sp|Q93WL3|CLPT1_ARATH ----> ATP-dependent Clp protease ATP-binding subunit CLPT1, chloroplastic

Intron 1 GTCAGTACCA ... TTTACTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	23.05	138	41.1	15.1
A2	23.38	117	35.1	17.1
A3	20.97	143.1	37.6	23.4
A4	19.56	83	19.9	9.3
A5	23.89	70.1	22	6.3
A6	21.7	670.1	184.8	78.6
A7	21.52	935.1	254.9	120.6
A8	18.6	952	215.6	149
A9	19.96	864.5	214.3	131.9
A10	22.86	764.1	224	108.9

>TRINITY_DN118332_c0_g1_i2 from sample A1 / Example spliced isoform

ATTGAATGTGAAGCAAATTTTAATGTGGGTATTCCAAAGCATAGACTGAGCTTTATGTTGGGATAAGAAGACACCATTTGAAATTTGATTCGAAGCAATACTTCGAGCGGAAGCCATGGCTGCTCAAATGTTCCCCGTGGCATCATCATCTTCTGCCAAAACTTTGCCCCGTTCTTCGCATCTTCAGTCTCGTTATTCAT
CTCTATCTGCAATTAAATCTCATGCCATTTCTACATTTTGCAGTCCACTTCCCCTAAACAGACTTTTCATGTTGAAACCAGAGACCTCGTTTGCGAGTAACTGGGATTTCGAGTGTACCAGGAAGCCATTATCCCGTTCTCTACGATCACGACGTGGACACCAGCCTGTATTCATGATGCTCCCTACAGCAAACCCAGAA
AGGGCCTCCCGTGACAAACCTGTTAAATGGTCTGCTAGAGCTATAAAATCTTTCAGCATGGCAGAATTAGAAGCTCGCAAAATGAAATACCCTACAACTGGCACAGAAGCTCTTCTTATGGGCATTTTGGCGGAAGGCACCAGCCCTGCTTCCAAGTATTTACGGGCTAATGGAGTAACACTCTTCAAAGTTCGGGATGA
AACAGTTAAATTGCTAGGAAAATCTTATCCACTTTACACCAGTCCAGAGCATCCAACAATAACTGAACCTGCACAGAAGGCATTGGATTGGGCTGTTGATGAGAAGATTAAATCGGGGGAAAGTGGCGAGGTAACAACAACTCACATGCTACTTGGAATCTGGGCTCAAAAGGGCTTTGCTGGTCAACTAATATTGGCTA
ATCTTGGATTTGATGATAAGAACGCTGAAGAACTTGCTGAGTCTATAAAGGAAGAAGTTGCCTTGAGTTCAAAATAAAAGAATTTTCTACCTTTGCTATATCTGTTTCATGCCACAAGTTACAGGAAGACCTATGCATGTACATTCTGCATTTGTGTCTCAAGTCCATCCAGAAGTTAATGACCTTACAACATACAGTTG
TGAACCCTAAGCAAACATACTGTAAAATTATTTCTACATGCAACATGGGGGCAGCTATACCTCTCTTCATGATTGTGATGAAATGCAACAGAGTTTGCATATTTCTGCATACAATCTAGATTACAGAATGGTGGGATCAATAGTTGACAAAATTCATCAGATGTGTTTGATAGGGAATCTGCAATGATTTCATTTGAATA
AACGGGAAAATACAAAATGATTTGTTGTATGAGTACACAGTAAAAGGTACTATTGCTAGTGGAATCTCTCAGGATTACTATCTTTGCATAACTATGACAATCCAGAGACAACTTTATCTCCAATATTTTTTCAAGAATTTCAGTTTTTCATTCTAAAGAAACATATTTTATTATTCC

>TRINITY_DN118332_c0_g1_i1 from sample A1 / Example unspliced isoform:

ATTGAATGTGAAGCAAATTTTAATGTGGGTATTCCAAAGCATAGACTGAGCTTTATGTTGGGATAAGAAGACACCATTTGAAATTTGATTCGAAGCAATACTTCGAGCGGAAGCCATGGCTGCTCAAATGTTCCCCGTGGCATCATCATCTTCTGCCAAAACTTTGCCCCGTTCTTCGCATCTTCAGTCTCGTTATTCAT
CTCTATCTGCAATTAAATCTCATGCCATTTCTACATTTTGCAGTCCACTTCCCCTAAACAGACTTTTCATGTTGAAACCAGAGACCTCGTTTGCGAGTAACTGGGATTTCGAGTGTACCAGGAAGCCATTATCCCGTTCTCTACGATCACGACGTGGACACCAGCCTGTATTCATGATGCTCCCTACAGCAAACCCAGAA
AGGGCCTCCCGTGACAAACCTGTTAAATGGTCTGCTAGAGCTATAAAATCTTTCAGCATGGCAGAATTAGAAGCTCGCAAAATGAAATACCCTACAACTGGCACAGAAGCTCTTCTTATGGGCATTTTGGCGGAAGGCACCAGCCCTGCTTCCAAGTATTTACGGGCTAATGGAGTAACACTCTTCAAAGTTCGGGATGA
AACAGTTAAATTGCTAGGAAAATCTTATCCACTTTACACCAGTCCAGAGCATCCAACAATAACTGAACCTGCACAGAAGGCATTGGATTGGGCTGTTGATGAGAAGATTAAATCGGGGGAAAGTGGCGAGGTAACAACAACTCACATGCTACTTGGAATCTGGGCTCAAAAGGGCTTTGCTGGTCAACTAATATTGGCTA
ATCTTGGATTTGATGATAAGAACGCTGAAGAACTTGCTGAGTCTgtcagtaccaagttcttctcttcacttggaaagacattttccactttgtcagaagtttctgggcttaagctgctgtgatcttgtagatttattattttatagtaactttgtacttttctaactttttgagaatactaatacttgtgcacatgtgat
gaatttactacagATAAAGGAAGAAGTTGCCTTGAGTTCAAAATAAAAGAATTTTCTACCTTTGCTATATCTGTTTCATGCCACAAGTTACAGGAAGACCTATGCATGTACATTCTGCATTTGTGTCTCAAGTCCATCCAGAAGTTAATGACCTTACAACATACAGTTGTGAACCCTAAGCAAACATACTGTAAAATTAT
TTCTACATGCAACATGGGGGCAGCTATACCTCTCTTCATGATTGTGATGAAATGCAACAGAGTTTGCATATTTCTGCATACAATCTAGATTACAGAATGGTGGGATCAATAGTTGACAAAATTCATCAGATGTGTTTGATAGGGAATCTGCAATGATTTCATTTGAATAAACGGGAAAATACAAAATGATTTGTTGTATG
AGTACACAGTAAAAGGTACTATTGCTAGTGGAATCTCTCAGGATTACTATCTTTGCATAACTATGACAATCCAGAGACAACTTTATCTCCAATATTTTTTCAAGAATTTCAGTTTTTCATTCTAAAGAAACATATTTTATTATTCC

Intron 2 GTCTCGTTAT ... TTGAAACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	64.52	33	55	65
A2	80.52	15	67	57
A3	73.41	23	68	59
A4	64.06	23	40	42
A5	55.26	17	20	22
A6	61.72	120	196	191
A7	62.69	172	286	292
A8	66.04	100	180	209
A9	66.71	140	289	272
A10	69.44	92	213	205

>TRINITY_DN102159_c0_g1_i2 from sample A4 / Example spliced isoform

ATTGAATGTGAAGCAAATTTTAATGTGGGTATTCCAAAGCATAGACTGAGCTTTATGTTGGGATAAGAAGACACCATTTGAAATTTGATTCGAAGCAATACTTCGAGCGGAAGCCATGGCTGCTCAAATGTTCCCCGTGGCATCATCATCTTCTGCCAAAACTTTGCCCCGTTCTTCGCATCTTCAAGACCTCGTTTGCG
AGTAACTGGGATTTCGAGTGTACCAGGAAGCCATTATCCCGTTCTCTACGATCACGACGTGGACACCAGCCTGTATTCATGATGCTCCCTACAGCAAACCCAGAAAGGGCCTCCCGTGACAAACCTGTTAAATGGTCTGCTAGAGCTATAAAATCTTTCAGCATGGCAGAATTAGAAGCTCGCAAAATGAAATACCCTAC
AACTGGCACAGAAGCTCTTCTTATGGGCATTTTGGCGGAAGGCACCAGCCCTGCTTCCAAGTATTTACGGGCTAATGGAGTAACACTCTTCAAAGTTCGGGATGAAACAGTTAAATTGCTAGGAAAATCTTATCCACTTTACACCAGTCCAGAGCATCCAACAATAACTGAACCTGCACAGAAGGCATTGGATTGGGCTG
TTGATGAGAAGATTAAATCGGGGGAAAGTGGCGAGGTAACAACAACTCACATGCTACTTGGAATCTGGGCTCAAAAGGGCTTTGCTGGTCAACTAATATTGGCTAATCTTGGATTTGATGATAAGAACGCTGAAGAACTTGCTGAGTCTATAAAGGAAGAAGTTGCCTTGAGTTCAAAATAAAAGAATTTTCTACCTTTG
CTATATCTGTTTCATGCCACAAGTTACAGGAAGACCTATGCATGTACATTCTGCATTTGTGTCTCAAGTCCATCCAGAAGTTAATGACCTTACAACATACAGTTGTGAACCCTAAGCAAACATACTGTAAAATTATTTCTACATGCAACATGGGGGCAGCTATACCTCTCTTCATGATTGTGATGAAATGCAACAGAGTT
TGCATATTTCTGCATACAATCTAGATTACAGAATGGTGGGATCAATAGTTGACAAAATTCATCAGATGTGTTTGATAGGGAATCTGCAATGATTTCATTTGAATAAACGGGAAAATACAAAATGATTTGTTGTATGAGTACACAGTAAAAGGTACTATTGCTAGTGGAATCTCTCAGGATTACTATCTTTGCATAACTAT
GACAATCCAGAGACAACTTTATCTCCAC

>TRINITY_DN102159_c0_g1_i1 from sample A4 / Example unspliced isoform:

ATTGAATGTGAAGCAAATTTTAATGTGGGTATTCCAAAGCATAGACTGAGCTTTATGTTGGGATAAGAAGACACCATTTGAAATTTGATTCGAAGCAATACTTCGAGCGGAAGCCATGGCTGCTCAAATGTTCCCCGTGGCATCATCATCTTCTGCCAAAACTTTGCCCCGTTCTTCGCATCTTCAgtctcgttattcat
ctctatctgcaattaaatctcatgccatttctacattttgcagtccacttcccctaaacagacttttcatgttgaaaccagAGACCTCGTTTGCGAGTAACTGGGATTTCGAGTGTACCAGGAAGCCATTATCCCGTTCTCTACGATCACGACGTGGACACCAGCCTGTATTCATGATGCTCCCTACAGCAAACCCAGAA
AGGGCCTCCCGTGACAAACCTGTTAAATGGTCTGCTAGAGCTATAAAATCTTTCAGCATGGCAGAATTAGAAGCTCGCAAAATGAAATACCCTACAACTGGCACAGAAGCTCTTCTTATGGGCATTTTGGCGGAAGGCACCAGCCCTGCTTCCAAGTATTTACGGGCTAATGGAGTAACACTCTTCAAAGTTCGGGATGA
AACAGTTAAATTGCTAGGAAAATCTTATCCACTTTACACCAGTCCAGAGCATCCAACAATAACTGAACCTGCACAGAAGGCATTGGATTGGGCTGTTGATGAGAAGATTAAATCGGGGGAAAGTGGCGAGGTAACAACAACTCACATGCTACTTGGAATCTGGGCTCAAAAGGGCTTTGCTGGTCAACTAATATTGGCTA
ATCTTGGATTTGATGATAAGAACGCTGAAGAACTTGCTGAGTCTATAAAGGAAGAAGTTGCCTTGAGTTCAAAATAAAAGAATTTTCTACCTTTGCTATATCTGTTTCATGCCACAAGTTACAGGAAGACCTATGCATGTACATTCTGCATTTGTGTCTCAAGTCCATCCAGAAGTTAATGACCTTACAACATACAGTTG
TGAACCCTAAGCAAACATACTGTAAAATTATTTCTACATGCAACATGGGGGCAGCTATACCTCTCTTCATGATTGTGATGAAATGCAACAGAGTTTGCATATTTCTGCATACAATCTAGATTACAGAATGGTGGGATCAATAGTTGACAAAATTCATCAGATGTGTTTGATAGGGAATCTGCAATGATTTCATTTGAATA
AACGGGAAAATACAAAATGATTTGTTGTATGAGTACACAGTAAAAGGTACTATTGCTAGTGGAATCTCTCAGGATTACTATCTTTGCATAACTATGACAATCCAGAGACAACTTTATCTCCAC