sp|Q84K90|RHIP1_ARATH ----> RGS1-HXK1-interacting protein 1

Intron 1 GTAATCTTTG ... CATTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	30.02	73	31	10.7
A2	14.07	46.7	7	12.3
A3	26.69	63.3	23	8.3
A4	21.79	44.7	12	14.7
A5	20.14	28	7	3
A6	21.38	128.3	34	15.3
A7	21.49	193.3	52	20
A8	25.62	141	48	14.3
A9	21.47	152.3	41	16.3
A10	20.8	155.7	40	18.3

>TRINITY_DN109599_c0_g1_i1 from sample A2 / Example spliced isoform

AGTCGACACAATAACGCTTTGACGTTAATGTAATAAGTTGGCCACTCTTACTGGTCATCGTTCTGTGATGACACAGACACCGAAAGTCCTCTGCCCTGCATAGTATATACCTCAATAAAATCCAATCAGTCACACATTGTTTCTCTGCGCATTCATTCTCTGGTGAAGAAGAAGAGCAGCAGAGAAAACCCTTGGAACTT
TAGGGTTTCCGGCGAAAACCCGCTAGGGATATAGGACCTTTTGAAGTCTTACATCAGGCACATGGCAGAAGCAACAGCGGATGTTCCATCTGCTCCTCCTCCATTTGCATCTGTAACAGAAATCGAGAATGCGGACGGTTCATCAAGAATTAGTGAAGGAAAAAATGAGGGAACGGAATCACAGAAGTCCGAGGTGGTGA
AGCCCTGGCACGTTTATACAGCGGAGCAGGCTCAGGAACTGAAGCGAACCGTGGTGGCATCCACTGACTCTGCGCTACGATCGGCAAGGGATCAAGTTGGAGAGTTGCAGGCAGTTTCTACTATTCACTACAGAACAGTTCTGGAATATGTACCAAGGCTAAGGAGCCAATATGGTATTTATGAAGATGCTTTCTTTGGA
AAACTTAAGGAGGGTGCACTTATTGCTCGTGAATACCCATTGTCAACATGCAGTGTAGCAGCTGGTCTTGGTCTTCTTCTTATGAGAAGTCCAAGGAGGTTTTTATTCCGCAATACTATTGGTCGATTCCAAAGTGAAGAGTCTTTGCTTACAAATGCAGAGAACAAGGTAAAGGACTTTAGACAATCGGTTGAGCTGCT
GAAGAATGAAAGCAAAAAGCTACAGGAGAGGGCAACACTTGCTGAAGAAGAGATGAAACGGGGTCAAATGAAGCTCAAGAATGCGGGAAATCAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAACAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGAAGGGAGGCATTAAAGCTTCGTGCAG
ATGTTGCATCAATGGCTTATGAGGCTAAACAGCAAAGGAATGCTCTGGTGAAACAAGTTTTGAAAATTACAAATAATGGCATTTCAGTTTGATTATTTGCAGATCAAAAAGTTATGATCCAAATCTCATATTGCCCTGTGGCTTAAGTTTGTGCACTTACATATTTTCTTTCAATTACCTTACCAGATAAGTTGTTGCAC
AAGTTTCAGAAAATAGTTACAAAACCAGTGCTCTCTGATGACATATTCTTTGTTTACAAAAAATCAGCAGTTTTCCCCTTTGTCAGTGGAAGGCTTTTTGAGGCTATTCTTGCTTTATGTTTAAAGCAAAATACCGGAAGTTTGGCCTTTCATTTTTCAGTAACCTTGTTAGATATGTGCTTGCATATCTTTTCATCCCT
TTCGAATCCAGTCAAACATGACATTGATTTCTCCAAGTCACCAAGATTAAAGGACGGCATGCAATTGTTTCATCTATTGAGGAATTCTTTGTCGGTTATCACTTTCCATGATTTCAATTGAAATAAGATGTTTGTTAAGCAAACAT

>TRINITY_DN109599_c0_g1_i5 from sample A2 / Example unspliced isoform:

AGTCGACACAATAACGCTTTGACGTTAATGTAATAAGTTGGCCACTCTTACTGGTCATCGTTCTGTGATGACACAGACACCGAAAGTCCTCTGCCCTGCATAGTATATACCTCAATAAAATCCAATCAGTCACACATTGTTTCTCTGCGCATTCATTCTCTGGTGAAGAAGAAGAGCAGCAGAGAAAACCCTTGGAACTT
TAGGGTTTCCGGCGAAAACCCGCTAGGGATATAGGACCTTTTGAAGTCTTACATCAGGCACATGGCAGAAGCAACAGCGGATGTTCCATCTGCTCCTCCTCCATTTGCATCTGTAACAGAAATCGAGAATGCGGACGGTTCATCAAGAATTAGTGAAGGAAAAAATGAGGGAACGGAATCACAGAAGTCCGAGGTGGTGA
AGCCCTGGCACGTTTATACAGCGGAGCAGGCTCAGGAACTGAAGCGAACCGTGGTGGCATCCACTGACTCTGCGCTACGATCGGCAAGGGATCAAGTTGGAGAGTTGCAGGCAGTTTCTACTATTCACTACAGAACAGTTCTGGAATATGTACCAAGGCTAAGGAGCCAATATGGTATTTATGAAGATGCTTTCTTTGGA
AAACTTAAGGgtaatctttgccatcttcctaggaatatatatatatatatatatggtgacataaacatgatttgcatatttgagtttttgaaatgactattgatgatgcagacatctttatgctatttaacatctaaaactgtttttatattttaagttgaatttggttagcattggttgcattttgcagAGGGTGCACT
TATTGCTCGTGAATACCCATTGTCAACATGCAGTGTAGCAGCTGGTCTTGGTCTTCTTCTTATGAGAAGTATGTCCTCGACTGGGGAATGGAAATTTTCAAACCACTTAACTGTATTGTTAGATTTTCTTTTTGGTAGGCTGTTCTTGCTTTGTAGATATACTGTCCAGAGAGTAATTATTTAGATTCATCTTGGCGGTG
ATTGAACTGAAGTTTGGTTAGCCTGGGAAACTGGAACAGTCTATCTCTAGTTTAACTCACAGCTTA

Intron 2 GTACATAAAA ... CATGCATCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	27.07	97	5	36
A2	25.49	76	0	26
A3	12.33	64	1	9
A4	23.68	58	1	18
A5	26.67	22	0	8
A6	16.18	171	1	33
A7	22.22	259	1	74
A8	23.12	219.5	2	66
A9	21.49	215.5	1	59
A10	18.37	200	7	45

>TRINITY_DN109599_c0_g1_i1 from sample A2 / Example spliced isoform

AGTCGACACAATAACGCTTTGACGTTAATGTAATAAGTTGGCCACTCTTACTGGTCATCGTTCTGTGATGACACAGACACCGAAAGTCCTCTGCCCTGCATAGTATATACCTCAATAAAATCCAATCAGTCACACATTGTTTCTCTGCGCATTCATTCTCTGGTGAAGAAGAAGAGCAGCAGAGAAAACCCTTGGAACTT
TAGGGTTTCCGGCGAAAACCCGCTAGGGATATAGGACCTTTTGAAGTCTTACATCAGGCACATGGCAGAAGCAACAGCGGATGTTCCATCTGCTCCTCCTCCATTTGCATCTGTAACAGAAATCGAGAATGCGGACGGTTCATCAAGAATTAGTGAAGGAAAAAATGAGGGAACGGAATCACAGAAGTCCGAGGTGGTGA
AGCCCTGGCACGTTTATACAGCGGAGCAGGCTCAGGAACTGAAGCGAACCGTGGTGGCATCCACTGACTCTGCGCTACGATCGGCAAGGGATCAAGTTGGAGAGTTGCAGGCAGTTTCTACTATTCACTACAGAACAGTTCTGGAATATGTACCAAGGCTAAGGAGCCAATATGGTATTTATGAAGATGCTTTCTTTGGA
AAACTTAAGGAGGGTGCACTTATTGCTCGTGAATACCCATTGTCAACATGCAGTGTAGCAGCTGGTCTTGGTCTTCTTCTTATGAGAAGTCCAAGGAGGTTTTTATTCCGCAATACTATTGGTCGATTCCAAAGTGAAGAGTCTTTGCTTACAAATGCAGAGAACAAGGTAAAGGACTTTAGACAATCGGTTGAGCTGCT
GAAGAATGAAAGCAAAAAGCTACAGGAGAGGGCAACACTTGCTGAAGAAGAGATGAAACGGGGTCAAATGAAGCTCAAGAATGCGGGAAATCAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAACAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGAAGGGAGGCATTAAAGCTTCGTGCAG
ATGTTGCATCAATGGCTTATGAGGCTAAACAGCAAAGGAATGCTCTGGTGAAACAAGTTTTGAAAATTACAAATAATGGCATTTCAGTTTGATTATTTGCAGATCAAAAAGTTATGATCCAAATCTCATATTGCCCTGTGGCTTAAGTTTGTGCACTTACATATTTTCTTTCAATTACCTTACCAGATAAGTTGTTGCAC
AAGTTTCAGAAAATAGTTACAAAACCAGTGCTCTCTGATGACATATTCTTTGTTTACAAAAAATCAGCAGTTTTCCCCTTTGTCAGTGGAAGGCTTTTTGAGGCTATTCTTGCTTTATGTTTAAAGCAAAATACCGGAAGTTTGGCCTTTCATTTTTCAGTAACCTTGTTAGATATGTGCTTGCATATCTTTTCATCCCT
TTCGAATCCAGTCAAACATGACATTGATTTCTCCAAGTCACCAAGATTAAAGGACGGCATGCAATTGTTTCATCTATTGAGGAATTCTTTGTCGGTTATCACTTTCCATGATTTCAATTGAAATAAGATGTTTGTTAAGCAAACAT

>TRINITY_DN109599_c0_g1_i7 from sample A2 / Example unspliced isoform:

GAATGAAAGCAAAAAGCTACAGgtacataaaattatgtataatggcagctatctgatttcttttttgttgtcttacttcacacgtgtgcatgttttgtctctatcaatcttggacttctcttcaatcattctttctcctgcgcagatgcttcatttaatctaaatttgatgttctttcctttcatgtttattgttttaat
gcagtcttcttttaggttgtagtgcccgatttcctccttatcttttttcattcccgtcttccaaatatttcaaggtttatacagaagtttactgctgcatttcaagtgttcctatttaaatagattgaagttaaaactgtagcaactacccatgtataccaaattgagacttgggaataaaaataacaaaatgatggcgt
tgtctctttgaaagtgatgaaactttgaagttctcttttcaatctggggaatgaattcaactttttaatactgttcatgcatcagGAGAGGGCAACACTTGCTGAAGAAGAGATGAAACGGGGTCAAATGAAGCTCAAGAATGCGGGAAATCAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAA
CAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGAAGGGAGGCATTAAAGCTTCGTGCAGATGTTGCATCAATGGCTTATGAGGCTAAACAGCAAAGGAATGCTCTGGTGAAACAAGTTTTGAAAATTACAAATAATGGCATTTCAGTTTGATTATTTGCAGATCAAAAAGTTATGATCCAAATCTCATATTGCCCTGTG
GCTTAAGTTTGTGCACTTACATATTTTCTTTCAATTACCTTACCAGATAAGTTGTTGCACAAGTTTCAGAAAATAGTTACAAAACCAGTGCTCTCTGATGACATATTCTTTGTTTACAAAAAATCAGCAGTTTTCCCCTTTGTCAGTGGAAGGCTTTTTGAGGCTATTCTTGCTTTATGTTTAAAGCAAAATACCGGAAG
TTTGGCCTTTCATTTTTCAGTAACCTTGTTAGATATGTGCTTGCATATCTTTTCATCCCTTTCGAATCCAGTCAAACATGACATTGATTTCTCCAAGTCACCAAGATTAAAGGACGGCATGCAATTGTTTCATCTATTGAGGAATTCTTTGTCGGTTATCACTTTCCATGATTTCAATTGAAATAAGATGTTTGTTAAGC
AAACAT

Intron 3 GTATGTACAT ... TTCTTAATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	17.52	86.3	2	18
A2	13.55	79	2	12
A3	13.52	41.3	0	6
A4	22.6	66	2	19
A5	17.04	21	0	4
A6	31.61	187.3	0	85
A7	25.53	290.7	0	98
A8	22.95	245.3	0	71
A9	24.62	244.7	0	78
A10	29.18	220.3	0	89

>TRINITY_DN98436_c1_g1_i7 from sample A4 / Example spliced isoform

ATGAATTCAACTTTTTAATACTGTTCATGCATCAGGAGAGGGCAACACTTGCTGAAGAAGAGATGAAACGGGGTCAAATGAAGCTCAAGAATGCGGGAAATCAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAACAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGAAGGGAGGCATTAAAG
CTTCGTGCAGATGTGGGTTTTGCTTCTTCCTTATTTAAATTCCTATGTTTCTTCTGTTTTCTTGTTTCATATCTGCTGGAACTTCTTCATCAAGTATAGTATGGTAATGGATACAGGCAAGTTGTAGATGGAAGAGGATTAATTTTTTTGTAATCTTTTGTCATATTTGTATGAGTTGATTGAATGATGTTAAGATCATG
TATAAAATTCTATGTTTCATGGGTACCGCTCCCAAGGGTTGGTGATTCCGTACCTGACATTCCCACGCCCCGGGAACTTAGGAGAAGGTAAGAAATGTTCCAAAATTGATGGGAATATCTTCTCGTACATGTGAGCTTTTAGGGTACGTTTTAGGGCCAGGTTTGCCATTCTGAGGTTGCATATCTGTAGTTTTCAGGAG
CTTGAGGATGCTACCTGTTGTGCATTCATTGGGAATCGGGATACATCACTGAAATGCTATTACTGTTGAATTGCTGGACAGATAAATGAATTCATGGAAAATTAA

>TRINITY_DN98436_c1_g1_i1 from sample A4 / Example unspliced isoform:

AACGGGGTCAAATGAAGCTCAAgtatgtacatcaatctgaccttatgttatgtttaatagattttgttttttaacataccctgcaatactaaacaacttcaagtagataaaattttttgagatattttctccgtaaatttgtatctctcagctcctttattgccaagtatttatttcttcttaatagGAATGCGGGAAAT
CAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAACAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGAAGGGAGGCATTAAAGCTTCGTGCAGATGTGGGTTTTGCTTCTTCCTTATTTAAATTCCTATGTTTCTTCTGTTTTCTTGTTTCATATCTGCTGGAACTTCTTCATCAAGTATAGTA
TGGTAATGGATACAGGCAAGTTGTAGATGGAAGAGGATTAATTTTTTTGTAATCTTTTGTCATATTTGTATGAGTTGATTGAATGATGTTAAGATCATGTATAAAATTCTATGTTTCATGGGTACCGCTCCCAAGGGTTGGTGATTCCGTACCTGACATTCCCACGCCCCGGGAACTTAGGAGAAGGTAAGAAATGTTCC
AAAATTGATGGGAATATCTTCTCGTACATGTGAGCTTTTAGGGTACGTTTTAGGGCCAGGTTTGCCATTCTGAGGTTGCATATCTGTAGTTTTCAGGAGCTTGAGGATGCTACCTGTTGTGCATTCATTGGGAATCGGGATACATCACTGAAATGCTATTACTGTTGAATTGCTGGACAGATAAATGAATTCATGGAAAA
TTAA

Intron 4 GTATGTCCTC ... TTGCCTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	10.26	70	8	15
A2	13.08	93	14	8
A3	27.78	52	20	4
A4	23.81	64	20	19
A5	10.71	25	3	1
A6	7.18	168	13	0
A7	12.29	264	37	1
A8	9.28	176	18	0
A9	10.22	202	23	0
A10	14.53	200	34	0

>TRINITY_DN98436_c1_g1_i4 from sample A4 / Example spliced isoform

CTCGAAAGAGAGAAACCCCTTTGTTAGTCGACACAATAACGCTTTGACGTTAATGTAATAAGTTGGCCACTCTTACTGGTCATCGTTCTGTGATGACACAGACACCGAAAGTCCTCTGCCCTGCATAGTATATACCTCAATAAAATCCAATCAGTCACACATTGTTTCTCTGCGCATTCATTCTCTGGTGAAGAAGAAGA
GCAGCAGAGAAAACCCTTGGAACTTTAGGGTTTCCGGCGAAAACCCGCTAGGGATATAGGACCTTTTGAAGTCTTACATCAGGCACATGGCAGAAGCAACAGCGGATGTTCCATCTGCTCCTCCTCCATTTGCATCTGTAACAGAAATCGAGAATGCGGACGGTTCATCAAGAATTAGTGAAGGAAAAAATGAGGGAACG
GAATCACAGAAGTCCGAGGTGGTGAAGCCCTGGCACGTTTATACAGCGGAGCAGGCTCAGGAACTGAAGCGAACCGTGGTGGCATCCACTGACTCTGCGCTACGATCGGCAAGGGATCAAGTTGGAGAGTTGCAGGCAGTTTCTACTATTCACTACAGAACAGTTCTGGAATATGTACCAAGGCTAAGGAGCCAATATGG
TATTTATGAAGATGCTTTCTTTGGAAAACTTAAGGAGGGTGCACTTATTGCTCGTGAATACCCATTGTCAACATGCAGTGTAGCAGCTGGTCTTGGTCTTCTTCTTATGAGAAGTCCAAGGAGGTTTTTATTCCGCAATACTATTGGTCGATTCCAAAGTGAAGAGTCTTTGCTTACAAATGCAGAGAACAAGGTAAAGG
ACTTTAGACAATCGGTTGAGCTGCTGAAGAATGAAAGCAAAAAGCTACAGGAGAGGGCAACACTTGCTGAAGAAGAGATGAAACGGGGTCAAATGAAGCTCAAGAATGCGGGAAATCAGATTCAGAGTCTTGTGCGTTCTGTATACAAAACTGAATCTCAAGCAACAGGTCTGATGGATAGTCTCAGAGAAATTCCTGGA
AGGGAGGCATTAAAGCTTCGTGCAGATGTTGCATCAATGGCTTATGAGGCTAAACAGCAAAGGAATGCTCTGGTGAAACAAGTTTTGAAAATTACAAATAATGGCATTTCAGTTTGATTATTTGCAGATCAAAAAGTTATGATCCAAATCTCATATTGCCCTGTGGCTTAAGTTTGTGCACTTACATATTTTCTTTCAAT
TACCTTACCAGATAAGTTGTTGCACAAGTTTCAGAAAATAGTTACAAAACCAGTGCTCTCTGATGACATATTCTTTGTTTACAAAAAATCAGCAGTTTTCCCCTTTGTCAGTGGAAGGCTTTTTGAGGCTATTCTTGCTTTATGTTTAAAGCAAAATACCGGAAGTTTGGCCTTTCATTTTTCAGTAACCTTGTTAGATA
TGTGCTTGCATATCTTTTCATCCCTTTCGAATCCAGTCAAACATGACATTGATTTCTCCAAGTCACCAAGATTAAAGGACGGCATGCAATTGTTTCATCTATTGAGGAATTCTTTGTCGGTTATCACTTTCCATGATTTCAATTGAAATAAGATGTTTGTTAAGCAAACATGGTATTTTC

>TRINITY_DN98436_c1_g1_i8 from sample A4 / Example unspliced isoform:

CTCGAAAGAGAGAAACCCCTTTGTTAGTCGACACAATAACGCTTTGACGTTAATGTAATAAGTTGGCCACTCTTACTGGTCATCGTTCTGTGATGACACAGACACCGAAAGTCCTCTGCCCTGCATAGTATATACCTCAATAAAATCCAATCAGTCACACATTGTTTCTCTGCGCATTCATTCTCTGGTGAAGAAGAAGA
GCAGCAGAGAAAACCCTTGGAACTTTAGGGTTTCCGGCGAAAACCCGCTAGGGATATAGGACCTTTTGAAGTCTTACATCAGGCACATGGCAGAAGCAACAGCGGATGTTCCATCTGCTCCTCCTCCATTTGCATCTGTAACAGAAATCGAGAATGCGGACGGTTCATCAAGAATTAGTGAAGGAAAAAATGAGGGAACG
GAATCACAGAAGTCCGAGGTGGTGAAGCCCTGGCACGTTTATACAGCGGAGCAGGCTCAGGAACTGAAGCGAACCGTGGTGGCATCCACTGACTCTGCGCTACGATCGGCAAGGGATCAAGTTGGAGAGTTGCAGGCAGTTTCTACTATTCACTACAGAACAGTTCTGGAATATGTACCAAGGCTAAGGAGCCAATATGG
TATTTATGAAGATGCTTTCTTTGGAAAACTTAAGGAGGGTGCACTTATTGCTCGTGAATACCCATTGTCAACATGCAGTGTAGCAGCTGGTCTTGGTCTTCTTCTTATGAGAAgtatgtcctcgactggggaatggaaattttcaaaccacttaactgtattgttagattttctttttggtaggctgttcttgctttgta
gatatactgtccagagagtaattatttagattcatcttggcggtgattgaactgaagtttggttagcctgggaaactggaacagtctatctctagtttaactcacagcttacctcctcagatactaatttcttaggttttccagcagtgtcttttgcaaatcaaatcacattgttgcagggtaaatgaaatctttgtata
cagcattttcagtttgcaacacttctatcctccctccgttcctcgggttctttgacagttccctcttacaaatttgatggaataacttcttgctgaataatctcaattctccatctttctgcaccagtctttctgtttggaattcagtcctactatgctgatcatggtcaagatttggttgaatgcataattccttgggg
tttctgaacttctatgttaatatgatcaatgatgcattaaagtttaaggtgctatttgcctgcagGTCCAAGGAGGTTTTTATTCCGCAATACTATTGGTCGATTCCAAAGTGAAGAGGTAGTTCTGGTTCACGTTTCTGCAAATTTCTTAATTTAGTTTGGGTTAGTGAAGAGGCAATTCATTTTCCTGTGAACTCTAG
ACCTAATTTGGATTCATATTTCTTTTTCTTCTTTTCATTTGAAAGTCTAGACTTGTGAAGTTGTGCTTGTTGGATAGTAATTGCACATGCGAATGCCCTATAAATATAGCCATTGGTGATATTTTGTTTGATTTAGCTCTCGTATGAGAAAGTAATGGCTGTTGGAAGTTTGATTGAATATGTGGAAGTTACGGTCCTGG
AAATTTTGTATTTAGTAGAAAATAAATTTTTGCTGAAACTAAAAGGATGATTGGAATTTCTAAATATAGACCAACAAAATTCTTCTAATACTTTTCCAATTGAAAGTTTATGTG