sp|P10978|POLX_TOBAC ----> Retrovirus-related Pol polyprotein from transposon TNT 1-94

Intron 1 GTCTTTATGG ... GAATCCTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	31.52	11.5	3	3.5
A2	20.16	17	4	6.5
A3	30.04	20.5	5.5	11
A4	7.73	15	1	4.5
A5	46.43	5.5	4.5	4
A6	28.93	59	22	5.5
A7	33.13	70.5	29	6.5
A8	35.17	45	20	6.5
A9	28.79	49.5	16	6.5
A10	29.66	45.5	15	4

>TRINITY_DN42899_c0_g1_i6 from sample A6 / Example spliced isoform

GTCTCTGTTACATGTGCTCTGCGGTCTCCGTGTTGTGTGTTCTCTGTTATTTGTATGCGTGGCTGTTTGTCTGTTTCGTTTTCTGAGAGCCTATCAGGAGGAAGAGAATGGTCGAGCTGGTTAACTGCAGAACTTACTGCTTTAATGGTGCGTATCCTTATCATGGAGTCATAGCCGGATCGCTTGGTGGAATTAACGTT
TATGCTTCTTTCGCAGCCTTTTTACAGGCTGTCGAAGACTGGACTTTGGAGCTAGAGAGTCATTTTCTATTGTCAAGATAGTTGATGGAAAGGATGTAGCGCAGTAGGAGCGCTATAAGATTAGATTGCTTATAATTGATGGATATGCATTCTTGGTTGCATCTTACTTAGTATTACTTTGCAACAAACTGCAAAAAGGG
ATATGGTCCACCCACCAAACTGGGTCAACCCACCATGGCACAGTGAAGAAGTCTAATGAAGCTAAACAGGGTAAGCTAGTGGCTGAAATTGAAGCTATTGAAGACCTTGAGCTGTAGCCGAGAGATGATCTTGGAAGAGATTGAAAGAATAGGGTCATTATTCAAGATGTGCTTGCAAATTTGAAGAGTACAGTTTGGAA
GGGGTGCCCCATTTTTAATTGGTAGAAGTCATCTTTATTGTCAGTTATTGGTAGAAGTCATCTTTACTGGTACAACTATTTGGGATAGATTAGCATATTGAAGGATTCTTATATGTAAATAATGGATTCTTACATGGACTCATGTTTCACATAAAACTGTAAGTGACCTTTATTTGTAAGAATATAAGTAGAAGCATTGT
TAGTATTGAATTTATGAATTTTAATATTTTAATTAAATAACATAATAATGGATATGTATGTGGCCAGCAGCATGTTTCCTC

>TRINITY_DN42899_c0_g1_i18 from sample A6 / Example unspliced isoform:

GTCTCTGTTACATGTGCTCTGCGGTCTCCGTGTTGTGTGTTCTCTGTTATTTGTATGCGTGGCTGTTTGTCTGTTTCGTTTTCTGAGAGCCTATCAGGAGGAAGAGAATGGTCGAGCTGGTTAACTGCAGAACTTACTGCTTTAATGGTGCGTATCCTTATCATGGAGTCATAGCCGGATCGCTTGGTGGAATTAACGTT
TATGCTTCTTTCGCAGCCTTTTTACAGGCTGTCGAAGACTGGACTTTGGAGCTAGAGAGTCATTTTCTATTGTCAAGATAGTTGATGGAAAGGATGTAGCGCAGTAGGAGCGCTATAAGAgtctttatggactttgcgtatttttccaagtcctgcacttatattttgtttggaatcctcagTTAGATTGCTTATAATTG
ATGGATATGCATTCTTGGTTGCATCTTACTTAGTATTACTTTGCAACAAACTGCAAAAAGGGATATGGTCCACCCACCAAACTGGGTCAACCCACCATGGCACAGTGAAGAAGTCTAATGAAGCTAAACAGGGTAAGCTAGTGGCTGAAATTGAAGCTATTGAAGACCTTGAGCTGTAGCCGAGAGATGATCTTGGAAGA
GATTGAAAGAATAGGGTCATTATTCAAGATGTGCTTGCAAATTTGAAGAGTACAGTTTGGAAGGGGTGCCCCATTTTTAATTGGTAGAAGTCATCTTTATTGTCAGTTATTGGTAGAAGTCATCTTTACTGGTACAACTATTTGGGATAGATTAGCATATTGAAGGATTCTTATATGTAAATAATGGATTCTTACATGGA
CTCATGTTTCACATAAAACTGTAAGTGACCTTTATTTGTAAGAATATAAGTAGAAGCATTGTTAGTATTGAATTTATGAATTTTAATATTTTAATTAAATAACATAATAATGGATATGTATGTGGCCAGCAGCATGTTTCCTC

Intron 2 GTAGATTGCT ... TCTTACTTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	58.14	9	10	15
A2	64.71	6	12	10
A3	54.93	16	20	19
A4	56.52	5	7	6
A5	9.09	5	0	1
A6	24.59	23	7	8
A7	65.62	11	16	26
A8	50.94	13	16	11
A9	56	11	12	16
A10	26.53	18	5	8

>TRINITY_DN46365_c1_g3_i3 from sample A10 / Example spliced isoform

AATACTATGGACTTTGGAGCTAGAGAGTCATTTTCTGTTGTCAAGATGGTCGATGGAAGGGATGTAGCACAGTAGGAGCGCTGTAAGATATGCTGCTGGCTGTTACATGATCATTGAATTTCCTCAAATAATTATGTTACGATGAATTCTAGCAGTTACTTTGCAACAAACTGCAAAAGGATATGGTCCACCCACCAAGG
CACAGTGAAGAAGTCTAATGAAGCTAAACAGGGTAAGCTAGTGGCTGAAATTGAAGCTATTGAAGACCGTGAGGTCAGTGTTTTGTTTTTTCACTTAATTTATTTTTCTCTTGAACACGATCTAAGAGATTCCTTTGGATTGTGGTTGCTTTGATAATACATA

>TRINITY_DN46365_c1_g3_i5 from sample A10 / Example unspliced isoform:

AATACTATGGACTTTGGAGCTAGAGAGTCATTTTCTGTTGTCAAGATGGTCGATGGAAGGGATGTAGCACAGTAGGAGCGCTGTAAGATATGCTGCTGGCTGTTACATGATCATTGAATTTCCTCAAATAATTATGTTACGATGAATTCTAGCAGgtagattgcttataattgatggatatgcattcttggttgcatctt
acttagTTACTTTGCAACAAACTGCAAAAGGATATGGTCCACCCACCAAGGCACAGTGAAGAAGTCTAATGAAGCTAAACAGGGCAGCTTGGATGATCGAAAGAACATTTCCGGTTATGTGTATCTCTTACATTTGGGACTGGTTTCATGGTCTTAAAAGAAATAGCCCATTGTCACTATTTTCTCAGCAGAAGCGGAAT
ACGTTGCAGCCACTTCAGCAGCTTGTCAGGCAGTTTGGTTACAAAGAAATCTAAGTGATCCTGGATATGAACAGAAAGCAGCAACTCAAATCTATTGTGACAACAATTCTGCTA

Intron 3 GTTACTTTGC ... AGCTAAACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	64.71	6	12	10
A2	62.5	3	6	4
A3	57.89	8	12	10
A4	36.36	14	2	14
A5	50	3	5	1
A6	55.56	18	19	26
A7	58.1	22	20	41
A8	50.48	26	16	37
A9	57.69	11	13	17
A10	68.75	10	20	24

>TRINITY_DN42899_c0_g1_i5 from sample A6 / Example spliced isoform

GGAGCTAGAGTCATTTTCTGTTGTCAAGATGGTCGATGGAAGGGATGTAGCACAGTAGGAGCGCTGTAAGATATGCTGCTGGCTGTTACATGATCATTGAATTTCCTCAAATAATTATGTTACGATGAATTCTAGCAGGCAGCTTGGATGATCGAAAGAGCACTTCCGGTTATGTGTATCTCTTACGTTTGAGACTGGTT
TCATGGTCTTAAAAGAAATAGCCCATTGTCACTATTTTCTCAGCAGAATCGGAATACGTTGCAGCCACTTCAGCAGCTTGTCAGGCAGTTTGGTTACAAAGAAATCTAAGTGATCCTGGATATGAACAGAAAGCAGCAACTCAAATCTATTGTGACAACAATTCTGCTATTGCTCTTTCAAAAAATCATGTCTTTCATAA
GAG

>TRINITY_DN42899_c0_g1_i8 from sample A6 / Example unspliced isoform:

GGAGCTAGAGTCATTTTCTGTTGTCAAGATGGTCGATGGAAGGGATGTAGCACAGTAGGAGCGCTGTAAGATATGCTGCTGGCTGTTACATGATCATTGAATTTCCTCAAATAATTATGTTACGATGAATTCTAGCAgttactttgcaacaaactgcaaaaggatatggtccacccaccaaggcacagtgaagaagtcta
atgaagctaaacagGGCAGCTTGGATGATCGAAAGAGCACTTCCGGTTATGTGTATCTCTTACGTTTGAGACTGGTTTCATGGTCTTAAAAGAAATAGCCCATTGTCACTATTTTCTCAGCAGAATCGGAATACGTTGCAGCCACTTCAGCAGCTTGTCAGGCAGTTTGGTTACAAAGAAATCTAAGTGATCCTGGATAT
GAACAGAAAGCAGCAACTCAAATCTATTGTGACAACAATTCTGCTATTGCTCTTTCAAAAAATCATGTCTTTCATAAGAG