sp|Q9LDD1|BRG3_ARATH ----> Probable BOI-related E3 ubiquitin-protein ligase 3

Intron 1 GTAAGGATGC ... GGTTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	12.93	64	12	7
A2	24.32	42	20	7
A3	20	46	17	6
A4	21.13	56	16	14
A5	25.58	16	5	6
A6	10.95	126	21	10
A7	12.57	160	32	14
A8	13.64	114	27	9
A9	15.54	125	34	12
A10	19.01	164	52	25

>TRINITY_DN116370_c2_g1_i3 from sample A2 / Example spliced isoform

CTCATTATATGTTATAGGAAAAACCCACCAAACCCTTCCATTGGCGGAAAGCGAACTTACAATGTGAACATCAACCTCGCCTCTCCACCATCTTCAGTTACAACGGCTCGCGAAATATGGGCTCCCCAGTCGTAGCGTAGACAAATTTGGAGGAGGTTGAGTTGAATTTCGCGTTCATCATCGTGTTGTGTGCGTGCATA
ATAATAATAATAATCATGGTGATATTGATGATGTAGCCGCTGTTGTGTACAGAGGCGGCCTTGGCCTTGGTGGCTGCTCAGATAAATCAACTCGGCTGCAATTTCTAGACCGATTGACCTCCCATGGATTCATTCATACCCATTTCGTATATAATACGAATATCCCAACTTCATCCATTCATGTAATCCGAAGAACATCA
GGTCTCTGCAATCTGCATTATCAGGATCGTTTCTGGTTCGAATCTTTGCCGTTTTTCAGTCTATCCCCAGATTGTTTGGAGGCTCAGAATGGCGGTTCAGGCACAGTACTCGTCCAATATGCGTAACAGGCACTTGTTTGCAGGTGAGAACAAGGGCTCCATTCCAATTGCTTTCTTTGGGCCTGGAAATTACATGGATC
ATCATCAGATTCAGCAGCAGCAACAGATTCAATCCCAATCCCAGAACCAATCCCCGGCTGTCAACGGGTTGCCCAGTCAGCCTCCGTACATCACCCAGTTTACTGCTTGTAACCGTGGACAACAGGCCACAGGCGCAGGCTTACATGGATCTGAGAATGATCTGGCCTGGAATTTATTGGCACCCAGGAAGAGGACCAGA
GAGCATGAGCTTCTGGAAAATTCTCAAATTTCATCTATTGATTTTCTGCAGAGCCAGCGCACTGCTCAGATTGCCCTTTCTCAGTCCAATGGAGCTGTTTCGACTGGGTTGCGGTTGTCATTGGATGATGAAAAACTGAATTCCTCCTGCAATATGTCGTTGGGTACTTCAAAGGTTTCCCTTATGAACGAAGAACTGAG
TGGAGTTTTACAGCAGCAGAATGCCGAGATTGACCAATTTTTAAGATCTCAGGAGGAGCAGTTCAGGCAAGCTCTGGATGAGAAAACTAGGAGGTTTCAGATGAATATCTTGGCTTCTCTCGAGGAAGCTGCACTAATGAAGCTCAGGGATAAGGATTTGGAGGTGGAAAACATGAATAAAAAAAACATGGAACTAGAAG
AGAAGATGAAGCAATTGAGCATGGAAGCACATGCATGGCAATATAGGGTGAAATGCAGTGAAACTATGATTAACGCCCTTAAATTCAATCTTCAGCAGGCTTATGCCCAAAACAGGGAGAGTAAGGAAGGATGTGGAGACAGTGAAGTAGATGATGCAGCTTCTTGTTTCAATGCTGATGGAGGTGATTTCCAGGCTTTC
ATCTACAAGGAGAATAGAGACTTAAAAGATCAGAGGACTTGCAAGGTATGCAGAAGCAATGATGTATGCATTCTTTTGCTGCCTTGCAGACATCTGTGCCTCTGCAAAGACTGTGAAAGTAGGCTTGAAGTTTGTCCCTTGTGCCGGTCATTTAAGAGTGCTAGCATGCAGATCTATATGTCATGAGTTGCCACTGTGAA
TAAATGCACCCTATGATTGTTTATGTTCCTTAGTGACCGATTTTATCTTTGGTCACCGCATTGATGTCATTTGGGTATGCATTGCATCTCCCTTGTGCTTGAATAGCTAGATCTACATGTGGACTGGGAATTTTGGAAGAGGCAACTTGGATTCTGGTCTCTGGCTGCTCTGGAATTTGAGCTTCTTAACCATGCAAGGA
ATTCCAAGTTGTAGGGTTCAACATTTTGTTCCGTGTTCATATTGACCTCTAAAATTAGTTTGGTGTTCATACTGACCTCTCCATTTAGTTTGATGTTCATATTGACCTTTAAACTACCATAATTCATGGTAAAAATAGATTTTTTTAAGGAGAGATGCCTAAATAGGCATTTGTAATGCTGATCTTGAAATACATTATTT
TGGGCACCTCTTTCATGAAGCTAAACTACTTAAGTCACCATTACATTGCAGTGGATTCTAAAGTGTGCATAGTTCTGAGATCATTGCACCGAGAGGAGCAAGGTGCTCTACAGCTCAGTATGGGGGAGATGTTGTAACGTTCGTTCCTAACAAAATAATTAAAAAATAATAATAAAAATTCATGGTGGC

>TRINITY_DN116370_c2_g1_i2 from sample A2 / Example unspliced isoform:

GCTCCTTGAATTTCAGATGTAGAGCTATTGTTAGAATCAAGGGATCAAGATTGATCGGGTTTTTTGGTTGGCAGGCACTTGTTTGCAGGTGAGAACAAGGGCTCCATTCCAATTGCTTTCTTTGGGCCTGGAAATTACATGGATCATCATCAGATTCAGCAGCAGCAACAGATTCAATCCCAATCCCAGAACCAATCCCC
GGCTGTCAACGGGTTGCCCAGTCAGCCTCCGTACATCACCCAGTgtaaggatgcctacatagctcggtttgaatcatttaggactttttgctatccgatgccaatatgattgttttatgggttttgcagTTACTGCTTGTAACCGTGGACAACAGGCCACAGGCGCAGGCTTACATGGATCTGAGAATGATCTGGCCTGG
AATTTATTGGCACCCAGGAAGAGGACCAGAGAGCATGAGCTTCTGGAAAATTCTCAAATTTCATCTATTGATTTTCTGCAGAGCCAGCGCACTGCTCAGATTGCCCTTTCTCAGTCCAATGGAGCTGTTTCGACTGGGTTGCGGTTGTCATTGGATGATGAAAAACTGAATTCCTCCTGCAATATGTCGTTGGGTACTTC
AAAGGTTTCCCTTATGAACGAAGAACTGAGTGGAGTTTTACAGCAGCAGAATGCCGAGATTGACCAATTTTTAAGATCTCAGGAGGAGCAGTTCAGGCAAGCTCTGGATGAGAAAACTAGGAGGTTTCAGATGAATATCTTGGCTTCTCTCGAGGAAGCTGCACTAATGAAGCTCAGGGATAAGGATTTGGAGGTGGAAA
ACATGAATAAAAAAAACATGGAACTAGAAGAGAAGATGAAGCAATTGAGCATGGAAGCACATGCATGGCAATATAGGGTGAAATGCAGTGAAACTATGATTAACGCCCTTAAATTCAATCTTCAGCAGGCTTATGCCCAAAACAGGGAGAGTAAGGAAGGATGTGGAGACAGTGAAGTAGATGATGCAGCTTCTTGTTTC
AATGCTGATGGAGGTGATTTCCAGGCTTTCATCTACAAGGAGAATAGAGACTTAAAAGATCAGAGGACTTGCAAGGTATGCAGAAGCAATGATGTATGCATTCTTTTGCTGCCTTGCAGACATCTGTGCCTCTGCAAAGACTGTGAAAGTAGGCTTGAAGTTTGTCCCTTGTGCCGGTCATTTAAGAGTGCTAGCATGCA
GATCTATATGTCATGAGTTGCCACTGTGAATAAATGCACCCTATGATTGTTTATGTTCCTTAGTGACCGATTTTATCTTTGGTCACCGCATTGATGTCATTTGGGTATGCATTGCATCTCCCTTGTGCTTGAATAGCTAGATCTACATGTGGACTGGGAATTTTGGAAGAGGCAACTTGGATTCTGGTCTCTGGCTGCTC
TGGAATTTGAGCTTCTTAACCATGCAAGGAATTCCAAGTTGTAGGGTTCAACATTTTGTTCCGTGTTCATATTGACCTCTAAAATTAGTTTGGTGTTCATACTGACCTCTCCATTTAGTTTGATGTTCATATTGACCTTTAAACTACCATAATTCATGGTAAAAATAGATTTTTTTAAGGAGAGATGCCTAAATAGGCAT
TTGTAATGCTGATCTTGAAATACATTATTTTGGGCACCTCTTTCATGAAGCTAAACTACTTAAGTCACCATTACATTGCAGTGGATTCTAAAGTGTGCATAGTTCTGAGATCATTGCACCGAGAGGAGCAAGGTGCTCTACAGCTCAGTATGGGGGAGATGTTGTAACGTTCGTTCCTAACAAAATAATTAAAAAATAAT
AATAAAAATTCATGGTGGC

Intron 2 GTTGAGTTGA ... TTGTGTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	70.49	18	8	43
A2	77.74	18	11.9	62.9
A3	75.43	19	19	58.4
A4	73.42	19	9.1	52.5
A5	80.95	8	11.9	34
A6	72.54	29	15.8	76.6
A7	75.33	58	31.4	177.1
A8	75.43	19	14.5	58.4
A9	73.89	50	23.3	141.5
A10	70.32	75	23.6	177.6

>TRINITY_DN111649_c0_g1_i3 from sample A1 / Example spliced isoform

GCGAACTTACAATGTGAACATCAACCCCGCCTCTCCACCATCTTCAGTTACAACGGCTCGCGAAATATGGGCTCCCCAGTCGTAGCGTAGACAAATTTGGAGGAGAGGCGGCCTTGGCCTTGGTGGCTGCTCAGATAAATCAACTCGGCTGCAATTTCTAGACCGATTGACCTCCCATGGATTCATTCATACCCATTTCG
TATATAATACGAATATCCCAACTTCATCCATTCATGTAATCCGAAGAACATCAGGTCTCTGCAATCTGCATTATCAGGATCGTTTCTGGTTCGAATCTTTGCCGTTTTTCAGTCTATCCCCAGATTGTTTGGAGGCTCAGAATGGCGGTTCAGGCACAGTACTCGTCCAATATGCGTAACAGG

>TRINITY_DN111649_c0_g1_i4 from sample A1 / Example unspliced isoform:

AAATTTGGAGGAGgttgagttgaatttcgcgttcatcatcgtgttgtgtgcgtgcataataataataataatcatgatgatattgatgatgtagccgctgttgtgtacagAGGCGGCCTTGGCCTTGGTGGCTGCTCAGATAAATCAACTCGGCTGCAATTTCTAGACCGATTGACCTCCCATGGATTCATTCATACCCA
TTTCGTATATAATACGAATATCCCAACTTCATCCATTCATGTAATCCGAAGAACATCAGGTCTCTGCAATCTGCATTATCAGGATCGTTTCTGGTTCGAATCTTTGCCGTTTTTCAGTCTATCCCCAGATTGTTTGGAGGCTCAGAATGGCGGTTCAGGCACAGTACTCGTCCAATATGCGTAACAGGTTTGTTTTTCTC
ATGTGGGAAGCAGTTTTTCCTTATTGTTTTTCCGTGGATTGAATGCAGATGCCGGGGTTTTTAAATGGCGAGGGTTTGATGTTTGTTTCTGAAATATCATTCCGTGGATTATTAAAATTTGAGGAATATAGCAGTACTCTTTAAAAGTAGGGCCATTGAGTTTATTCTCGGGACGTCAGAGATGGCTTTGATAGGCTCTT
TGAACTTCAATGGGACGGCATCCCGGGAGAGGATTTGGGGGTTGTTTTTTTTGGAGGCC

Intron 3 GTTTGTTTTT ... TGGTTGGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.29	61	11	24
A2	30.1	36	17	14
A3	27.63	55	14	28
A4	25	36	14	10
A5	22.64	41	10	14
A6	16.83	84	15	19
A7	20.66	144	32	43
A8	18.78	80	13	24
A9	19.49	126	39	22
A10	21.66	123	44	24

>TRINITY_DN105805_c0_g2_i4 from sample A3 / Example spliced isoform

CGAACTTACAATGTGAACATCAACCCCGCCTCTCCACCATCTTCAGTTACAACGGCTCGCGAAATATGGGCTCCCCAGTCGTAGCGTAGACAAATTTGGAGGAGGTTGAGTTGAATTTCGCGTTCATCATCGTGTTGTGTGCGTGCATAATAATAATAATAATCATGGTGATATTGATGATGTAGCCGCTGTTGTGTACA
GAGGCGGCCTTGGCCTTGGTGGCTGCTCAGATAAATCAACTCGGCTGCAATTTCTAGACCGATTGACCTCCCATGGATTCATTCATACCCATTTCGTATATAATACGAATATCCCAACTTCATCCATTCATGTAATCCGAAGAACATCAGGTCTCTGCAATCTGCATTATCAGGATCGTTTCTGGTTCGAATCTTTGCCG
TTTTTCAGTCTATCCCCAGATTGTTTGGAGGCTCAGAATGGCGGTTCAGGCACAGTACTCGTCCAATATGCGTAACAGGCACTTGTTTGCAGGTGAGAACAAGGGCTCCATTCCAATTGCTTTCTTTGGGCCTGGAAATTACATGGATCATCATCAGATTCAGCAGCAGCAACAGATTCAATCCCAATCCCAGAACCAAT
CCCCGGCTGTCAACGGGTTGCCCAGTCAGCCTCCGTACATCACCCAGTTTACTGCTTGTAACCGTGGACAACAGGCCACAGGCGCAGGCTTACATGGATCTGAGAATGATCTGGCCTGGAATTTATTGGCACCCAGGAAGAGGACCAGAGAGCATGAGCTTCTGGAAAATTCTCAAATTTCATCTATTGATTTTCTGCAG
AGCCAGCGCACTGCTCAGATTGCCCTTTCTCAGTCCAATGGAGCTGTTTCGACTGGGTTGCGGTTGTCATTGGATGATGAAAAACTGAATTCCTCCTGCAATATGTCGTTGGGTACTTCAAAGGTTTCCCTTATGAACGAAGAACTGAGTGGAGTTTTACAGCAGCAGAATGCCGAGATTGACCAATTTTTAAGATCTCA
GGAGGAGCAGTTCAGGCAAGCTCTGGATGAGAAAACTAGGAGGTTTCAGATGAATATCTTGGCTTCTCTCGAGGAAGCTGCACTAATGAAGCTCAGGGATAAGGATTTGGAGGTGGAAAACATGAATAAAAAAAACATGGAACTAGAAGAGAAGATGAAGCAATTGAGCATGGAAGCACATGCATGGCAATATAGGGTGA
AATGCAGTGAAACTATGATTAACGCCCTTAAATTCAATCTTCAGCAGGCTTATGCCCAAAACAGGGAGAGTAAGGAAGGATGTGGAGACAGTGAAGTAGATGATGCAGCTTCTTGTTTCAATGCTGATGGAGGTGATTTCCAGGCTTTCATCTACAAGGAGAATAGAGACTTAAAAGATCAGAGGACTTGCAAGGTATGC
AGAAGCAATGATGTATGCATTCTTTTGCTGCCTTGCAGACATCTGTGCCTCTGCAAAGACTGTGAAAGTAGGCTTGAAGTTTGTCCCTTGTGCCGGTCATTTAAGAGTGCTAGCATGCAGATCTATATGTCATGAGTTGCCACTGTGAATAAATGCACCCTATGATTGTTTATGTTCCTTAGTGACCGATTTTATCTTTG
GTCACCGCATTGATGTCATTTGGGTATGCATTGCATCTCCCTTGTGCTTGAATAGCTAGATCTACATGTGGACTGGGAATTTTGGAAGAGGCAACTTGGATTCTGGTCTCTGGCTGCTCTGGAATTTGAGCTTCTTAACCATGCAAGGAATTCCAAGTTGTAGGGTTCAACATTTTGTTCCGTGTTCATATTGACCTCTA
AAATTAGTTTGGTGTTCATACTGACCTCTCCATTTAGTTTGATGTTCATATTGACCTTTAAACTACCATAATTCATGGTAAAAATACATTTTTTTAAGGAGAGATGCCTAAATAGGCATTTGTAATGCTGATCTTGAAATACATTATTTTGGGCACCTCTTTCATGAAGCTAAACTACTTAAGTCACCATTACATTGCAG
TGGATTCTAAAGTGTGCATAGTTCTGAGATCATTGCACCGAGAGGAGCAAGGTGCTCTACAGCCCAGTATGGGGGAGATGTTGTCACGTTATGTAACGTAACGTTCCCAACCAGCATGGGGGCGC

>TRINITY_DN105805_c0_g2_i2 from sample A3 / Example unspliced isoform:

CGAACTTACAATGTGAACATCAACCCCGCCTCTCCACCATCTTCAGTTACAACGGCTCGCGAAATATGGGCTCCCCAGTCGTAGCGTAGACAAATTTGGAGGAGGTTGAGTTGAATTTCGCGTTCATCATCGTGTTGTGTGCGTGCATAATAATAATAATAATCATGGTGATATTGATGATGTAGCCGCTGTTGTGTACA
GAGGCGGCCTTGGCCTTGGTGGCTGCTCAGATAAATCAACTCGGCTGCAATTTCTAGACCGATTGACCTCCCATGGATTCATTCATACCCATTTCGTATATAATACGAATATCCCAACTTCATCCATTCATGTAATCCGAAGAACATCAGGTCTCTGCAATCTGCATTATCAGGATCGTTTCTGGTTCGAATCTTTGCCG
TTTTTCAGTCTATCCCCAGATTGTTTGGAGGCTCAGAATGGCGGTTCAGGCACAGTACTCGTCCAATATGCGTAACAGgtttgtttttctcatgtgggaagcagtttttccttattgtttttccgtggattgaatgcagatgccggggtttttaaatggcgagggtttgatgtttgtttctgaaatatcattccgtggat
tattaaaatttgaggaatatagcagtactctttaaaagtagggccattgagtttattctcgggacgtcagagatggctttgataggctctttgaacttcaatgggacggcatcccgggagaggatttgggggttgttttttttggagggcttaatgcaggttcctctggaaattatctccttgacgaaatgaacaacatg
ggccgatattgggaacaagatatggtattagggtttcaacagtatggcaagggctgtaaaaaacaaaacaggagttgggggttaagttttcttaagaacccaatccagaccacccttaaataaactatttttattttcttttgaaataataataagagcagctactgtctgtaagctccttgaatttcagatgtagagct
attgttagaatcaagggatcaagattgatcgggttttttggttggcagGCACTTGTTTGCAGGTGAGAACAAGGGCTCCATTCCAATTGCTTTCTTTGGGCCTGGAAATTACATGGATCATCATCAGATTCAGCAGCAGCAACAGATTCAATCCCAATCCCAGAACCAATCCCCGGCTGTCAACGGGTTGCCCAGTCAGC
CTCCGTACATCACCCAGTTTACTGCTTGTAACCGTGGACAACAGGCCACAGGCGCAGGCTTACATGGATCTGAGAATGATCTGGCCTGGAATTTATTGGCACCCAGGAAGAGGACCAGAGAGCATGAGCTTCTGGAAAATTCTCAAATTTCATCTATTGATTTTCTGCAGAGCCAGCGCACTGCTCAGATTGCCCTTTCT
CAGTCCAATGGAGCTGTTTCGACTGGGTTGCGGTTGTCATTGGATGATGAAAAACTGAATTCCTCCTGCAATATGTCGTTGGGTACTTCAAAGGTTTCCCTTATGAACGAAGAACTGAGTGGAGTTTTACAGCAGCAGAATGCCGAGATTGACCAATTTTTAAGATCTCAGGAGGAGCAGTTCAGGCAAGCTCTGGATGA
GAAAACTAGGAGGTTTCAGATGAATATCTTGGCTTCTCTCGAGGAAGCTGCACTAATGAAGCTCAGGGATAAGGATTTGGAGGTGGAAAACATGAATAAAAAAAACATGGAACTAGAAGAGAAGATGAAGCAATTGAGCATGGAAGCACATGCATGGCAATATAGGGTGAAATGCAGTGAAACTATGATTAACGCCCTTA
AATTCAATCTTCAGCAGGCTTATGCCCAAAACAGGGAGAGTAAGGAAGGATGTGGAGACAGTGAAGTAGATGATGCAGCTTCTTGTTTCAATGCTGATGGAGGTGATTTCCAGGCTTTCATCTACAAGGAGAATAGAGACTTAAAAGATCAGAGGACTTGCAAGGTATGCAGAAGCAATGATGTATGCATTCTTTTGCTG
CCTTGCAGACATCTGTGCCTCTGCAAAGACTGTGAAAGTAGGCTTGAAGTTTGTCCCTTGTGCCGGTCATTTAAGAGTGCTAGCATGCAGATCTATATGTCATGAGTTGCCACTGTGAATAAATGCACCCTATGATTGTTTATGTTCCTTAGTGACCGATTTTATCTTTGGTCACCGCATTGATGTCATTTGGGTATGCA
TTGCATCTCCCTTGTGCTTGAATAGCTAGATCTACATGTGGACTGGGAATTTTGGAAGAGGCAACTTGGATTCTGGTCTCTGGCTGCTCTGGAATTTGAGCTTCTTAACCATGCAAGGAATTCCAAGTTGTAGGGTTCAACATTTTGTTCCGTGTTCATATTGACCTCTAAAATTAGTTTGGTGTTCATACTGACCTCTC
CATTTAGTTTGATGTTCATATTGACCTTTAAACTACCATAATTCATGGTAAAAATACATTTTTTTAAGGAGAGATGCCTAAATAGGCATTTGTAATGCTGATCTTGAAATACATTATTTTGGGCACCTCTTTCATGAAGCTAAACTACTTAAGTCACCATTACATTGCAGTGGATTCTAAAGTGTGCATAGTTCTGAGAT
CATTGCACCGAGAGGAGCAAGGTGCTCTACAGCCCAGTATGGGGGAGATGTTGTCACGTTATGTAACGTAACGTTCCCAACCAGCATGGGGGCGC