sp|Q9FLF0|RS92_ARATH ----> Small ribosomal subunit protein uS4y

Intron 1 GTATCCTATG ... CTGCCTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	15.05	98	7.6	17.4
A2	20.07	109	12.8	27.4
A3	9.09	112	11.6	11.2
A4	10.89	67	4.8	8.2
A5	26.68	24	0.4	8.8
A6	15.81	628.4	53.8	118.2
A7	13.69	612.4	46	97.2
A8	14.02	777.6	56.8	126.9
A9	12.4	717.2	60.2	101.8
A10	15.31	475.7	45.6	86.4

>TRINITY_DN45081_c0_g1_i9 from sample A7 / Example spliced isoform

AAGCAATTTATATGGGAAAGAAAAGACATTTTAGGGGATTGGACGTAACTGTAAGTATAGGTAAAGAATCCCTACTTCCCTACTCGAGCCGCTGCAAGACGAGATTCTCTGCAAAGAAGAAGAAAGTTACCAAAATATTTGCAGACTAAGAACACTGCACGGGATTTAGACACGAATCGCTCAGCGATGTGCAGACCCTA
AATTGTCCAGCGTCAGACCAACGGATTTAGAACAAAATTAGTGCCCTAGCATCGATAGATTTGTGCCCTTATCTGCAAGAGAGAGGCAAAGGCACTGCAACTTTGAGTGATTCGGGCTGGAACTTGAAGCTATAACACCATGAGGAAGCTTAAATTTCATGAGAAGAAGCTGTTGAAGAAGGTCAATTTTCTAGAATGGA
AAAGAGAAAGAGGACAGAGGGAGGCCCTCGTCATGCGTCGCTACCTTATCACTGGAAGAGATGACTACAAGAAGTATAATATATTATGTGGGATGATTACCAAGCTGGTGAATATTTTGAAGCAGGTTGATCCAAAAGACCCTTTTCGAGTAGAGATGACTGATCGTCTGTTAGAAAAGTTATATAATATTGGAGTAATT
CCCACGAAGAAGAGCTTGGCTTTGTGTGACAAGTTATCAGTTTCTTCCTTTTGCAGGCGCCGGTTAGCTACAGTTCTCGTAAGGTTACATTTTGCAGAACGCTTAAAGGAAGCTGTCACGTACATTGAACAAGGCCATATCCGTGTTGGCCCAGACACTGTTACAGATCCAGCATTTCTGGTGACAAGGACTTTTGAAGA
CTTTGTTACATGGGTTGACACATCGAAGATCAAGAGGAAAGTGTTGCAATACAATGAGCGTTTGGATGATTACGATCTTCTCAATTAGGATTCTGGAGTGCTGATTTAGGGTTCTTATACCTGCCATGTTCTCTCATTTTTGAAAGGACAATCTCATTGCAGATTTGCTAATTGTACATTCTGATCTTTCAGATCTTTTA
ACTTCCCATGTCTTTATCCTATGATGTAGCTCGTTCTTGTGAGCCTTCAAAACTATGAATCACTAAGTTAAAAGGATAATGTTTTCAGTTCTTTTAATCTTCATATCTGCTATCATTTTCTGTAGCGTTATCGTAAGTGGGATCACCAAGTTGGAAGGATTATATATGTATTGAAATTTAAATTATGTGGTCAGTTGCTC
AAAGTCCTCGTTTCCCTTGGACTGTATTTGTTGTCAATTGCTTAGAAATGGACTTACACAGCTCAAATTGAATTAAGAATTCAATTCTGTACCATTTAATTTGTTCAGGAAATGACAATGCACTCCAAGCTAGTTGTATCAATGTATACTCACAAAGGTACTAGTAATTTACAGAGAGTAGCTACCTATATACTGTAGTA
GTGGCCATACGTAGTGAAATTTTCTGTCGGGCCAGCTCCCGTTGCCTCGGTGGTTCAAGAAGCTGCCTATGTTCAATGAAAAATTGGAAATATTCCACATGATACATGGCCTATTCCATAGTGTTTACGGGCAGGAATTGCATGGCATTGTGTCTAAGAGGTTTTATCTAGAGGCCTGTCCTCTTTTATGAAGCTTCCTA
TACTATTTCAAGACAACACATAGCATTGCAATCCAAATCTAGTTGAGGTTTTTTATATGATAACTTTAGAAATTTGTTGTTGGTGAAATTCTTGCAGCTTCTTTTAGATTTAATGTGGAAGGACTTTTGGTTTCTAGTTACACTTGTCTAAGTGATTTTTTCTTACATGGACGGAATCTTCTTTGGATATTGCTTTGTAG
AGATCTAGATTTCAAAGGGAACTGAACATATCCTTCCTCCTATCCTATAAA

>TRINITY_DN45081_c0_g1_i7 from sample A7 / Example unspliced isoform:

TGTCACGTACATTGAACAAGGCCgtatcctatgtctagttttatctttgtaaatctttgttgtatataatgtgtagtaccatataactggacaatggcttcttacaaaattgtaatatctggcctcgacccaacatgtttaaaagattttaaatctaggtagcagctagcagtgtaataaatcatttagttaacaaattt
tgggaattgtatatctagataatcatgcagttggcttgttgaagggttcatttcaaaaaatgtaaagttttccttgactgcctttagATATCCGTGTTGGCCCGGACACTGTTACAGATCCAGCATTTCTGGTGACAAGGACTTTTGAAGACTTTGTTACATGGGTTGACACATCGAAGATCAAGAGGAAAGTGTTGCAA
TACAATGAGCGTTTGGATGATTACGATCTTCTCAATTAGGATTCTGGAGTGCTGATTTAGGGTTCTTATACCTGCCATGTTCTCTCATTTTTGAAAGGACAATCTCATTGCAGATTTGCTAATTGTACATTCTGATCTTTCAGATCTTTTAACTTCCCATGTCTTTATCCTATGATGTAGCTCGTTCT

Intron 2 GTATCCTACA ... CTGTCTTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	7.6	98	9.2	18.2
A2	11.42	109	16.4	24
A3	9.71	112	13.6	10.2
A4	8.47	67	7.2	7.2
A5	1.6	24	0.4	8
A6	8.39	629.2	64.8	108.4
A7	7.69	612.4	58	92.4
A8	7.94	778.6	77.2	123.4
A9	8.24	718	73.8	103
A10	9.5	475.7	58.8	83.4

>TRINITY_DN43402_c1_g3_i5 from sample A8 / Example spliced isoform

AGAGAGGCAAAGGCACTGCAACTTTGAGTGATTCGGGCTGGAACTTGAAGCTATAACACCATGAGGAAGCTTAAATTTCATGAGAAGAAGCTGTTGAAGAAGGTCAATTTTCTAGAATGGAAAAGAGAAAGAGGACAGAGGGAGGCCCTCGTCATGCGTCGCTACCTTATCACTGGAAGAGATGATTACAAGAAGTATAA
TATACTGTGTGGAATGATCACCAAGCTGGTGAATATTTTGAAACAGGTTGATCCAAAAGACCCTTTTCGAATAGAGATGACTGATCGTCTGCTAGAAAAATTATATAATATTGGAGTAATTCCCACGAAGAAGAGCTTGGCTTTGTGTGACAAGATATCGGTTTCTTCCTTTTGCAGGCGCCGATTAGCTACAGTTCTTG
TAAGGTTGCATTTTGCAGAACGCTTGAAGGAAGCTGTCACGTACATTGAACAAGGCCATATCCGTGTTGGCCCGGACACTGTTACAGATCCAGCATTTCTGGTGACAAGGACTTTTGAAGACTTTGTTACATGGGTTGACACATCGAAGATCAAGAGGAAAGTGTTGCAATACAATGAGCGTTTGGATGATTATGATCTT
CTCAACTAGGAATCTGGAGGGTTCATTTAGGGTTCTTATATCTGCCATGTTCTCTCATTTTTGAAAGGACAATCTCATTGCAGATTTGCTAATTGTACATTCTGATCTTTTGGATCTTTTAACTTCCCATGTCTTTATCCTATGATGTAGCTCGTTCTTGTGAGCCTTCAAAACTATGAATCACTAAGTTAAAAGGATAA
TGTTTTCAGTTCTTTTAATCTTCATATCTGCTATCATTTTCTGTAGCGTTATCGTAAGTGGGATCACCAAGTTGGAAGGATTATATATGTATTGAAATTTAAATTATGTGGTCAGTTGCTCAAAGTCCTCGTTTCCCTTGGACTGTATTTGTTGTCAATTGCTTAGAAATGGACTTACACAGCTCAAATTGAATTAAGAA
TTCAATTCTGTACCATTTAATTTGTTCAGGAAATGACAATGCACTCCAAGCTAGTTGTATCAATGTATACTCACAAAGGTACTAGTAATTTACAGAGAGTAGCTACCTATATACTGTAGTAGTGGCCATACGTAGTGAAATTTTCTGTCGGGCCAGCTCCCGTTGCCTCGGTGGTTCAAGAAGCTGCCTATGTTCAATGA
AAAATTGGAAATATTCCACATGATACATGGCCTATTCCATAGTGTTTACGGGCAGGAATTGCATGGCATTGTGTCTAAGAGGTTTTATCTAGAGGCCTGTCCTCTTTTATGAAGCTTCCTATACTATTTCAAGACAACACATAGCATTGCAATCCAAATCTAGTTGAGGTTTTTTATATGATAACTTTAGAAATTTGTTG
TTGGTGAAATTCTTGCAGCTTCTTTTAGATTTAATGTGGAAGGACTTTTGGTTTCTAGTTACACTTGTCTAAGTGATTTTTTCTTACATGGACGGAATCTTCTTTGGATATTGCTTTGTAGAGATCTAGATTTCAAAGGGAACTGAACATATCCTTCCTCCTATCCTATAAATAGTTGC

>TRINITY_DN43402_c1_g3_i6 from sample A8 / Example unspliced isoform:

TGTCACGTACATTGAACAAGGCCgtatcctatgtctagttttatctttgtaaatctttgttgtatataatgtgtagtaccatataactggacagtgccttcataaaaaaaaatgtaatatttggccttgacccaacatggttggaagactctaaatctaggtggcagctagcagtgtaatgcatcattaattaaattttt
ttgggcattgcatatctagataatcatgggttggcttgttgaacagttcatttcaaaaaatgtttgcataagttttctttgactgtctttagATATCCGTGTTGGCCCAGACACTGTTACAGATCCAGCATTTCTGGTGACAAGGACTTTTGAAGACTTTGTTACATGGGTTGACACATCGAAGATCAAGAGGAAAGTGT
TGCAATACAATGAGCGTTTGGATGATTA

Intron 3 GTAAAGAATC ... TCTGCAAGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	68.29	26	53	59
A2	61.81	38	45	78
A3	63.26	44.5	52.3	101
A4	50.7	35	31	41
A5	62.22	17	24	32
A6	54.63	232	175	383.5
A7	54.95	312	243	518
A8	49.23	267	152.3	365.5
A9	56.25	303.3	283.8	496
A10	55.72	259	218	434

>TRINITY_DN114579_c4_g1_i6 from sample A2 / Example spliced isoform

AAAGAAGATGTTAAAAGTTACTTGTAAACTTATTGGAAGCAATTTATATGGGAAAGAAAGACATTTTAGGGGATTGGACGTAACTGTAAGTATAGAGAGGCAAAGGCACTGCAACTTTGAGTGATTCGGGCTGGAACTTGAAGCTATAACACCATGAGGAAGCTTAAATTTCATGAGAAGAAGCTGTTGAAGAAGGTCAA
TTTTCTAGAATGGAAAAGAGAAAGAGGACAGAGGGAGGCCCTCGTCATGCGTCGCTACCTTATCACTGGAAGAGATGACTACAAGAAGTATATCTGTGCATTACCTTCTGCATCGTTTTTCCTTTCATATCTTTGGAACGAATAGATTTCTAAGTATAGTACTTTTATGCTTTGAATATATGCC

>TRINITY_DN114579_c4_g1_i7 from sample A2 / Example unspliced isoform:

AAAGAAGATGTTAAAAGTTACTTGTAAACTTATTGGAAGCAATTTATATGGGAAAGAAAGACATTTTAGGGGATTGGACGTAACTGTAAGTATAGgtaaagaatccctacttccctacccgagccgctgcaagacgagattctctgcaaagaagaagaaagttaccaaaatatttgcagactaagaacactgcacgggat
ttagacacgaatcgctcagcgatgtgcagaccctaaattgtccagcgtcagaccaacggatttagaacaaaattagtgccctagcatcgatagatttgtgcccttatctgcaagagAGAGGCAAAGGCACTGCAACTTTGAGTGATTCGGGCTGGAACTTGAAGCTATAACACCATGAGGAAGCTTAAATTTCATGAGAA
GAAGCTGTTGAAGAAGGTCAATTTTCTAGAATGGAAAAGAGAAAGAGGACAGAGGGAGGCCCTCGTCATGCGTCGCTACCTTATCACTGGAAGAGATGACTACAAGAAGTATAATATATTATGTGGGATGATTACCAAGCTGGTGAATATTTTGAAGCAGGTTGATCCAAAAGACCCTTTTCGAGTAGAGATGACTGATC
GTCTGTTAGAAAAGTTATATAATATTGGAGTAATTCCCACGAAGAAGAGCTTGGCTTTGTGTGACAAGTTATCAGTTTCTTCCTTTTGCAGGCGCCGGTTAGCTACAGTTCTCGTAAGGTTACATTTTGCAGAACGCTTAAAGGAAGCTGTCACGTACATTGAACAAGGCCATATCCGTGTTGGCCCGGACACTGTTACA
GATCCAGCATTTCTGGTGACAAGGACTTTTGAAGACTTTGTTACATGGGTTGACACATCGAAGATCAAGAGGAAAGTGTTGCAATACAATGAGCGTTTGGATGATTACGATCTTCTCAATTAGGATTCTGGAGTGCTGATTTAGGGTTCTTATACCTGCCATGTTCTCTCATTTTTGAAAGGACAATCTCATTGCAGATT
TGCTAATTGTACATTCTGATCTTTCAGATCTTTTAACTTCCCATGTCTTTATCCTATGATGTAGCTCGTTCTTGTGAGCCTTCAAAACTATGAATCACTAAGTTAAAAGGATAATGTTTTCAGTTCTTTTAATCTTCATATCTGCTATCATTTTCTGTAGCGTTATCGTAAGTGGGATCACCAAGTTGGAAGGATTATAT
ATGTATTGAAATTTAAATTATGTGGTCAGTTGCTCAAAGTCCTCGTTTCCCTTGGATTGCATCTGGTGTCAATTGTTTAGAAATGGACTTATGCAGCTGAAATTGAATTAATAATTAATTCTATACCATTTAGTTTGTTCAGGAC