sp|Q9FKS0|UKL1_ARATH ----> Uridine/cytidine kinase UKL1, chloroplastic

Intron 1 GCTTGTGTAA ... TTACATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80.97	3.9	13.9	20
A2	70.79	3	8	6.6
A3	74.27	3	7.9	9.6
A4	50.8	15.3	14	17.1
A5	55.16	6.8	8	8.6
A6	62.39	68.2	103.5	122.1
A7	74.55	28.7	73.9	94.7
A8	65.11	58.8	87.7	130.9
A9	59.57	40	44.9	72.7
A10	63.33	20.9	36.8	35.1

>TRINITY_DN111673_c0_g2_i2 from sample A3 / Example spliced isoform

ATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTGATGAAATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGGATT
ACCAATACCATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAATGCTCTACTTGGAGGATGGCATTTTCATGGCATCA

>TRINITY_DN111673_c0_g2_i4 from sample A3 / Example unspliced isoform:

ATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTGATGAAATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGGATT
ACCAATACCATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAATGCTCTACTTGGAGgcttgtgtaattggaatgagtggagctggaggccactctgatccatctttagcacgc
atgttcagaaagtttactttttcactaattgtaacacctttacatgtagGATGGCATTTTCATGGCATTATCTGTCTACCTTACTGGCAGAAAACTCTTCCTACGCAGTTGATGACCCTGCTTGTGTTTACAAACACAATAGATTTGTCATGGAAATATGTTTTGCCACTCTGGTCTACAGATTCACCGAATGCATTTGT
GCAATGATTCACTGTGATTTATTTGTGCAATGATTTGCTTAATCACATCAAGGAACTCTACACAGCTGATGCACAGAGAATCAACAACTCTGCACACAGAGATGACAGCAGAAGTATCCACGCACAGGAATAAAATTAAAACAAAAATGCAGATAGGCATTCACAATATAATTCTAAAAGCACACATTATTCCCAGAAAC
AACCACA

Intron 2 GTAAGATTCC ... TTACATGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	84	4	9	21
A2	70	3	4	7
A3	75	3	6	9
A4	52.94	16	10	18
A5	53.33	7	5	8
A6	63.48	71.3	46.7	124
A7	76.83	30	17	99.5
A8	68.21	62	25	133
A9	64.41	42	27	76
A10	61.4	22	15	35

>TRINITY_DN109319_c2_g1_i1 from sample A4 / Example spliced isoform

CTTCTTTCAGAAGAATCCATTCCGTCTCTCACGACGTGCGCTATTTTGTTAAGTAGCCTAGCCAGAGGGAATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTG
ATGAAATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGTATTACCAATAACATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAAT
GCTCTACTTGGAGGATGGCATTTTCATGGCATCATCTGTCTACCTTACTGGCAGAAAACTCTTCCTACGCAGTTGATGACCCTGCTTGTGTTTACAAACACAATAGATTTGTCATGGAAATATGTTTTGCCACTCTGGTCTACAGATTCACCGAATGCATTTGTGCAATGATTCACTGTGATTTATTTGTGCAATGATTT
GCTTAATCACATCAAGGAACTCTACACAGCTGATGCACAGAGAATCAACAACTCTGCACACAGAGATGACAGCAGAAGTATCCACGCACAGGAATAAAATTAAAACAAAAATGCAGATAGGCATTCACAATATAATTCTAAAAGCACACATTATTCCCAGAAACAACCACAATTCTGAAATATTTGTTTATTGAAGATGG
ACTGCTCCTAGATTACATTCCAATAGAGCCACTCTCTGGAACTCCATGCTTCCCTCAGCCTCCACAGCTTCAACCTGAGAACTCACAGCCTCCTCTTTTCTGTTTTGTCCCTCATCACAGCAAGGAATTTACATATATTTGACCGCTGGAGGAATACCAAACAGTTTAACTACCATAGATTCAGTTCGTCTTGTTGCACA
TTCTCTCCACTATCTTATAGGCTTTATTGTTTTTGAGTATACATTGG

>TRINITY_DN109319_c2_g1_i3 from sample A4 / Example unspliced isoform:

CTTCTTTCAGAAGAATCCATTCCGTCTCTCACGACGTGCGCTATTTTGTTAAGTAGCCTAGCCAGAGGGAATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTG
ATGAAATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGTATTACCAATAACATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAAT
GCTCTACTTGGAGgtaagattcccattgatcccaacgtttgcaaatttcaaaatccttttaaattacagtctgaggtttgtaatatgggttgctacaggcttgtgtaattggaatgagtggagctggaggccactctgatccatctttagcacgcatgttcagaaagtttactttctcactaattgtaacacctttacat
gtagGATGGCATTTTCATGGCATCATCTGTCTACCTTACTGGCAGAAAACTCTTCCTACGCAGTTGATGACCCTGCTTGTGTTTACAAACACAATAGATTTGTCATGGAAATATGTTTTGCCACTCTGGTCTACAGATTCACCGAATGCATTTGTGCAATGATTCACTGTGATTTATTTGTGCAATGATTTGCTTAATCA
CATCAAGGAACTCTACACAGCTGATGCACAGAGAATCAACAACTCTGCACACAGAGATGACAGCAGAAGTATCCACGCACAGGAATAAAATTAAAACAAAAATGCAGATAGGCATTCACAATATAATTCTAAAAGCACACATTATTCCCAGAAACAACCACAATTCTGAAATATTTGTTTATTGAAGATGGACTGCTCCT
AGATTACATTCCAATAGAGCCACTCTCTGGAACTCCATGCTTCCCTCAGCCTCCACAGCTTCAACCTGAGAACTCACAGCCTCCTCTTTTCTGTTTTGTCCCTCATCACAGCAAGGAATTTACATATATTTGACCGCTGGAGGAATACCAAACAGTTTAACTACCATAGATTCAGTTCGTCTTGTTGCACATTCTCTCCA
CTATCTTATAGGCTTTATTGTTTTTGAGTATACATTGG

Intron 3 GTATGTTCTC ... TGATTCGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	63.08	2.7	4	5
A2	100	0	1	1
A3	66.67	1	2	2
A4	100	0	3	0
A5	33.33	2	1	1
A6	14.29	3	1	0
A7	36.36	7	4	4
A8	35.04	4.7	3	2
A9	27.27	4	0	3
A10	31.25	22	5	15

>TRINITY_DN42672_c0_g1_i7 from sample A8 / Example spliced isoform

GGAACCATTGAATCTATGAAATTGTTAGGGAAGCAGATTCTAAACTACTGAAGCAATTAATGTGCATAATAGCCTTCTGCACCAGGGATGCTCCTGCATTAACAATACAACTTTTCCATTCACTGTGACCAGGGTTGACGCTGTTAGATGGCCTAGCCATTGAATTCATGTAATTTGAGGGAACATGAATGGAGGATTGC
TAGAAAAACATAGAGACAGAGAAGGGAGAGTAAAAGCCATCAACCTTGCTGCAGCAAACAGTCTATAAGAACCAGGGACTGTTTATAGCTGTAACGTAGGCAGTGTTATCCCCAAAAATGTATGAGCATTTTGAGATTTTCAGAGGCTGATCGTAGCAGCTCTGTTTGAGGAGGAAATTGCTATCATGACAGTGGATGAT
ACTGCTGGTTGATGCTGTAGATTAAGGACACAGCCGCAATCAATTTTCAGATTCATTAGGGGTTGTATGGCAGCGAATCTGAGCATTCTTTGGCCCACAGTAGATTCCTTCAAAGGACTGTTTCAGCTTCGTAGATCTGTGATTTTTGCACAGTTACACACAGCAGGGTGATAGTACTTGTTCAGTGGCAATGAAGGCGA
GCGATGACTGTTCTTCATACCCAGATCTTGGTGCATTCCCTACAGCATGACGTCTTGCATTTCTTGAGGACTTGCCAATGGCAGACTATGTGACAGCAGATTATTTCCAGTAGTGCTTCTCAGCATAGATCGTTCTCTGTTGATCGATCTACACCGGAGTTGACTTATGCGAAAAGTTGTGTGGAGTATCAATTATACGA
AGTGGGGAAAGCATTGCGTGAATGTTGCAAAGTAATCAAAATTGAAAAAATTTCAATCCATCGTGATGGAGATAATTTTAAACAGCTGATTTACGTGAAACTACCAAATGATATTTCTGAATCCCATGTTTTGTCCTTGATCCAGTTCAGCTGGGCAGGCTATTGAACTTTTAATGCAGAAGTCTGGTGCCAGAATCGCA
TATCATATTCC

>TRINITY_DN42672_c0_g1_i4 from sample A8 / Example unspliced isoform:

GGAACCATTGAATCTATGAAATTGTTAGGGAAGCAGATTCTAAACTACTGAAGCAATTAATGTGCATAATAGCCTTCTGCACCAGGGATGCTCCTGCATTAACAATACAACTTTTCCATTCACTGTGACCAGGGTTGACGCTGTTAGATGGCCTAGCCATTGAATTCATGTAATTTGAGGGAACATGAATGGAGGATTGC
TAGAAAAACATAGAGACAGAGAAGGGAGAGTAAAAGCCATCAACCTTGCTGCAGCAAACAGTCTATAAGAACCAGGGACTGTTTATAGCTGTAACGTAGGCAGTGTTATCCCCAAAAATGTATGAGCATTTTGAGATTTTCAGAGGCTGATCGTAGCAGCTCTGTTTGAGGAGGAAATTGCTATCATGACAGTGGATGAT
ACTGCTGGTTGATGCTGTAGATTAAGGACACAACCCCAATCAATTTTCAGATTCATTAGGGGTTGTATGGCAGCGAATCTGAGCATTCTTTGGgtatgttctctgattcaaatgcatgatctaaatagaagagtagttcctgtagcaacatattgaagacctgtgccatagaattagtagaacattcttacattttttga
catgctacattgacatggatgatttgtgatgattcgcagCCCACAGTAGATTCCTTCAAAGGACTGTTTCAGCTTCGTAGATCTGTGATTTTTGCACAGTTACACACAGCAGGGTGATAGTACTTGTTCAGTGGCAATGAAGGCGAGCGATGACTGTTCTTCATACCCAGATCTTGGTGCATTCCCTACAGCATGACGTC
TTGCATTTCTTGAGGACTTGCCAATGGCAGACTATGTGACAGCAGATTATTTCCAGTAGTGCTTCTCAGCATAGATCGTTCTCTGTTGATCGATCTACACCGGAGTTGACTTATGCGAAAAGTTGTGTGGAGTATCAATTATACGAAGTGGGGAAAGCATTGCGTGAATGTTGCAAAGTAATCAAAATTGAAAAAATTTC
AATCCATCGTGATGGAGATAATTTTAAACAGCTGATTTACGTGAAACTACCAAATGATATTTCTGAATCCCATGTTTTGTCCTTGATCCAGTTCAGCTGGGCAGGCTATTGAACTTTTAATGCAGAAGTCTGGTGCCAGAATCGCATATCATATTCC

Intron 4 GTAAGATTCC ... GTTGCTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	41.76	13.9	9	11
A2	38.46	8	4	6
A3	45	8	6	7
A4	45.1	14	10	13
A5	33.33	8	5	3
A6	30.78	103.5	46.6	45.4
A7	30.32	73.9	17	47.3
A8	30.38	87.8	25	51.6
A9	40.03	45	27	33
A10	26.81	36.9	15	12

>TRINITY_DN132828_c4_g1_i3 from sample A1 / Example spliced isoform

GCGGCAGAATACACCAATGTATGAGCGACTGGAGATAGATATCCAAGATAGGGCAGAAGATAACACAGGAACATAGCAACAGGTTTGAAGCCTTCAGGTGTGGCTGTCCCATACATATACACTCCAACTATTCTCAATCTCCATCTGAATCTGCTCACTATGTTTTCCATTTCGAAGATTTCACTTGCTGTTATTCCTCA
ACCTCCTCCCTATCATTCTTCAAACAACAACAACAATAAGCGCACCACCCATACCATTTTCCTTGTTAAAAGCCTCGCATACTACACTCGCGCTACACATTCCTCCCACACTCTCCATGGCAATACAGAGAAGCACATTAGAAGATTGTGTTACACCAGCAGGCTTCTGGAGGCAGTGGAGACCTTCAACCATATGCTTC
TTTCAGAAGAATCCATTCCGTCTCTCACGACGTGCGCTATTTTGTTAAGTAGCCTAGCCAGAGGGAATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTGATGA
AATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGTATTACCAATAACATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAATGCTC
TACTTGGAGGCTTGTGTAATTGGAATGAGTGGAGCTGGAGGCCACTCTGATCCATCTTTAGCACGCATGTTCAGAAAGTTTACTTTCTCACTAATTGTAACACCTTTACATGTAGGATGGCATTTTCATGGCATCATCTGTCTACCTTACTGGCAGAAAACTCTTCCTACGCAGTTGATGACCCTGCTTGTGTTTACAAA
CACAATAGATTTGTCATGGAAATATGTTTTGCCACTCTGGTCTACAGATTCACCGAATGCATTTGTGCAATGATTCACTGTGATTTATTTGTGCAATGATTTGCTTAATCACATCAAGGAACTCTACACAACTGATGCACAGC

>TRINITY_DN132828_c4_g1_i2 from sample A1 / Example unspliced isoform:

GCGGCAGAATACACCAATGTATGAGCGACTGGAGATAGATATCCAAGATAGGGCAGAAGATAACACAGGAACATAGCAACAGGTTTGAAGCCTTCAGGTGTGGCTGTCCCATACATATACACTCCAACTATTCTCAATCTCCATCTGAATCTGCTCACTATGTTTTCCATTTCGAAGATTTCACTTGCTGTTATTCCTCA
ACCTCCTCCCTATCATTCTTCAAACAACAACAACAATAAGCGCACCACCCATACCATTTTCCTTGTTAAAAGCCTCGCATACTACACTCGCGCTACACATTCCTCCCACACTCTCCATGGCAATACAGAGAAGCACATTAGAAGATTGTGTTACACCAGCAGGCTTCTGGAGGCAGTGGAGACCTTCAACCATATGCTTC
TTTCAGAAGAATCCATTCCGTCTCTCACGACGTGCGCTATTTTGTTAAGTAGCCTAGCCAGAGGGAATCGACATGAATTAGCGTTCTCCGTTTACAGAGTTATGACTGAAGCAGTGTGGATCGTGAGAAGGGTTTGGGGCAAGTTTGGCCTTTTTACCACTAGAAATAGTGCTGATTTTGATGTTGGATTGCTGTGATGA
AATAGCACTGATTGGGACGTCCTTCAGCTTCATTTTCTTGGGGCATCTCTGTAATGGCCTTGGATTACCAATACCATCTGTCTCAGTGGGCGATTCACAGTGGTTTGGAACCATAATGGCAATCTCAGTGACATGGTCTATGGCTGCCAGGTCATTTCGGTCATGGAGAATGATCATTGTTGGGGAGACCGGCAATGCTC
TACTTGGAGgtaagattcccattgatcccaacgtttgcaaatttcaaaatccttttaaattacagtctgaggtttgtaatatgggttgctacagGCTTGTGTAATTGGAATGAGTGGAGCTGGAGGCCACTCTGATCCATCTTTAGCACGCATGTTCAGAAAGTTTACTTTCTCACTAATTGTAACACCTTTACATGTAG
GATGGCATTTTCATGGCATCATCTGTCTACCTTACTGGCAGAAAACTCTTCCTACGCAGTTGATGACCCTGCTTGTGTTTACAAACACAATAGATTTGTCATGGAAATATGTTTTGCCACTCTGGTCTACAGATTCACCGAATGCATTTGTGCAATGATTCACTGTGATTTATTTGTGCAATGATTTGCTTAATCACATC
AAGGAACTCTACACAACTGATGCACAGC