sp|Q8LDV3|Y4320_ARATH ----> Uncharacterized protein At4g13200, chloroplastic

Intron 1 GTGTGTGTGC ... ATCTATACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	12	19	5
A2	35	13	12	2
A3	88.89	1	14	2
A4	82.35	3	23	5
A5	38.46	4	4	1
A6	60.26	61	108	77
A7	53.61	45	74	30
A8	59.37	64	115	72
A9	62.23	61	118	83
A10	63.93	22	53	25

>TRINITY_DN36490_c0_g1_i1 from sample A6 / Example spliced isoform

ATGATTTCAGGCCCACACTTGGCAATCTTATAGATATAATGTTTTTAATTTTGAAACTGTTCTCTATTCCTTCTGAAAATGCTACCTACCCTTCATTCACATTTTTAGAAGAACCCTTCATTCGCATTACAACATATAACTGTATTCCAATCATTGTTTACGGTCTCTTCGGTGGATAACCAACAGGAACACCAAGAAAA
ATGGCAGTAAGCATGTCAGTTTATGGACTCTCCAATTTTTTAAACACCCATTATAACGCTCGCTCATCTTCTCAAAGCGATGGAATTTCATTGCATCTGCGCATTCATACTTGGCGTGGGAATGGACTTCAGAAGAAGAACAAACAGCGCCCCCTCAGCGTAGGAGCTCAGTGCAGCAACACTCCACCAGGTCAAAGTGA
TAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATAGGGACAACCGTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGGTTGTTGGAGCTACTGCTGTCGGTATTCATTATTTGTATTAAAGTCATGCTATCC
TTGTCTAGTGAAACAACCTGATTTCTTTGTAAATAACATTATACTGCTAGAATTTCAGCTTTTATTGTTTGCTTGGTTTGCTATTTTCTGTTTCAATTTGCAATCAAATGTATTATTTCTATTTATTTCTTCCTAGATGAGTGCATATCTTGGTCTGTATGTTGACTATGTTCTACTATAATAACTTTCACTACTAAGTG
GTGTCAATAATCCATTAGTAAGTAGACCAC

>TRINITY_DN36490_c0_g1_i3 from sample A6 / Example unspliced isoform:

ATGATTTCAGGCCCACACTTGGCAATCTTATAGATATAATGTTTTTAATTTTGAAACTGTTCTCTATTCCTTCTGAAAATGCTACCTACCCTTCATTCACATTTTTAGAAGAACCCTTCATTCGCATTACAACATATAACTGTATTCCAATCATTGTTTACGGTCTCTTCGGTGGATAACCAACAGGAACACCAAGAAAA
ATGGCAGTAAGCATGTCAGTTTATGGACTCTCCAATTTTTTAAACACCCATTATAACGCTCGCTCATCTTCTCAAAGCGATGGAATTTCATTGCATCTGCGCATTCATACTTGGCGTGGGAATGGACTTCAGAAGAAGAACAAACAGCGCCCCCTCAGCGTAGGAGCTCAGTGCAGCAACACTCCACCAGGTCAAAGTGA
TAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATAGGGACAACCGTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGgtgtgtgtgccaaatcctgactattttaaagggaagcaattaatatggagtgaca
actattatttaatatgaactacgtaggaggaataaaatgcccaaattgcactgcttctgtaggcaccacctgtaatatgattgctgtgaagtctgaaatcaatgcctatctatacagGTTGTTGGAGCTACTGCTGTCGGTATTCATTATTTGTATTAAAGTCATGCTATCCTTGTCTAGTGAAACAACCTGATTTCTTT
GTAAATAACATTATACTGCTAGAATTTCAGCTTTTATTGTTTGCTTGGTTTGCTATTTTCTGTTTCAATTTGCAATCAAATGTATTATTTCTATTTATTTCTTCCTAGATGAGTGCATATCTTGGTCTGTATGTTGACTATGTTCTACTATAATAACTTTCACTACTAAGTGGTGTCAATAATCCATTAGTAAGTAGACC
AC

Intron 2 GTACGATGAT ... ACTCCACCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	72.22	5	0	13
A2	69.57	7	0	16
A3	72.73	9	0	24
A4	80	4	0	16
A5	85.71	2	0	12
A6	83.23	28	0	139
A7	74.43	45	6	131
A8	76.62	36	2	118
A9	82.04	30	2	137
A10	77.92	34	1	120

>TRINITY_DN43091_c0_g1_i1 from sample A10 / Example spliced isoform

GTGGAACACAAGAAAATACACCCACCATGACTAAACTACTATACAAATGATGTTTAAGCAGTGATGGAAATTGGAACTAGCGGCGAGGACATGGAGAATAGTGTGACACGAGGATTGGGGTCAAAGTGATAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATAGGGA
CAACCGTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGG

>TRINITY_DN43091_c0_g1_i3 from sample A10 / Example unspliced isoform:

GTGGAACACAAGAAAATACACCCACCATGACTAAACTACTATACAAATGATGTTTAAGCAGTGATGGAAATTGGAACTAGCGGCGAGGACATGGAGAATAGTGTGACACGAGGATTGGGgtacgatgatttcaggcccacacttggcaatcttatagatataatgtttttaattttgaaactgttctctattccttctga
aaatgctacctacccttcattcacatttttagaagaacccttcattcgcattacaacatataactgtattccaatcattgtttacggtctcttcggtggataaccaacaggaacaccaagaaaaatggcagtaagcatgtcagtttatggactctccaattttttaaacacccattataacgctcgctcatcttctcaaa
gcgatggaatttcattgcatctgcgcattcatacttggcgtgggaatggacttcagaagaagaacaaacagcgccccctcagcgtaggagctcagtgcagcaacactccaccagGTCAAAGTGATAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATAGGGACAACC
GTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGGAAGAGGTGCTGGAAAGGGCCAGAATAACCAGGGATAAAGCTGCCCGTGAAGCTCTGGGAAAGGAGCAAGTAAAGGAACCATCGACTTCATCTTATACTAGTACAACCTCAGTGTCACCAGAATCAAGTCC
TGTTTCTGAGAGTACAGCTTCACCAATAGTACCAAGCTCTTCCAATGGTATTTCTGGGCCACTACCAACGGAATTTAATGAAAATTAGCGACATCAAGTTGGAGTCTGAATTTGTCCCAGAAGAGTTCACGGGATATGTGCATATCACAGGCATTGGATACAGATACTCTAGGGAGAAAATAGATGTTAGCAAGCAAACC
CTTGACTTTCAGGAAGAGGTGCTGGAAAGGGCCA

Intron 3 GTACGATGAT ... TAACCAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	56.76	16	0	21
A2	60	8	0	12
A3	65.12	15	0	28
A4	66.67	11	0	22
A5	60	4	0	6
A6	64.29	50	0	90
A7	59.02	84	6	121
A8	62.89	59	2	100
A9	60.16	102	2	154
A10	58.7	57	1	81

>TRINITY_DN43091_c0_g1_i2 from sample A10 / Example spliced isoform

GTGGAACACAAGAAAATACACCCACCATGACTAAACTACTATACAAATGATGTTTAAGCAGTGATGGAAATTGGAACTAGCGGCGAGGACATGGAGAATAGTGTGACACGAGGATTGGGGAACACCAAGAAAAATGGCAGTAAGCATGTCAGTTTATGGACTCTCCAATTTTTTAAACACCCATTATAACGCTCGCTCAT
CTTCTCAAAGCGATGGAATTTCATTGCATCTGCGCATTCATACTTGGCGTGGGAATGGACTTCAGAAGAAGAACAAACAGCGCCCCCTCAGCGTAGGAGCTCAGTGCAGCAACACTCCACCAGGTCAAAGTGATAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATA
GGGACAACCGTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGGAAGAGGTGCTGGAAAGGGCCAGAATAACCAGGGATAAAGCTGCCCGTGAAGCTCTGGGAAAGGAGCAAGTAAAGGAACCATCGACTTCATCTTATACTAGTACAACCTCAGTGTCACCAGA
ATCAAGTCCTGTTTCTGAGAGTACAGCTTCACCAATAGTACCAAGCTCTTCCAATGGTATTTCTGGGCCACTACCAACGGAATTTAATGAAAATTAGCGACATCAAGTTGGAGTCTGAATTTGTCCCAGAAGAGTTCACGGGATATGTGCATATCACAGGCATTGGATACAGATACTCTAGGGAGAAAATAGATGTTAGC
AAGCAAGTTTCATTTGTATGGTGTTTCGGCCTAGTCACACTTAATGGAGTATTAAGCTTGGTTAATTGCACAAGAATGCACTGTCTGGTTGTTTATTAATTTCCAATAACAGGGTCTTTGTAACGAGAAGCAGAGCGTAGCCAGTGGAAACAATAATGTCCCAGAAACTATAGCTATCTAATATCTCACTTCTTCCTTAT
CCTTAATACCTTTTTCACACATAAATATATCTTACTATTAATAAAGCGAAATAGTAAATAGGAACATTACATCAGGACTTCAAACCGTAAAATCATATACCATACT

>TRINITY_DN43091_c0_g1_i3 from sample A10 / Example unspliced isoform:

GTGGAACACAAGAAAATACACCCACCATGACTAAACTACTATACAAATGATGTTTAAGCAGTGATGGAAATTGGAACTAGCGGCGAGGACATGGAGAATAGTGTGACACGAGGATTGGGgtacgatgatttcaggcccacacttggcaatcttatagatataatgtttttaattttgaaactgttctctattccttctga
aaatgctacctacccttcattcacatttttagaagaacccttcattcgcattacaacatataactgtattccaatcattgtttacggtctcttcggtggataaccaacagGAACACCAAGAAAAATGGCAGTAAGCATGTCAGTTTATGGACTCTCCAATTTTTTAAACACCCATTATAACGCTCGCTCATCTTCTCAAA
GCGATGGAATTTCATTGCATCTGCGCATTCATACTTGGCGTGGGAATGGACTTCAGAAGAAGAACAAACAGCGCCCCCTCAGCGTAGGAGCTCAGTGCAGCAACACTCCACCAGGTCAAAGTGATAGTAAAGCTGTACTGGATGCATTCTTCCTTGGTAAGGCTTTTGCTGAAGCAGTTAATGAACGGATAGGGACAACC
GTTGGAGAGATTTTGAGTGAGATTGGAAGGTGGCAGGCAGAGACACAAAAGCAAACCCTTGACTTTCAGGAAGAGGTGCTGGAAAGGGCCAGAATAACCAGGGATAAAGCTGCCCGTGAAGCTCTGGGAAAGGAGCAAGTAAAGGAACCATCGACTTCATCTTATACTAGTACAACCTCAGTGTCACCAGAATCAAGTCC
TGTTTCTGAGAGTACAGCTTCACCAATAGTACCAAGCTCTTCCAATGGTATTTCTGGGCCACTACCAACGGAATTTAATGAAAATTAGCGACATCAAGTTGGAGTCTGAATTTGTCCCAGAAGAGTTCACGGGATATGTGCATATCACAGGCATTGGATACAGATACTCTAGGGAGAAAATAGATGTTAGCAAGCAAACC
CTTGACTTTCAGGAAGAGGTGCTGGAAAGGGCCA