoform

CGGTACCTCATTTTTACTGTTTGGTGATCCACATACAAACCAGAAGAGTTAGAGTAACGAGTTCATCGCCTGCACGGGTCGGGGAGGCGCTTCTTCTTCTAACCGAGCAGGGCAGGGCAGGGCAGGGCAGGCGAGTTTTAAGTGGACCGACATGTAGCAAGGGCATTGTCATGTCAACAAAGCTTTCTCCTCCTTCACTT
AATTAAAGTGGGACGAAACTCATTCTTGCTTGCTCTTCCATCTCTATTTCTGGTTCCCAGGGGAGGAAGGCAAAGAGATATATAAACAGCAATTTCATAGATGACGGAGTTCCCCAAGCATTGGATGACAAGTTACGTCCAAGACAAGAAGCCATGAGCGGCTTAGAAAAGAAACCGATTCTTCGAGATCGCAGCACGCA
ATCATGGCCGACCACGACGGAAGAACAAGAACGCTGGCAAGAAAGATTTCTCCATCAATTCAACCAGCAAAGCACTGCATTCGATGGCAAAGAAGGATTATCTTTAGGGCAAAGTTCCACGCGATATTTAGGGGAGGAGGAAAGCAGAACAGGTAATTATAATTCCAATGATAGTAATATTAACCCTAACTTGACGGCAG
GTCCGAAGACTGAACACATAGGTGTTGTTTCCGACAATGAAGGAATAATCGCACAAGCTCAAAATCCTTGGCCCTCTTCTGCACTACTCCAACTACCGAACTCGGAACATAATTATGCTAAACGTCCCCGGCAATCAGGCTCCAATTATCTGCCGGGAAATTCACATCATTCTTTCCAGTCTAATTTCATAAACACTATG
TCGTCGGGAAGCGGTGCCAATTTTCCAGGACCGATGTTCAGGCAATCGAAGGTAGAATCTCCTCAGCAGCAGCAGAGAAATACACATAGTCCATACAGCTTACACAGCGCTGGGACGGTTATATCGCCCTATCAGAACCCGCGGAATGAAACCCCAGCTCCTCCTCCTTCTCCTCCTCCAGATCCTAGATCCCTGCAGTC
CTTGAGAGAGGCTATTCAGTTAGCCGTCGGCAGATTATTTAGGGAACCAGAAACGCATACTGAGCATATGCCGATGCAACTTCAAAATCTTTTGGAATACTCCGATGCTACTCCGTCTGTTACTGTGGAAATGGAAGGCCGTTCAATTTGCCAGAGGATTTTCCTTGAAGAACACTCGTGTTATGAAAGCTTTGCGCAGG
CTCTCAGAGAAATGTTTGTGGTGAACATTCTGGCCTTAGACGGTCAGGAAGCTGATCTAATTAATAGCAGAGACTACTGCAATCTTTCAAACGCGATTCCAGGCCATTTTATTGCATATGAAGATAAGGAAGGCGACTTGCTTCTTGCGGGAGATCTTTCCTGGAAAGATTTTGTTCGAGCAGTAAAGAAAATCCGAATT
TTACCGGCCAAAAATCGGCAAGGCAGAGTACGCAAGAGAGAATCATAATTTACTTTTACTACACTACATGGATAGATTTACATTCACCCCCTTCAGATGCGTATATGTGTAATTTGTTCTCTTGCGTATTAAATTTTGAATCCATTACTGAATCCGTGGCTACAGACTCTTCTTTTTAAATCTTTCTTCGACTTTTACTT
ATAAATGCATTTACTCTCATAAAGTATTCATGACCTCATCAGTCCGGTCGTGGAGAAGGTGGAAGCCCAAACGCTATGCGTTTCCTTATCATGTTGTAGATGACCGAAATCTCCAGATGATATTTTACATAAAAAACCAAACCCCTTAGGAAATACGTTGTGTGATGGTACTTTTCCCGGACCAACACATCCTTGTCATT
GCAGGATTCTCCAGATTTTGTGTAATTGCAACATTATCAATGGTAATTACCATTACAACAATATTCATATTTCTAAGGAAATGGATTTGAAGATGGGTTTAGTTTTTGGATAAAAGAGTTTTCAAAAAGGCAGTATGTGCATTTACAGGCAGGTGCAGTTACAAAATTATCGAATGATATTAAATTCAGATCATTCATTA
TTATTATTAGA

>TRINITY_DN105414_c0_g1_i2 from sample A1 / Example unspliced isoform:

CGGTACCTCATTTTTACTGTTTGGTGATCCACATACAAACCAGAAGAGTTAGAGTAACGAGTTCATCGCCTGCACGGGTCGGGGAGGCGCTTCTTCTTCTAACCGAGCAGGGCAGGGCAGGGCAGGGCAGGCGAGTTTTAAGTGGACCGACATGTAGCAAGGGCATTGTCATGTCAACAAAGCTTTCTCCTCCTTCACTT
AATTAAAGTGGGACGAAACTCATTCTTGCTTGCTCTTCCATCTCTATTTCTGGTTCCCAGGGGAGGAAGGCAAAGAGATATATAAACAGCAATTTCATAGATGACGGAGTTCCCCAAGCATTGGATGACAAGTTACGTCCAAGACAAGAAGCCATGAGCGGCTTAGAAAAGAAACCGATTCTTCGAGATCGCAGCACGCA
ATCATGGCCGACCACGACGGAAGAACAAGAACGCTGGCAAGAAAGATTTCTCCATCAATTCAACCAGCAAAGCACTGCATTCGATGGCAAAGAAGGATTATCTTTAGGGCAAAGTTCCACGCGATATTTAGGGGAGGAGGAAAGCAGAACAGGTAATTATAATTCCAATGATAGTAATATTAACCCTAACTTGACGGCAG
GTCCGAAGACTGAACACATAGGTGTTGTTTCCGACAATGAAGGAATAATCGCACAAGCTCAAAATCCTTGGCCCTCTTCTGCACTACTCCAACTACCGAACTCGGAACATAATTATGCTAAACGTCCCCGGCAATCAGGCTCCAATTATCTGCCGGGAAATTCACATCATTCTTTCCAGTCTAATTTCATAAACACTATG
TCGTCGGGAAGCGGTGCCAATTTTCCAGGACCGATGTTCAGGCAATCGAAGGTAGAATCTCCTCAGCAGCAGCAGAGAAATACACATAGTCCATACAGCTTACACAGCGCTGGGACGGTTATATCGCCCTATCAGAACCCGCGGAATGAAACCCCAGCTCCTCCTCCTTCTCCTCCTCCAGATCCTAGATCCCTGCAGTC
CTTGAGAGAGGCTATTCAGTTAGCCGTCGGCAGATTATTTAGGGAACCAGAAACGCATACTGAGCATATGCCGATGCAACTTCAAAATCTTTTGGAATACTCCGATGCTACTCCGTCTGTTACTGTGGAAATGGAAGGCCGTTCAATTTGCCAGAGGATTTTCCTTGAAGAACACTCGTGTTATGAAAGCTTTGCGCAGG
CTCTCAGAGAAATGTTTGTGGTGAACATTCTGGCCTTAGACGGTCAGGAAGCTGATCTAATTAATAGCAGAGACTACTGCAATCTTTCAAACGCGATTCCAGGCCATTTTATTGCATATGAAGATAAGGAAGGCGACTTGCTTCTTGCGGGAGATCTTTCCTGGAAgtaagtctgcagtacttgttttcattttcactat
ttgagataaaagatataatattttcttgtccatgcatgcttagttttcaaaatcatgctctatcgtttcccctcatctctatcattcaaactaagtaattaggttttccatgatattcatctatttatttgctgtccgatttcatcgtgtttgtccgtcatttttgacgagtttattgaatcagAGATTTTGTTCGAGCA
GTAAAGAAAATCCGAATTTTACCGGCCAAAAATCGGCAAGGCAGAGTACGCAAGAGAGAATCATAATTTACTTTTACTACACTACATGGATAGATTTACATTCACCCCCTTCAGATGCGTATATGTGTAATTTGTTCTCTTGCGTATTAAATTTTGAATCCATTACTGAATCCGTGGCTACAGACTCTTCTTTTTAAATC
TTTCTTCGACTTTTACTTATAAATGCATTTACTCTCATAAAGTATTCATGACCTCATCAGTCCGGTCGTGGAGAAGGTGGAAGCCCAAACGCTATGCGTTTCCTTATCATGTTGTAGATGACCGAAATCTCCAGATGATATTTTACATAAAAAACCAAACCCCTTAGGAAATACGTTGTGTGATGGTACTTTTCCCGGAC
CAACACATCCTTGTCATTGCAGGATTCTCCAGATTTTGTGTAATTGCAACATTATCAATGGTAATTACCATTACAACAATATTCATATTTCTAAGGAAATGGATTTGAAGATGGGTTTAGTTTTTGGATAAAAGAGTTTTCAAAAAGGCAGTATGTGCATTTACAGGCAGGTGCAGTTACAAAATTATCGAATGATATTA
AATTCAGATCATTCATTATTATTATTAGA

Intron 2 GTAATTATAA ... GACAATGAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	86.39	29	188.3	180
A2	89.47	20	169	171
A3	89.15	25	187	224
A4	89.91	15	146.3	121
A5	91.94	10	105	123
A6	91.8	42	438.3	502
A7	90.39	95	857.3	931
A8	88.83	80	580	693
A9	89.9	92	762.3	876
A10	92.48	70	806	915

>TRINITY_DN114596_c1_g4_i11 from sample A3 / Example spliced isoform

GGGGAGGAGGAAAGCAGAACAGGAATAATCGCACAAGCTCAAAATCCTTGGCCCTCTTCTGCACTACTCCAACTACCGAACTCGGAACATAATTATGCTAAACGTCCCCGGCAATCAGGCTCCAATTATCTGCCGGGAAATTCACATCATTCTTTCCAGTCTAATTTCATAAACACTATGTCGTCGGGAAGCGGTGCCAA
TTTTCCAGGACCGATGTTCAGGCAATCGAAGGTAGAATCTCCTCAGCAGCAGCAGAGAAATACACATAGTCCATACAGCTTACACAGCGCTGGGACGGTTATATCGCCCTATCAGAACCCGCGGAATGAAACCCCAGCTCCTCCTCCTTCTCCTCCTCCAGATCCTAGATCCCTGCAGTCCTTGAGAGAGGCTATTCAGT
TAGCCGTCGGCAGATTATTTAGGGAACCAGAAACGCATACTGAGCATATGCCGATGCAACTTCAAAATCTTTTGGAATACTCCGATGCTACTCCGTCTGTTACTGTGGAAATGGAAGGCCGTTCAATTTGCCAGAGGATTTTCCTTGAAGAACACTCGTGTTATGAAAGCTTTGCGCAGGCTCTCAGAGAAATGTTTGTG
GTGAACATTCTGGCCTTAGACGGTCAGGAAGCTGATCTAATTAATAGCAGAGACTACTGCAATCTTTCAAACGCGATTCCAGGCCATTTTATTGCATATGAAGATAAGGAAGGCGACTTGCTTCTTGCGGGAGATCTTTCCTGGAAAGATTTTGTTCGAGCAGTAAAGAAAATCCGAATTTTACCGGCCAAAAATCGGCA
AGGCAGAGTACGCAAGAGAGAATCATAATTTACTTTTACTACACTACATGGATAGATTTACATTCACCCCCTTCAGATGCGTATATGTGTAATTTGTTCTCTTGCGTATTAAATTTTGAATCCATTACTGAATCCGTGGCTACAGACTCTTCTTTTTAAATCTTTCTTCGACTTTTACTTATAAATGCATTTACTCTCAT
AAAGTATTCATGACCTCATCAGTCCGGTCGTGGAGAAGGTGGAAGCCCAAACGCTATGCGTTTCCTTATCATGTTGTAGATGACCGAAATCTCCAGATGATATTTTACATAAAAAACCAAACCCCTTAGGAAATACGTTGTGTGATGGTACTTTTCCCGGACCAACACATCCTTGTCATTGCAGGATTCTCCAGATTTTG
TGTAATTGCAACATTATCAATGGTAATTACCATTACAACAATATTCATATTTCTAAGGAAATGGATTTGAAGATGGGTTTAGTTTTTGGATAAAAGAGTTTTCAAAAAGGCAGTATGTGCATTTACAGGCAGGTGCAGTT

>TRINITY_DN114596_c1_g4_i5 from sample A3 / Example unspliced isoform:

AAGCAAGTATACGCCGCTCTCCACGGTACCTCATTTTTACTGTTTGGTGATCCACATACAAACCAGAAGAGTTAGAGTAACGAGTTCATCGCCTGCACGGGTCGGGGAGGCGCTTCTTCTTCTAACCGAGCAGGGCAGGGCAGGGCAGGGCAGGCGAGTTTTAAGTGGACCGACATGTAGCAAGGGCATTGTCATGTCAA
CAAAGCTTTCTCCTCCTTCACTTAATTAAAGTGGGACGAAACTCATTCTTGCTTGCTCTTCCATCTCTATTTCTGGTTCCCAGGGGAGGAAGGCAAAGAGATATATAAACAGCAATTTCATAGATGACGGAGTTCCCCAAGCATTGGATGACAAGTTACGTCCAAGACAAGAAGCCATGAGCGGCTTAGAAAAGAAACCG
ATTCTTCGAGATCGCAGCACGCAATCATGGCCGACCACGACGGAAGAACAAGAACGCTGGCAAGAAAGATTTCTCCATCAATTCAACCAGCAAAGCACTGCATTCGATGGCAAAGAAGGATTATCTTTAGGGCAAAGTTCCACGCGATATTTAGGGGAGGAGGAAAGCAGAACAGgtaattataattccaatgatagtaa
tattaaccctaacttgacggcaggtccgaagactgaacacataggtgttgtttccgacaatgaagGAATAATCGCACAAGCTCAAAATCCTTGGCCCTCTTCTGCACTACTCCAACTACCGAACTCGGAACATAATTATGCTAAACGTCCCCGGCAATCAGGCTCCAATTATCTGCCGGGAAATTCACATCATTCTTTCC
AGTCTAATTTCATAAACACTATGTCGTCGGGAAGCGGTGCCAATTTTCCAGGACCGATGTTCAGGCAATCGAAGGTAGAATCTCCTCAGCAGCAGCAGAGAAATACACATAGTCCATACAGCTTACACAGCGCTGGGACGGTTATATCGCCCTATCAGAACCCGCGGAATGAAACCCCAGCTCCTCCTCCTTCTCCTCCT
CCAGATCCTAGATCCCTGCAGTCCTTGAGAGAGGCTATTCAGTTAGCCGTCGGCAGATTATTTAGGGAACCAGAAACGCATACTGAGCATATGCCGATGCAACTTCAAAATCTTTTGGAATACTCCGATGCTACTCCGTCTGTTACTGTGGAAATGGAAGGCCGTTCAATTTGCCAGAGGATTTTCCTTGAAGAACACTC
GTGTTATGAAAGCTTTGCGCAGGCTCTCAGAGAAATGTTTGTGGTGAACATTCTGGCCTTAGACGGTCAGGAAGCTGATCTAATTAATAGCAGAGACTACTGCAATCTTTCAAACGCGATTCCAGGCCATTTTATTGCATATGAAGATAAGGAAGGCGACTTGCTTCTTGCGGGAGATCTTTCCTGGAAAGATTTTGTTC
GAGCAGTAAAGAAAATCCGAATTTTACCGGCCAAAAATCGGCAAGGCAGAGTACGCAAGAGAGAATCATAATTTACTTTTACTACACTACATGGATAGATTTACATTCACCCCCTTCAGATGCGTATATGTGTAATTTGTTCTCTTGCGTATTAAATTTTGAATCCATTACTGAATCCGTGGCTACAGACTCTTCTTTTT
AAATCTTTCTTCGACTTTTACTTATAAATGCATTTACTCTCATAAAGTATTCATGACCTCATCAGTCCGGTCGTGGAGAAGGTGGAAGCCCAAACGCTATGCGTTTCCTTATCATGTTGTAGATGACCGAAATCTCCAGATGATATTTTACATAAAAAACCAAACCCCTTAGGAAATACGTTGTGTGATGGTACTTTTCC
CGGACCAACACATCCTTGTCATTGCAGGATTCTCCAGATTTTGTGTAATTGCAACATTATCAATGGTAATTACCATTACAACAATATTCATATTTCTAAGGAAATGGATTTGAAGATGGGTTTAGTTTTTGGATAAAAGAGTTTTCAAAAAGGCAGTATGTGCATTTACAGGCAGGTGCAGTT