sp|Q9LK22|PUX1_ARATH ----> Plant UBX domain-containing protein 1

Intron 1 GTAATATATG ... CATTGCTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80	4	17	15
A2	85.19	2	9	14
A3	75.44	7	19	24
A4	80.95	2	8	9
A5	100	0	9	8
A6	80.28	7	18	39
A7	88.41	4	27	34
A8	85.71	6	40	32
A9	85.42	7	37	45
A10	86.89	4	22	31

>TRINITY_DN97994_c0_g1_i5 from sample A3 / Example spliced isoform

GTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCGTCCGA
ATGTACAGCTGTAGGTTTTCAACTGATCGGGAGGCCTAGCAGTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGG

>TRINITY_DN97994_c0_g1_i3 from sample A3 / Example unspliced isoform:

GTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCGTCCGA
ATGTACAGgtaatatatgaccaatcggacaaaaccccgactctcacatccaagaaatacgtaacagtaatcacagagacttggcgcttttgatttgcgcggaaacacatcgaattgcagtggtctgattcaaattgaacaggattcttacctaaatacattgcttagCTGTAGGTTTTCAACTGATCGGGAGGCCTAGCA
GTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGGCTAAGCTTGCATCAGCCGCTAGGGAACTGGGACGAGAAGTACATGTTTTTGTCAATCCAGCTGCTAGAAATTCAGATGACCCAAAACCTCTTTCAGACGA
GCCAGATGACTTTTATGAGTTTACCACAGAGGATTATATTCGACTATTGGCAAGCAAGAAAGAAGGTGAATTTTAGGTTGGTTTATGGTTTCTGGAATTCAGGTTCTGTAGGCTGATAGGTCCCCTAATTCAACATATGCAAATAATGAAATTACTGTGTGATGAATTGTGAACATGCTACCATGCATAATGGAGCCATG
GTTATTGTTTCTTTTCAAATGGTGCTGGCAATGGGAAAATGCAGTCACTGCCTAAAGCTGTTATATAGTATATACATAGAGAATGCTTTGGGAAGCAAATATGCTTTTTCATTCTGAGCTAAATTACTTCAATGGCAACAGAAAGCATTTTGAAGACCC

Intron 2 GTGAATTTTA ... ATGGCAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	27.78	13	5	0
A2	33.33	14	7	0
A3	47.37	10	9	1
A4	33.33	8	4	0
A5	40	6	4	0
A6	22.08	60	17	0
A7	29.73	52	22	2
A8	18.64	48	11	0
A9	31.91	64	30	1
A10	16.67	40	8	1

>TRINITY_DN97994_c0_g1_i1 from sample A3 / Example spliced isoform

GTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCGTCCGA
ATGTACAGGTAATATATGACCAATCGGACAAAACCCCGACTCTCACATCCAAGAAATACGTAACAGTAATCACAGAGACTTGGCGCTTTTGATTTGCGCGGAAACACATCGAATTGCAGTGGTCTGATTCAAATTGAACAGGATTCTTACCTAAATACATTGCTTAGCTGTAGGTTTTCAACTGATCGGGAGGCCTAGCA
GTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGGCTAAGCTTGCATCAGCCGCTAGGGAACTGGGACGAGAAGTACATGTTTTTGTCAATCCAGCTGCTAGAAATTCAGATGACCCAAAACCTCTTTCAGACGA
GCCAGATGACTTTTATGAGTTTACCACAGAGGATTATATTCGACTATTGGCAAGCAAGAAAGAAGAAAGCATTTTGAAGACCAAAAAACTCCGTGATGCAGAGCAGGCTGCTTGCAGAGCGAAGATAACTAAGGCGGTAATAAAGGTGCAATTTCCCGATGATTATCTAATACAGACAACTTTTCAGCCATCAGAAACCA
TTTCAATGCTGATGGATCTGTTAAAAAAAGTGATTGCACAACCAAATGTGCCATTTTACATTTATACAACACCCCCAAAGAAAAGAATCACAGATTTGACAAAGGATTTTTATTCTGCTAATCTTGTACCTGGTGCACTCGTGCGTTTCCATTATGATGTGCCGGAAGAGGAAGAGAAGGGCCCCTTTCTACGTGACGAT
ATTATGGCTTTGTGTGATCTGCATTCTATACTTGAAACAAAAGAAGCAGAAAAGGCAGCTGAACCTGAACCTATTGCTGTAGAGCCTCC

>TRINITY_DN97994_c0_g1_i3 from sample A3 / Example unspliced isoform:

GTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCGTCCGA
ATGTACAGGTAATATATGACCAATCGGACAAAACCCCGACTCTCACATCCAAGAAATACGTAACAGTAATCACAGAGACTTGGCGCTTTTGATTTGCGCGGAAACACATCGAATTGCAGTGGTCTGATTCAAATTGAACAGGATTCTTACCTAAATACATTGCTTAGCTGTAGGTTTTCAACTGATCGGGAGGCCTAGCA
GTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGGCTAAGCTTGCATCAGCCGCTAGGGAACTGGGACGAGAAGTACATGTTTTTGTCAATCCAGCTGCTAGAAATTCAGATGACCCAAAACCTCTTTCAGACGA
GCCAGATGACTTTTATGAGTTTACCACAGAGGATTATATTCGACTATTGGCAAGCAAGAAAGAAGgtgaattttaggttggtttatggtttctggaattcaggttctgtaggctgataggtcccctaattcaacatatgcaaataatgaaattactgtgtgatgaattgtgaacatgctaccatgcataatggagccatg
gttattgtttcttttcaaatggtgctggcaatgggaaaatgcagtcactgcctaaagctgttatatagtatatacatagagaatgctttgggaagcaaatatgctttttcattctgagctaaattacttcaatggcaacagAAAGCATTTTGAAGACCC

Intron 3 GTCTGTGCTG ... CCCATTTGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	27.78	13	4	6
A2	33.33	13	10	3
A3	21.43	11	3	3
A4	30.77	9	6	2
A5	14.29	3	0	1
A6	18.37	40	5	13
A7	32.47	52	18	32
A8	31.65	27	18	7
A9	20.61	52	12	15
A10	28.4	29	10	13

>TRINITY_DN105156_c0_g1_i5 from sample A2 / Example spliced isoform

GATCTGTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCG
TCCGAATGTACAGGTAATATATGACCAATCGGACAAAACCCCGACTCTCACATCCAAGAAATACGTAACAGTAATCACAGAGACTTGGCGCTTTTGATTTGCGCGGAAACACATCGAATTGCAGTGGTCTGATTCAAATTGAACAGGATTCTTACCTAAATACATTGCTTAGCTGTAGGTTTTCAACTGATCGGGAGGCC
TAGCAGTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGGCTAAGCTTGCATCAGCCGCTAGGGAACTGGGACGAGAAGTACATGTTTTTGTCAATCCAGCTGCTAGAAATTCAGATGACCCAAAACCTCTTTCA
GACGAGCCAGATGACTTTTATGAGTTTACCACAGAGGATTATATTCGACTATTGGCAAGCAAGAAAGAAGAAAGCATTTTGAAGACCAAAAAACTCCGTGATGCAGAGCAGGCTGCTTGCAGAGCGAAGATAACTAAGGCGGTAATAAAGGTGCAATTTCCCGATGATTATCTAATACAGACAACTTTTCAGCCATCAGA
AACCATTTCAATGCTGATGGATCTGTTAAAAAAAGTGATTGCACAACCAAATGTGCCATTTTACATTTGTGAGTTCATTTTACCCTTCAATCCTTCACAGAAAAGTAGGTTGACAACATGTGATTGGACTTTTACTGAAGTTTTGTAATCAAAGCTTCCAGTAAACAAATTTTTGAGTTTATTATGTTAAAGATTTTGTG
TCAAGGTGTTAAAAGAGCA

>TRINITY_DN105156_c0_g1_i3 from sample A2 / Example unspliced isoform:

GATCTGTCTACTTTGCATTCCATTCCAAAATACGCAAGAATATGAAGCTTAATTTCTTGTTAAGTAACCCCCAAAAAACCACTTTGATATTTAGAAAATATGCTTAACCTACTCAACAAACCCACTGTAACGGGAGAGGAACCGTAAGGCGAGCGTAGAAGCGTGGTTAGCCTACCCTTAACTGTACAATATAACATCCG
TCCGAATGTACAGGTAATATATGACCAATCGGACAAAACCCCGACTCTCACATCCAAGAAATACGTAACAGTAATCACAGAGACTTGGCGCTTTTGATTTGCGCGGAAACACATCGAATTGCAGTGGTCTGATTCAAATTGAACAGGATTCTTACCTAAATACATTGCTTAGCTGTAGGTTTTCAACTGATCGGGAGGCC
TAGCAGTTTTAGAAATAAAATTAGTTCGACTGGGTGAGAAGACAAACAAGGCACACATACCGCAGAGAGACAAGGTTCTAATCATGGATGCAGCAGAAGCCCAGgtctgtgctgagaatggaagtgccaaaaggagaagaatagtagatgtgggcgcaaacccatttgagGCTAAGCTTGCATCAGCCGCTAGGGAACTG
GGACGAGAAGTACATGTTTTTGTCAATCCAGCTGCTAGAAATTCAGATGACCCAAAACCTCTTTCAGACGAGCCAGATGACTTTTATGAGTTTACCACAGAGGATTATATTCGACTATTGGCAAGCAAGAAAGAAGAAAGCATTTTGAAGACCAAAAAACTCCGTGATGCAGAGCAGGCTGCTTGCAGAGCGAAGATAAC
TAAGGCGGTAATAAAGGTGCAATTTCCCGATGATTATCTAATACAGACAACTTTTCAGCCATCAGAAACCATTTCAATGCTGATGGATCTGTTAAAAAAAGTGATTGCACAACCAAATGTGCCATTTTACATTTGTGAGTTCATTTTACCCTTCAATCCTTCACAGAAAAGTAGGTTGACAACATGTGATTGGACTTTTA
CTGAAGTTTTGTAATCAAAGCTTCCAGTAAACAAATTTTTGAGTTTATTATGTTAAAGATTTTGTGTCAAGGTGTTAAAAGAGCA