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

Intron 1 GTACCAATGT ... GATTCCCAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	16.57	219	45	42
A2	19.42	193	59	34
A3	15.64	267	49	50
A4	17.47	153	38.9	25.9
A5	15.11	132	28	19
A6	16.27	2957	608	541
A7	15.25	1865	363.1	308.1
A8	15.02	2009	346	364
A9	15.86	1886	348	363
A10	14.35	1525	273	238

>TRINITY_DN120080_c8_g1_i2 from sample A1 / Example spliced isoform

AGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGGTATATGGTTTCAGCAGGGGCTTGCACGAAACTT
GTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTAGATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCA
TAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGTTCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCT
TTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGTTTTTGGTACTTTTTTTGCACCATTTTTTTGTCCAGAGACTTTCAGATGTGCAGCCTGAAAAGTTACAAATGACTACCACTTATATTTTGCTTTAATCTCTTAGTGTCTGTAGAAAAATGAGAATGGCAGTTTTCAGTAAGCATCTATGT
GGTCACGTTCTCTTAGGTTTTCCAAAGGAATTAGGTAGTCTTCTCATGTCTTCTCTTGCCCAATGTTACAATACACTATATCTCGATCAAAAGTATGAGCCTTAACTGCAATTGAGGGCTAGGGAACTTAAGC

>TRINITY_DN120080_c8_g1_i3 from sample A1 / Example unspliced isoform:

AGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGgtaccaatgttttcatacttggcatctcttcaaa
acgcacccaacattgcaggctgcagcagtgatttgtgcatgtgagagagatgacctttgggcttcagattcccaagGTATATGGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTA
GATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGT
TCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCTTTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGTTTTTGGTACTTTTTTTGCACCATTTTTTTGTCCAGAGAC
TTTCAGATGTGCAGCCTGAAAAGTTACAAATGACTACCACTTATATTTTGCTTTAATCTCTTAGTGTCTGTAGAAAAATGAGAATGGCAGTTTTCAGTAAGCATCTATGTGGTCACGTTCTCTTAGGTTTTCCAAAGGAATTAGGTAGTCTTCTCATGTCTTCTCTTGCCCAATGTTACAATACACTATATCTCGATCAA
AAGTATGAGCCTTAACTGCAATTGAGGGCTAGGGAACTTAAGC

Intron 2 GTGAGAGAGA ... GATTCCCAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	14.92	219	25.6	38.4
A2	12.9	193	26.4	28.6
A3	14.08	267	35	43.8
A4	11.35	153	18	19.6
A5	13.95	132	18.4	21.4
A6	14.25	2957	386.8	491.4
A7	13.56	1865	208.6	292.6
A8	14.61	2009	230	343.8
A9	15.97	1886	220	358.4
A10	13.02	1525	169.2	228.4

>TRINITY_DN118306_c3_g1_i1 from sample A3 / Example spliced isoform

GAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGGTATATGGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGC
AAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTAGATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTG
AACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGTTCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCTTTTGCTCC
TTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGTTTTTGGTACTTTTTTTGCAC

>TRINITY_DN118306_c3_g1_i5 from sample A3 / Example unspliced isoform:

GAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGgtgagagagatgacctttgggcttcagattcccaagGTATAT

GGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTAGATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTG
GCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGTTCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTG
AATGTTTTAAATGATTTTGATACATTCTTTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGTTTTTGGTACTTTTTTTGCAC

Intron 3 GTCTTGCAGC ... GAAGTGAAAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	14.79	219	31	45
A2	14.98	193	32	36
A3	13.31	267	35	47
A4	14.29	153	24	27
A5	16.46	132	30	22
A6	15.24	2957	476	587
A7	13.42	1865	246	332
A8	14.05	2009	277	380
A9	15.22	1886	267	410
A10	12.93	1525	188	265

>TRINITY_DN42090_c2_g2_i1 from sample A6 / Example spliced isoform

AGGGCGCTAGCGGTACACTAACGAGGAGCATAAAGTCACAAATTTAAGAAATAATACAAGGCATACATGAAGACATGCATAGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAG
CGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGGTATATGGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTAGATCATTGAGTTCAGACCTACTGTATTTAC
AAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGTTCTTATGCTGTCATAACAGTATGAACCTTT
TGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCTTTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGC

>TRINITY_DN42090_c2_g2_i3 from sample A6 / Example unspliced isoform:

AGGGCGCTAGCGGTACACTAACGAGGAGCATAAAGTCACAAATTTAAGAAATAATACAAGGCATACATGAAGACATGCATAGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAG
CGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGgtcttgcagcttggatctgacaaccgtgggacgtggagcaacattcaggagaaatgattgcgaagtgaaagGTATATGGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATA
AAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTAGATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTC
CAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGTTCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCTTTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCG
GC

Intron 4 GTATTACACA ... ATTTATACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	21.21	9.8	2.8	3.4
A2	13.25	10.6	1.8	1.4
A3	20.34	18.6	4.8	4
A4	36.08	9.8	5.4	2.8
A5	10	2	0.4	2
A6	4.92	108.8	7.8	4.4
A7	6.61	74.8	7.4	0.4
A8	5.8	63.6	5.2	2.4
A9	6.5	62.6	6	2.2
A10	5.47	71.8	6.4	0

>TRINITY_DN120080_c8_g1_i3 from sample A1 / Example spliced isoform

AGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGGTACCAATGTTTTCATACTTGGCATCTCTTCAAA
ACGCACCCAACATTGCAGGCTGCAGCAGTGATTTGTGCATGTGAGAGAGATGACCTTTGGGCTTCAGATTCCCAAGGTATATGGTTTCAGCAGGGGCTTGCACGAAACTTGTACTGGCAAGTTTTACTGCTGGTGTTTTTGTGGGATTTACATTGAATAAAAGTTTTCGACGTCTAGTTCGGAGGTGGCTGAAGAAATTA
GATCATTGAGTTCAGACCTACTGTATTTACAAAGTGTATTGAGTGATAGAGTTCATGCAGTTATTCTGCATACTAACTTCTGGCTTTTCGTTTATGTGTTTCTGTTTTCATAACAGTGAACATTTTGTATTTTTGACTTTTATTATAATATAGCTCTTCCAAATATGCAGCCATTGAAATGTTGAACTTTTCTTTTTGGT
TCTTATGCTGTCATAACAGTATGAACCTTTTGTATACTTGGGAGTTCATCAAACTACACAACTCTTTCAAACATGCAGCCTGAATGTTTTAAATGATTTTGATACATTCTTTTGCTCCTTTGACTGAATATTATTAATATATGTAAAAATAGCATACCGGTTTTTGGTACTTTTTTTGCACCATTTTTTTGTCCAGAGAC
TTTCAGATGTGCAGCCTGAAAAGTTACAAATGACTACCACTTATATTTTGCTTTAATCTCTTAGTGTCTGTAGAAAAATGAGAATGGCAGTTTTCAGTAAGCATCTATGTGGTCACGTTCTCTTAGGTTTTCCAAAGGAATTAGGTAGTCTTCTCATGTCTTCTCTTGCCCAATGTTACAATACACTATATCTCGATCAA
AAGTATGAGCCTTAACTGCAATTGAGGGCTAGGGAACTTAAGC

>TRINITY_DN120080_c8_g1_i4 from sample A1 / Example unspliced isoform:

AGACAATCGAAAAAAACAAATAGAAGAGAGACATGTCTCCTTCATTCAGGAAGGCAGGCAGTCCGGGGGGGTTTTCTGCGGCCGTGCAAGATGGTTTTGACTATGTGCAAGGAGGGAGAGCGGCCATGGCCGGATCATCCGATATAATAGTTCGCAGTCAACCCAGGTACCAATGTTTTCATACTTGGCATCTCTTCAAA
ACGCACCCAACATTGCAGGCTGCAGCAGTGATTTGTGCATgtattacacattttataattttattgtgaaaccagatttctgtcaggccttggttaactccaagctgaatgattttattgattgtaaatggtttatttatacagGTGAGAGAGATGACCTTTGGGCTTCAGATTCCCAAGGTATGTGCCTCTTCATCTTC
ATAACTGAAAGCAAATATTTACAATAATTCACAAGAGGAACCCTTGTAGGATTATGTTTCCAACATTCCCCCCTTAATTCGAAGGGGTGTTTGTGAGTCCAAGCATCTTTCTGAACTTTTCAAGCTTTTCTCTTCCAAGCGATTTGGTGAAGATGTCTG