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

Intron 1 GTATTCTGTT ... TTTGATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	20.86	478	157	95
A2	22.34	419	167	74
A3	19.51	491	158	80
A4	22.65	321	125	63
A5	20.46	276	81	61
A6	19.15	5287	1560	945
A7	19.36	2952	895	522
A8	19.76	2824	901	490
A9	19.37	3086	958	525
A10	19	2379	731	385

>TRINITY_DN44231_c0_g1_i1 from sample A7 / Example spliced isoform

CACAACCATTGGGGAAGAGGAGGGAAGAGGGACCGAGGTAAGTAAACCCTAAGGGACGCTTTTAGACATGAAGTTATAGGTTAAAGATCTAGTTTCCCCTTGCAATCGCATTGAAAAGGATTTTAGGGTTTTTGTATGAAGCGGTAGGGTTTGTCACATTCAATAGAATGCGTTAGGGGGAGGCTTTGTTGGTGCTTGAT
TGTGAGTCCGGAGGAGTAGGAAGAGCAGCAGAGGAGGAGGAGAGATGGTGCACGTCGTTTTTTACCGCAACTATGGAAAGACGTTCAAGAAGCCCCGCCGCCCTTACGAGAAGGAGCGGCTGGACGCAGAGCTGAAATTGGTTGGAGAATACGGGCTGCGAAACAAGAGAGAGCTCTGGAGGGTTCAATACACATTGAGC
CGCATACGAAATGCGGCGCGTATGCTTCTGACGCTGGATGAGAAAAACCCTCGTCGGATTTTCGAAGGAGAAGCCCTGCTGCGGCGTATGAACAGGTATGGCCTCCTGGACGAAACCCAAAGCAAGCTTGATTACGTCCTCGCTCTTACTGTCGAGAACTTCCTCGAGCGCCGTCTTCAGACTCTCGTCTTCAAATCCGG
CATGGCCAAGTCCATCCATCACGCCCGTGTTCTCATCAGGCAACGTCACATCAGAGTTGGTAGGCAGGTCGTGAATATTCCGTCTTTCATGGTAAGAGTTGACTCGCAAAAGCACATTGATTTCTCACTTACAAGTCCACTTGGTGGGGGACGTCCCGGACGTGTGAAACGAAAGAACATGAAGGCAGCATCAAAGAAGG
CTGCTGGTGGAGATGGAGAGGAAGAGGATGAGGAATGAGGAATAGCAGTATTATCGGCCAAGAAAAATTAGCTTCACAATCTCTTCTTTAGTGTGAAGCATTTAGATTTTGTTAAGACATACTAGCCGAGTTTTCTGGCTGCTGCGACAACTGGTTGTAAAACTTCGGCAATAGGTTTGGATAAATCTTAAATTTGGTAA
TAGTCAGCAATAGCATACATTTTAAATTTTGTCAGTTTACTGGCTTATGCAAGATGTTTGGTTTGTTAAACATTGGCAATAGGTTAGAATACACTTTAAAATTTGCTGGACTTTGATTATAGTCCAGAGTTCTGTGACAGTAAACGGCAAATGTTGATTTATTTCATTCCAGTTACTGAAAATTTAAATTTTGCACATTT
AATTATGTCGTAGTAATATTATCTTTTGTTTATGTATTTTAAATTTGACAATAGTCAGCATACATTTTTAAATTTTGTCAATTTACTGTTTACTGCAAGATGTTTGGTTTGTTAA

>TRINITY_DN44231_c0_g1_i3 from sample A7 / Example unspliced isoform:

CACAACCATTGGGGAAGAGGAGGGAAGAGGGACCGAGGTAAGTAAACCCTAAGGGACGCTTTTAGACATGAAGTTATAGGTTAAAGATCTAGTTTCCCCTTGCAATCGCATTGAAAAGGATTTTAGGGTTTTTGTATGAAGCGGTAGGGTTTGTCACATTCAATAGAATGCGTTAGGGGGAGGCTTTGTTGGTGCTTGAT
TGTGAGTCCGGAGGAGTAGGAAGAGCAGCAGAGGAGGAGGAGAGATGGTGCACGTCGTTTTTTACCGCAACTATGGAAAGACGTTCAAGAAGCCCCGCCGCCCTTACGAGAAGGAGCGGCTGGACGCAGAGCTGAAATTGGTTGGAGAATACGGGCTGCGAAACAAGAGAGAGCTCTGGAGGGTTCAATACACATTGAGC
CGCATACGAAATGCGGCGCGTATGCTTCTGACGCTGGATGAGAAAAACCCTCGTCGGATTTTCGAAGGAGAAGCCCTGCTGCGGCGTATGAACAGGTATGGCCTCCTGGACGAAACCCAAAGCAAGCTTGATTACGTCCTCGCTCTTACTGTCGAGAACTTCCTCGAGCGCCGTCTTCAGACTCTCGTCTTCAAATCCGG
CATGGCCAAGTCCATCCATCACGCCCGTGTTCTCATCAGGCAACGTCACATCAGgtattctgttctattctattcgtttctattgttaaataatcataaaagattttgcccattttaatcagcccacattgattctgaagaggctaaattacttgtttagggtatgaaactccatacaagatctgtattacaaatagggc
atattttggggcagtatttctttttactagttcgcccttcctcaatccgggagaatataaatcaatgtggtcatattatactatttaaacctgaagcacggttcacaatcccaaaacatattgcagggagacttgatccctagtgaggtctataaaattaccctgctttcactgactcagcaagtcgcctttgatgcaat
atgctacttttgactagcagccctgatcgagggtatatgtcctatcaaagtcggtcaggatttgaacctgaaatcatctgaatagaagatcgtgctagcacaggtagtgagaccaccagcttttgaacccaggttctctagacaatgtttggaccgatctcttccggctaatactgttaaatagaaaaggcccagtctaa
atggaattgagaaaggcaaacttatctgtttagggtatacaaatacatagatgatccactctacgaacattttatctttgaataagggctgctattgaggagttaatattctgtcaaagtgacccgagaataaactagcataaactagcagagatccttctcaaccctggatctctggatcttataagtggtgataggtt
tgcagttgggctttttaaattcctctgggtgttaaatagatgtatggttaaaatggatctatgctagtttattgtaatctatggtttatatagtttgagaagtgaattttcaaatttaagaaacaccattattgagatttattgagattgtcagctgataaactgattttctagtctcttagtctcagtgttcaatagtt
ccaagctttcaaataactgggaaaaacaaagatactactggtgttgacttttcttgggatgcctgacaaattatctcatctctctttctgagctatacggtactccacttcagattatgacaaattatctcatccctctttctgagctatacggtactccacttcagattacgcaaatctttggttgttatcaacgcttg
ttttgtctacttgagagtttttgacgagacacagtagaacgaattgtttctgatgtcaatttcatacacaccaaacgattgcttcaatccaacctacataatttctacttgccttcttaagggcttacataagctccaccttatctgtggtagcttataacgtttgcctgaatgagcaatcaccagactttaattctcct
tttgccaaggcttgcgtcaacatgaaactttgaagcctccaactcaaatcatatttatcttcccaatggcacaaggtgttagtttccattgaatataggagccaagaattttaatgaaaggcatagcctgctgaatatagtagtgattgtggagatctattgtaggccaaatttacaaatggcatgtgctctttactagt
accgaatatggatgatgtttactggttccaagtgttagtgatgtaatgggtacagtgcatccatgttgtgtttaatgggtacattgcatacatattgcgtttacacgtttttagagtaaatttctactgcagtgctttaggaatctctgcttattagatggttttgtttgatgcagAGTTGGTAGGCAGGTCGTGAATAT
TCCGTCTTTCATGGTAAGAGTTGACTCGCAAAAGCACATTGATTTCTCACTTACAAGTCCACTTGGTGGGGGACGTCCCGGACGTGTGAAACGAAAGAACATGAAGGCAGCATCAAAGAAGGCTGCTGGTGGAGATGGAGAGGAAGAGGATGAGGAATGAGGAATAGCAGTATTATCGGCCAAGAAAAATTAGCTTCACA
ATCTCTTCTTTAGTGTGAAGCATTTAGATTTTGTTAAGACATACTAGCCGAGTTTTCTGGCTGCTGCGACAACTGGTTGTAAAACTTCGGCAATAGGTTTGGATAAATCTTAAATTTGGTAATAGTCAGCAATAGCATACATTTTAAATTTTGTCAGTTTACTGGCTTATGCAAGATGTTTGGTTTGTTAAACATTGGCA
ATAGGTTAGAATACACTTTAAAATTTGCTGGACTTTGATTATAGTCCAGAGTTCTGTGACAGTAAACGGCAAATGTTGATTTATTTCATTCCAGTTACTGAAAATTTAAATTTTGCACATTTAATTATGTCGTAGTAATATTATCTTTTGTTTATGTATTTTAAATTTGACAATAGTCAGCATACATTTTTAAATTTTGT
CAATTTACTGTTTACTGCAAGATGTTTGGTTTGTTAA

Intron 2 GTAAGTGCCT ... TTGTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	12.82	1120.5	17.3	167.8
A2	11.72	1452.3	19	196.3
A3	10.69	1860	34.3	226.5
A4	12.38	1290.3	26.8	185.3
A5	10.5	1248	24.8	150.3
A6	11.66	16338.5	268.5	2205.5
A7	11.23	10708.5	172.5	1380.8
A8	11.07	6632.3	101.5	845.3
A9	11.21	9578.3	144.8	1235.3
A10	10.72	9474	157.5	1160.3

>TRINITY_DN109411_c0_g1_i3 from sample A2 / Example spliced isoform

CTCCACGACCATGTAAAATAACACAACCATTGGGGAAGAGGAGGGAAGAGGGACCGAGGTAAGTAAACCCTAAGGGACGCTTTTAGACATGAAGTTATAGGTTAAAGATCTAGTTTCCCCTTGCAATCGCATTGAAAAGGATTTTAGGGTTTTTGTATGAAGCGGTAGGGTTTGTCACATTCAATAGAATGCGTTAGGGG
GAGGCTTTGTTGGTGCTTGATTGTGAGTCCGGAGGAGTAGGAAGAGCAGCAGAGGAGGAGGAGAGATGGTGCACGTCGTTTTTTACCGCAACTATGGAAAGACGTTCAAGAAGCCCCGCCGCCCCTACGAGAAGGAGCGGCTGGACGCAGAGCTGAAATTGGTTGGAGAATACGGGCTACGAAACAAGAGAGAGCTCTGG
AGGGTTCAATACACATTGAGCCGCATACGAAATGCGGCGCGTATGCTTCTGACGCTGGATGAGAAAAACCCTCGTCGGATTTTCGAAGGAGAAGCCCTGCTGCGGCGTATGAACAGGTATGGCCTCCTGGACGAAACCCAAAGCAAGCTTGATTACGTCCTCGCTCTTACTGTCGAGAACTTCCTCGAGCGCCGTCTTCA
GACTCTCGTCTTCAAATCCGGCATGGCCAAGTCCATCCATCACGCCCGTGTTCTCATCAGGCAACGTCACATCAGAGTTGGTAGGCAGGTCGTGAATATTCCGTCTTTCATGGTAAGAGTTGACTCGCAAAAGCACATTGATTTCTCACTTACAAGTCCACTTGGTGGGGGACGTCCCGGTCGTGTGAAACGAAAGAACA
TGAAGGCAGCATCAAAGAAGGCTGCTGGTGGAGATGGAGAGGAAGAGGATGAGGAATGAGGAATAGCAGTATTATCGGCCAAGAAAAATTAGCTTCACAATCTCTTCTTTAGTGTGAAGCATTTAGATTTTGTTAAGACATACTAGCCGAGTTTTCTGGCTGCTGCGACAACTGGTTGTAAAACTTCGGCAATAGGTTTG
GATAAATCTTAAATTTGGTAATAGTCAGCAATAGCATACATTTTAAATTTTGTCAGTTTACTGGCTTATGCAAGATGTTTGGTTTGTTAAACATTGGCAATAGGTTAGAATACACTTTAAAATTTGCTGGACTTTGATTATAGTCCAGAGTTCTGTGACAGTAAACGGCAAATGTTGATTTATTTCATTCCAGTTACTGA
AAATTTAAATTTTGCAC

>TRINITY_DN109411_c0_g1_i4 from sample A2 / Example unspliced isoform:

CTCCACGACCATGTAAAATAACACAACCATTGGGGAAGAGGAGGGAAGAGGGACCGAGGTAAGTAAACCCTAAGGGACGCTTTTAGACATGAAGTTATAGGTTAAAGATCTAGTTTCCCCTTGCAATCGCATTGAAAAGGATTTTAGGGTTTTTGTATGAAGCGGTAGGGTTTGTCACATTCAATAGAATGCGTTAGGGG
GAGGCTTTGTTGGTGCTTGATTGTGAGTCCGGAGGAGTAGGAAGAGCAGCAGAGGAGGAGGAGAGATGGTGCACGTCGTTTTTTACCGCAACTgtaagtgcctgtcttgcatttcctgatcctcattctccattttcctttctttcatagccctctgtttctgtgttttattgaattgtataagccttccttgtttgcag


ATGGAAAGACGTTCAAGAAGCCCCGCCGCCCCTACGAGAAGGAGCGGCTGGACGCAGAGCTGAAATTGGTTGGAGAATACGGGCTACGAAACAAGAGAGAGCTCTGGAGGGTTCAATACACATTGAGCCGCATACGAAATGCGGCGCGTATGCTTCTGACGCTGGATGAGAAAAACCCTCGTCGGATTTTCGAAGGAGAA
GCCCTGCTGCGGCGTATGAACAGGTATGGCCTCCTGGACGAAACCCAAAGCAAGCTTGATTACGTCCTCGCTCTTACTGTCGAGAACTTCCTCGAGCGCCGTCTTCAGACTCTCGTCTTCAAATCCGGCATGGCCAAGTCCATCCATCACGCCCGTGTTCTCATCAGGCAACGTCACATCAGAGTTGGTAGGCAGGTCGT
GAATATTCCGTCTTTCATGGTAAGAGTTGACTCGCAAAAGCACATTGATTTCTCACTTACAAGTCCACTTGGTGGGGGACGTCCCGGTCGTGTGAAACGAAAGAACATGAAGGCAGCATCAAAGAAGGCTGCTGGTGGAGATGGAGAGGAAGAGGATGAGGAATGAGGAATAGCAGTATTATCGGCCAAGAAAAATTAGC
TTCACAATCTCTTCTTTAGTGTGAAGCATTTAGATTTTGTTAAGACATACTAGCCGAGTTTTCTGGCTGCTGCGACAACTGGTTGTAAAACTTCGGCAATAGGTTTGGATAAATCTTAAATTTGGTAATAGTCAGCAATAGCATACATTTTAAATTTTGTCAGTTTACTGGCTTATGCAAGATGTTTGGTTTGTTAAACA
TTGGCAATAGGTTAGAATACACTTTAAAATTTGCTGGACTTTGATTATAGTCCAGAGTTCTGTGACAGTAAACGGCAAATGTTGATTTATTTCATTCCAGTTACTGAAAATTTAAATTTTGCAC