sp|P54774|CDC48_SOYBN ----> Cell division cycle protein 48 homolog

Intron 1 GTAAGTCAGA ... CATATTCCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	24.4	127	39	43
A2	25.22	169	62	52
A3	21.77	221	68	55
A4	23.45	173	44	62
A5	23.86	67	19	23
A6	16.85	37	10	5
A7	25.19	144	52	45
A8	29.32	47	12	27
A9	23.17	121	48	25
A10	22.59	197	63	52

>TRINITY_DN120328_c1_g1_i4 from sample A2 / Example spliced isoform

GAAAGAAGGAATTACATTGTCCAGTTTGGAATTGCACTAGATCCGCAAGAAAGACTGGTGTATCGTAGAGGTCTCCTCCTGCCTGCTTTCGGTTGATCTATTCCCTACACTTTGTCGTTGCATTTGCGTGGTTTGAAAGTTAACAATGGCGGGAGAATCATCGGAATCCAACGAGGTAACAAAGAGGGACTTTAGCACTG
CAATACTTGAGCGTAAGAAGGCTCCTAATCGCCTAGTTGTGGATGAAGCCATTAACGATGATAATTCTATGGTGGCCCTTAATCCCCAAACAATGGAACAGTTGCAGCTATTCAGGGGTGATACGGTCCTTCTTAAGGGTAAAAAGAGAAAGGATACAGTTTGCGTAGTTCTGGGCGATGATAGCTGTGCAGAGCATGCA
ATTAGAATGAACAGAGTTGTTAGATCAAATCTGAGAGTAAGATTGGGGGATGTGGTGTCTGTTCATCAGTGCCCAGATGTCAAGTATGGGAAGCGTGTCCATATTCTTCCTATAGATGACACTATTGAGGGTCTTACAGGCGACCTGTTTGATGCCTACTTGAAACCCTACTTCCAGGAAGCCTATCGCCCTGTGAGAAA
AGGAGACCTATTTCTTGTGCGAGGAGGGATGCGCAGTGTGGAATTTAAAATCATCGGGACAGATCCTGGTGAATATTGTATTGTTTCTCCGGACACTGAAATCTTTTGTGAAGGAGATCCAATAAAACGAGAAGATGAAGAGAAATTGAATGAAGTTGGTTATGATGATATTGGTGGTGTCAGAAAACAAATGGCACAAA
TCAGGGAACTAGTTGAACTACCCCTTCGACATCCCCAGCTTTTCAAAGCTATTGGTGTGAAGCCACCTAAGGGTGTTTTGCTTTATGGTCCTCCTGGTTCAGGAAAAACCTTGATTGGCAGGGCAGTGGCAAATGAGACCGGGTGTTTCTTTTTCTTGATTAATGGTCCTGAAATTATGTCAAAAATGGCTGGAGAGAGT
GAAAGCAATCTCAGAAAGGCTTTTCAAGAAGCAGAGAACAATGCTCCCTCCATCATTTTCATCGATGAGATTGACTCCATAGCTCCCAAGAGGGAGAAAACACACGGTGAAGTAGAGAGACGCATTGTATCTCAACTGTTGACATTGATGGATGGCCTTAAAGCTCGAGCTCACGTGATTGTGATGGGAGCAACAAATAG
GCCCAACAGCATTGATCCAGCGCTTAGAAGATTTGGTAGGTTTGATCGTGAAATTGAAATTGGGGTTCCAGATGAAGTTGGTCGATTGGAGGTTCTTCGCATTCACACAAAGAACATGAAGCTTGCTGAAGAAGTTGATCTTGAACATATTGCCAAGAATACACATGGACATGTGGGGGCAGACCTTGCAGCTCTTTGCA
CTGAGGCTGCACTACAGTGTATCAGAGAAAAAATGGATGTAATTGATTTGGATGATGAGACAATCGATGCTGAAATCCTGAATTCTATGGCCGTTACAAATGAGCACTTTAGGGCTGCTTTGGGCACTAGCAACCCCTCTGCCCTAATAGGTAGGCACTTCAAGGTCAAAACAAATCACGATAGTATTAAATACTTCTTG
GAACATATACTCTCTTCAGA

>TRINITY_DN120328_c1_g1_i9 from sample A2 / Example unspliced isoform:

GAAAGAAGGAATTACATTGTCCAGTTTGGAATTGCACTAGATCCGCAAGAAAGACTGGTGTATCGTAGAGGTCTCCTCCTGCCTGCTTTCGGTTGATCTATTCCCTACACTTTGTCGTTGCATTTGCGTGGTTTGAAAGTTAACAATGGCGGGAGAATCATCGGAATCgtaagtcagaaaagcttctcatctcttttctt
atccccttaaatctggaatagaatttataagaatggcgaaattgggcactgtggcaaggctgattccattaatatacatattgcttcaatcaatatattgtttgttgacagtctgttgcttgttaatttaatcaattcatttttcttccatattccagCAACGAGGTAACAAAGAGGGACTTTAGCACTGCAATACTTGA
GCGTAAGAAGGCTCCTAATCGCCTAGTTGTGGATGAAGCCATTAACGATGATAATTCTATGGTGGCCCTTAATCCCCAAACAATGGAACAGTTGCAGCTATTCAGGGGTGATACGGTCCTTCTTAAGGTTCCTCCTTGCTCTATTATGGCATTGCAAATTATTCCTTCTTTCCAATGGTCTTGAATTCTCTCTATTTGCT
TCTTAACAATTGAAATCACG

Intron 2 GTATGAAAAA ... CTTGTGCCAG

Found issues: Low number of reads

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	64.71	3	7	4
A2	55.56	4	7	3
A3	52	6	7	6
A4	-1	0	0	0
A5	100	0	4	1
A6	60	2	4	2
A7	33.33	6	2	4
A8	75	1	3	3
A9	29.41	6	3	2
A10	46.67	4	1	6

>TRINITY_DN44800_c4_g2_i6 from sample A9 / Example spliced isoform

CTGAAATGGTGACGTAAGTCTTGGAATCGGCATCCCAAGAGCCGGCGGTGCGATGCCGTCAGCGTCTGCTCGTTTGTTTAATGCATGACAGGATGTTGAAGCCACGTTGTAGAGGGCGTTGAAGCCACGTTGAGTGGTGACGTAAGTCTTGAAATGGGGGCAGTACGGGTCTAGGCATTTGTTTAATGCATGGCAGGTTG
ACATGACAGGGAGCAGCAGGTTGAAGCCAACATTCGAGGCATAAAGTCTTGAGCGGGGTGACGGTCCTTCCATGGTTTCATCTTGGTTGGGCGGAGGAGAAGTCCAAGGTCGGGGATCGCGTATTCGTCTGCATTTGTTGCCTTGTTATAATCCTGGCGCTTGGTGAAGTAGAGAGACGCATTGTATCTCAACTGTTGAC
ATTGATGGATGGCCTTAAAGCTCGAGCTCACGTGATTGTGATGGGAGCAACAAATAGGCCCAACAGCATTGATCCAGCGCTTAGAAGATTTGGTAGGTTTGATCGTGAAATTGAAATTGGAGTTCCAGATGAAGTTGGTCGATTGGAGGTTCTTCGCATCCACACAAAGAATATGAAGCTTGCTGAAGAAGTTGATCTTG
AACATATTGCCAAGAATACACATGGACATGTGGGGGCAGACCTTGCAGCTCTTTGCACTGAGGCTGCACTATAGTGTATCAGAGAAAAAAATGGATGTAATTGATTTGGATGATGAGACAATCGATGCTGAAATCCTGAATTCTATGGCCGTTACAAATGAGCACTTTAGGGCTGCTTTGGGCACTAGCAACCCCTCTGC
CCTAATAGGTAGGCACTTCAAGGTCAAAACAAATCACGATAGTATTAAATGCTTCTTGGAACATATACTCTCTTCAGAAGAGTAAGAAAAATGGGTATAACCAAGATGTTGGAATATGACTTTGAAATCATCTATAAAAAAGGGAAACATAATGTGGTGGTATATGCACTCTACATAAAAGATGAGGATGTTGAGGAAGT
ACTTTGTGCAATTTATGTTGTACAACCTGATTAGGTAGTAGTAGCAAGGGAAGAATGGAAGAATGACCTATATGTGTGGACACTCATCAAAAGCTACAAAGGGATACCAATGTATCTGATACTTTTGTGTGGAAAAATGATTCACTATGGTATAAGGATTTCTTGTATATATGTAAGAACCCCCAATTCAAACAAAAGAT
CCTTTTCGAATTACACACCTCTCCTATAGGTGGCCATTCAGGATTCCTAAACACCTACCACAGGGTCAAGAAGGAATTCTGGATAAAGTCTTAAATTTGACGTTCAAATGTTCACGGCAGAATGTTTGGTATACCAACAAAATAAGGTTGAAACAGTTAAGACCTCGAGTCTTCTACAACCATTAGATATACCTTGTCGG
CGATGGGAGGAAGTTTCGATGGATTTTATCATAAGTAATACTCAAGTTAGAAGGAAAGAATTTTATTATGGTGGTTGTTGACAGACTCACAAAGTATGCTCACGTTTTTGCACTCTCTCGCCCTTTTAATGCAAGTACTATAGTTGTATCCTTCATGGAAACAATTCATAAGTTACATGGAAACCCAAAGATTATTGTAA
GTGATAGAGATCCAATTTACACTGGAAAATTTTGGACTGAAATATTTTTTTGTTTAGGTACCCAGTTGGTTCATAATTCATCTTATCATTCTCAACCTGATGGGAAAAATGAGATGGTGAACAAATGTTTGGAAGGATGTCTTCGCTGCTTTGCATCTAATAAGCAAACACAATGGGCG

>TRINITY_DN44800_c4_g2_i11 from sample A9 / Example unspliced isoform:

CTGAAATGGTGACGTAAGTCTTGGAATCGGCATCCCAAGAGCCGGCGGTGCGATGCCGTCAGCGTCTGCTCGTTTGTTTAATGCATGACAGGATGTTGAAGCCACGTTGTAGAGGGCGTTGAAGCCACGTTGAGTGGTGACGTAAGTCTTGAAATGGGGGCAGTACGGGTCTAGGCATTTGTTTAATGCATGGCAGGTTG
ACATGACAGGGAGCAGCAGGTTGAAGCCAACATTCGAGGCATAAAGTCTTGAGCGGgtatgaaaaacacctgctagctcatagcgtattgtagtttgtgagtattgaaacaaattgataaggtttggcttgtgccagGGTGACGGTCCTTCCATGGTTTCATCTTGGTTGGGCGGAGGAGAAGTCCAAGGTCGGGGATCG
CGTATTCGTCTGCATTTGTTGCCTTGTTATAATCCTGGCGCTTGGTGAAGTAGAGAGACGCATTGTATCTCAACTGTTGACATTGATGGATGGCCTTAAAGCTCGAGCTCACGTGATTGTGATGGGAGCAACAAATAGGCCCAACAGCATTGATCCAGCGCTTAGAAGATTTGGTAGGTTTGATCGTGAAATTGAAATTG
GAGTTCCAGATGAAGTTGGTCGATTGGAGGTTCTTCGCATCCACACAAAGAATATGAAGCTTGCTGAAGAAGTTGATCTTGAACATATTGCCAAGAATACACATGGACATGTGGGGGCAGACCTTGCAGCTCTTTGCACTGAGGCTGCACTATAGTGTATCAGAGAAAAAAATGGATGTAATTGATTTGGATGATGAGAC
AATCGATGCTGAAATCCTGAATTCTATGGCCGTTACAAATGAGCACTTTAGGGCTGCTTTGGGCACTAGCAACCCCTCTGCCCTAATAGGTAGGCACTTCAAGGTCAAAACAAATCACGATAGTATTAAATGCTTCTTGGAACATATACTCTCTTCAGAAGAGTAAGAAAAATGGGTATAACCAAGATGTTGGAATATGA
CTTTGAAATCATCTATAAAAAAGGGAAACATAATGTGGTGGTATATGCACTCTACATAAAAGATGAGGATGTTGAGGAAGTACTTTGTGCAATTTATGTTGTACAACCTGATTAGGTAGTAGTAGCAAGGGAAGAATGGAAGAATGACCTATATGTGTGGACACTCATCAAAAGCTACAAAGGGATACCAATGTATCTGA
TACTTTTGTGTGGAAAAATGATTCACTATGGTATAAGGATTTCTTGTATATATGTAAGAACCCCCAATTCAAACAAAAGATCCTTTTCGAATTACACACCTCTCCTATAGGTGGCCATTCAGGATTCCTAAACACCTACCACAGGGTCAAGAAGGAATTCTGGATAAAGTCTTAAATTTGACGTTCAAATGTTCACGGCA
GAATGTTTGGTATACCAACAAAATAAGGTTGAAACAGTTAAGACCTCGAGTCTTCTACAACCATTAGATATACCTTGTCGGCGATGGGAGGAAGTTTCGATGGATTTTATCATAAGTAATACTCAAGTTAGAAGGAAAGAATTTTATTATGGTGGTTGTTGACAGACTCACAAAGTATGCTCACGTTTTTGCACTCTCTC
GCCCTTTTAATGCAAGTACTATAGTTGTATCCTTCATGGAAACAATTCATAAGTTACATGGAAACCCAAAGATTATTGTAAGTGATAGAGATCCAATTTACACTGGAAAATTTTGGACTGAAATATTTTTTTGTTTAGGTACCCAGTTGGTTCATAATTCATCTTATCATTCTCAACCTGATGGGAAAAATGAGATGGTG
AACAAATGTTTGGAAGGATGTCTTCGCTGCTTTGCATCTAATAAGCAAACACAATGGGCG

Intron 3 GTGAGTAGTT ... CATTTATCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	18.06	253.3	54	1
A2	24.64	203.3	65	1
A3	22.64	245.3	70	0
A4	16.26	208.3	39	0
A5	21.66	134.3	36	3
A6	18.38	223	49	0
A7	18.79	504.3	114	2
A8	18.18	366.7	79	0
A9	21.44	426.7	113	0
A10	20.21	408	101	0

>TRINITY_DN111478_c0_g2_i5 from sample A5 / Example spliced isoform

TGGTCCTCCTGGTTCAGGAAAAACCTTGATTGCCAGGGCAGTGGCAAATGAGACTGGAGCTTTCTTTTTCTTAATTAATGGTCCTGAAATTATGTCAAAACTTGCTGGAGAAAGTGAAAGCAATCTTAGAAAGGCTTTTGAAGAAGCAGAGAAAAATGCTCCTTCTATTATTTTCATTGACGAAATTGACTCCATAGCTC
CAAAGAGGGAGAAAACAAATGGTGAAGTAGAGAGGCGCATTGTATCTCAACTTTTGACATTGATGGATGGTCTAAAATCTCGATCTCATGTGATTGTCATGGGAGCAACAAATAGGCCGAACAGCATTGATCCAGCACTTAGAAGGTTTGGCAGGTTTGATCGTGAAATTGACATTGGGGTTCCAGATGAAGTTGGTCGA
CTGGAGGTTCTTCGCATCCACACAAAAAATATGAAACTTGCTGAAGATGTTGATCTTGAACGTATTTCAAAGAATACACATGGTTATGTTGGGGCAGATCTTGCAGCTCTTTGCACTGAGGCCGCACTGCAGTGTATTAGGGAAAAAATGGATGTCATTGACTTGGAAGATGAAACAATTGATGCGGAAGTTCTGAATTC
TATGGCTGTTACAAACGAGAACTTTAGGGCTGCTTTGGGCACTAGCAACCCCTCTGCCCTCCGTGAGACTGTTGTGGAGGTGCCAAATGTTTCTTGGGAAGATGTTGGGGGTCTGGAAAATGTCAAGAGAGAGCTTCAGGAGGTAATAAAATTTAATATATTTTTCAATTT

>TRINITY_DN111478_c0_g2_i1 from sample A5 / Example unspliced isoform:

CTTCTTATTCATTGAAACCCATTTGACTTATAGATTCTGCAAAGCTGGTCGGTTCGGTTGGCTGCCCCTCCCCTCACGAGGTGTACTAATAAAAGAAACAAGTTGAGCTTTTATTGTAATACATGATGGGATTGTGATTTTTAGCATACGATTCTCCGGAGAGTCTCTACTTACTTTTTCCCTGCGCTGGTCGTTGGTAG
TGGTGGGTGAAAATAGGAAGGGGAGGCCACTGATACATACCATCAGATCGCATTCATTGATTAGAGATCTTCTTTTGCGTCCTCCTCTCTTCTGTAGTTTTTTTTTTTTCTATCGTTGCATCTCCTGAAATCGACAATGGCGAGCTCAATACCGGGAGAATCATCTGAAGGGAAAGGAACAAAGAAAGACTTTAGTACTG
CAATACTTGAGCGTAAGAAGTCTCCTAATCGGTTAGTTGTAGATGAAGCCATAAATGATGAGAATTCTGTGGTGGCTCTTCATTCAAAAACAATGGAAACGTTGCAGCTTTTCCGGGGTGATACCATCCTTATTAAGGGTAAAAAGAGAAAGGATACGGTTTGCATTGTTCTGGTTGATGATACATGTGAAGAGCATAAG
ATCAGAATGAACAAGGTTGTTCGGTCAAATCTAAGAGTAAGATTAGGGGATGTAGTATCTGTTCATCAGTGCCCAGATGTTAAGTATGGGAAGCGTGTGCATATTCTTCCTATAGATGACACAATCGAAGGTGTTACAGGAAACTTGTTCGATGTGTACTTGAAGTCTTACTTCTTGGAAGCCTATCGCCCAGTAAGAAA
AGGAGACCTTTTTCTAGTACGAGGAGGAATGAGAAGTGTGGAATTTAAAATCATTGAGACAGACCCGGGTGAATATTGTGTTGTTTCTCCAGACACCGAAATTTTTTGTGAGGGAGAGCCAATAAAACGAGAAGATGAAGACAGATTGGATGAAGTTGGCTATGATGATGTTGGTGGTGTAAGGAAACAAATGGCACAAA
TCAGGGAACTAGTTGAATTACCCCTACGGCATCCACAACTTTTCAAATCCATTGGTGTGAAGCCCCCAAAAGGTATTTTGCTTTTTGGTCCTCCTGGTTCAGGAAAAACCTTGATTGCCAGGGCAGTGGCAAATGAGACTGGAGCTTTCTTTTTCTTAATTAATGGTCCTGAAATTATGTCAAAACTTGCTGGAGAAAGT
GAAAGCAATCTTAGAAAGGCTTTTGAAGAAGCAGAGAAAAATGCTCCTTCTATTATTTTCATTGACGAAATTGACTCCATAGCTCCAAAGAGGGAGAAAACAAATGGTGAAGTAGAGAGGCGCATTGTATCTCAACTTTTGACATTGATGGATGGTCTAAAATCTCGATCTCATGTGATTGTCATGGGAGCAACAAATAG
GCCGAACAGCATTGATCCAGCACTTAGAAGGTTTGGCAGGTTTGATCGTGAAATTGACATTGGGGTTCCAGATGAAGTTGGTCGACTGGAGGTTCTTCGCATCCACACAAAAAATATGAAACTTGCTGAAGATGTTGATCTTGAACGTATTTCAAAGAATACACATGGTTATGTTGGGGCAGATCTTGCAGCTCTTTGCA
CTGAGGCCGCACTGCAGTGTATTAGGGAAAAAATGGATGTCATTGACTTGGAAGATGAAACAATTGATGCGGAAGTTCTGAATTCTATGGCTGTTACAAATGAGCACTTTCAGGCTGCACTGGGCTCTAGTAACCCCTCTGCCCTCCGTGAGACTgtgagtagttataaacttggatatagagagagcctgagcaagatt
tgttgttttgtttccattgcttttatattaagcatgatacatatctccactgaagttaatcatttcatttatcagGTTGTGGAGGTGCCAAATGTTTCTTGGGAAGATGTTGGGGGTCTGGAAAATGTCAAGAGAGAGCTTCAGGAGGTAATAAAATTTAATATATTTTTCAATTT