sp|A8MS41|CCR4D_ARATH ----> Carbon catabolite repressor protein 4 homolog 4

Intron 1 GTAAATTTTA ... CAATGTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	83.75	1.4	7	2
A2	66.67	1	2	0
A3	47.86	2.2	2	1
A4	-1	0	0	3
A5	100	0	2	0
A6	67.09	26	53	11.9
A7	56.52	10	13	2.6
A8	68	8	17	10.7
A9	72.41	8	21	11.1
A10	95.45	1	21	4

>TRINITY_DN32884_c0_g1_i1 from sample A6 / Example spliced isoform

GCGCTCTTGCTCATTTGGCCTCTTCAAACGCGTCCGAATACCCCGCCATTTGATTCCAAATATGTATAATACTGCATTTAAATCTACCGGATGCCATTATTCAATATTCTCGGAGGCCCAAAACAAGTGACAATATAGGACACTGGGCAAATTGCTGGAATCAGTAACTGAACAATCCCATCGGGTATCCACTATTAGTC
AATAGTATTACTCCATTTCTGTGAAAAGTCCTCCTCAGAATCTCTTTGAACAAATTCTCCAAACATTATTCTTTCCCTATCGAATACCCACATGTATGGAAGTGCGATATTCTCAAATCAGTTGGTGGCTGGCCTTCACACGATTTTCAGAGCCCGCGTGCCTTCCATAGGGAGCTTCTCAACAGCAGTACAAGCTTGTG
GGCTTTCTCGTACTCGGGCCTTTTCAAGACCAATGACAGGAGCAGTCTCACCATGCTTTCCTGAATTTATTCCTGTGGATGATAAAGAATGGGCTGTCAAAAACATATCAGAGGGGTCCATTATCCGCGTTGTCTCATACAATATTCTTGCTCAGGCATACGTAAAGAGCACATTATTTCCACACTCTCCATCACATTCC
CTGAAATGGAAGGCTCGTTCACAATCTCTCCTATCACTACTAAAAAGTTTGGAGGCTAACTTCTTATGTCTACAGGAATTAGATGAATTTGAAACATTTTACAAAGGAAACATGGACATGCAAGGGTACTCAAGTGTATATATCCAACGAGGTGGACGCAAGCGTGATGGCTGTGGCATCTTTTACAAGCGTGAGCGAGC
AGAGCTAATTTTAGAAGAGGATATTGATTACAATGACCTTGTACCTGCTGATGAAGATCCAGAAAATTCAGACAAGGTGAAAGATGAAGAAAACTTAAGTTCTAATAACAGCAGAGGATCCCCACAAACTGATTTACTGGATGACAGAGGAGATCCAGACGACCCTAGGGTGAGATTGAAGCGAGATTGTGTTGGACTGT
TAACAGCATTCAAACTTCTAGATCCCCCACACCACGTGATTGTTCTCGCAAACACACATATTTACTGGGATCCTGAATGGGCAGATGTAAAGCTTGCACAAGCAAAGTATCTTCTATTACGTCTTACCCAATTTAAGAACACAGTCTCAGAAAGATTCAGTTGTAACCCTCTAGTCATTGTTGCAGGTGACTTCAATTCT
ACTCCTGGAGATGAGGTGTATCAATACCTTACATCAGGGATTTCACAATCGAGTAAAGGATATTCTTCCATTGGCAATGAGCCAGAAGCATCTGAACAGAGCCCAATAGCATTACATAGTCTTTATTCATTTATTGGAGGAGAACCTCCATTTACAAATTACACACCTGGATTCACTGGAACACTTGATTATATTTTGTT
CTCAAGCTCTGAGCACATGCAGCCTGTCAGCTTTCTCAAACTGCCATCTGTGGAATCCCCTGACATTCTTGGTGGATTGCCAAATGAAAATCATCCCAGTGATCACTTGCCCATTGGAGCAGATTTTGAAATTCGTTAGAACACAATAGCTTCTTATGATGAACATTGTATATTCATAATATTGAAGTGAAGCCAAATGC
TCGTAATCCACTTTGATACAGAAATCTGAGTTTCTTTAAGGATACAATTTTTTTCTATCATTTGTGCAAACATTCCAAGATCTGAGTTTCATTAAGGATGTACTTTTTTCTACCAAACTTGTTGATGAAGTAATTTATTCATGGCTGATATCATTTTTTTAAT

>TRINITY_DN32884_c0_g1_i3 from sample A6 / Example unspliced isoform:

GCGCTCTTGCTCATTTGGCCTCTTCAAACGCGTCCGAATACCCCGCCATTTGATTCCAAATATGTATAATACTGCATTTAAATCTACCGGATGCCATTATTCAATATTCTCGGAGGCCCAAAACAAGTGACAATATAGGACACTGGGCAAATTGCTGGAATCAGTAACTGAACAATCCCATCGGGTATCCACTATTAGTC
AATAGTATTACTCCATTTCTGTGAAAAGTCCTCCTCAGAATCTCTTTGAACAAATTCTCCAAACATTATTCTTTCCCTATCGAATACCCACATGTATGGAAGTGCGATATTCTCAAATCAGTTGGTGGCTGGCCTTCACACGATTTTCAGAGCCCGCGTGCCTTCCATAGGGAGCTTCTCAACAGCAGTACAAGCTTGTG
GGCTTTCTCGTACTCGGGCCTTTTCAAGACCAATGACAGGAGCAGTCTCACCATGCTTTCCTGAATTTATTCCTGTGGATGATAAAGAATGGGCTGTCAAAAACATATCAGAGGGGTCCATTATCCGCGTTGTCTCATACAATATTCTTGCTCAGATGGAAGGCTCGTTCACAATCTCTCCTATCACTACTAAAAAGTTT
GGAGGCTAACTTCTTATGTCTACAGGAATTAGATGAATTTGAAACATTTTACAAAGGAAACATGGACATGCAAGGGTACTCAAGTGTATATATCCAACGAGGTGGACGCAAGCGTGATGGCTGTGGCATCTTTTACAAGCGTGAGCGAGCAGAGCTAATTTTAGAAGAGGATATTGATTACAATGACCTTGTACCTGCTG
ATGAAGATCCAGAAAATTCAGACAAGGTGAAAGATGAAGAAAACTTAAGTTCTAATAACAGCAGAGGATCCCCACAAACTGATTTACTGGATGACAGAGGAGATCCAGACGACCCTAGGGTGAGATTGAAGCGAGATTGTGTTGGACTGTTAACAGCATTCAAACTTCTAGATCCCCCACACCACGTGATTGTTCTCGCA
AACACACATATTTACTGGGATCCTGAATGGGCAGATGTAAAGCTTGCACAAGCAAAGTATCTTCTATTACGTCTTACCCAATTTAAGAACACAGTCTCAGAAAGATTCAGTTGTAACCCTCTAGTCATTGTTGCAGGTGACTTCAATTCTACTCCTGGAGATGAGGTGTATCAATACCTTACATCAGGGATTTCACAATC
GAGTAAAGGATATTCTTCCATTGGCAATGAGCCAGAAGCATCTGAACAGAGCCCAATAGCATTACATAGTCTTTATTCATTTATTGGAGGAGAACCTCCATTTACAAATTACACACCTGGATTCACTGGAACACTTGATTATATTTTGTTCTCAAGCTCTGAGCACATGCAGCCTGTCAGCTTTCTCAAACTGCCATCTG
TGGAATCCCCTGACATTCTTGGTGGATTGCCAAATGAAAATCATCCCAGTGATCACTTGCCCATTGGAGCAGATTTTGAAATTCGTTAGAACACAATAGCTTCTTATGATGAACAgtaaattttaaagaactttaaactttcttgatgttattctctgcttctttatttattatagagaataaacgttgctcttttatct
atattgacaattaggttacatttcttagtctcagacctgtttatttatggctgatatcatttttttaatactaactgaccaatggaacaatgtgcagTTGTATATTCATAATATTGAAGTGAAGCCAAATGCTCGTAATCCACTTTGATACAGAAATCTGAGTTTCTTTAAGGATACAATTTTTTTCTATCATTTGTGCA
AACATTCCAAGATCTGAGTTTCATTAAGGATGTACTTTTTTCTACCAAACTTGTTGATGAAGTAATTTATTCATGGCTGATATCATTTTTTTAAT

Intron 2 GTGACTTCAA ... TGGAGATGAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	90.04	2.5	22	23
A2	75.75	5	15	15
A3	78.79	6	22	18
A4	80.43	2.5	10	9
A5	100	0	2	2
A6	75.23	17	52	49
A7	79.53	11.5	45	40
A8	74.47	18	49	53
A9	71.9	21	51	53
A10	88.09	2.5	18	14

>TRINITY_DN105118_c0_g1_i1 from sample A2 / Example spliced isoform

AACGCGTCCGAATACCCCGCCATTTGATTCCAAATATGTATAATACTGCATTTAAATCTACCGGATGCCATTATTCAATATTCTCGGAGGCCCAAAACAAGTGACAATATAGGACACTGGGCAAATTGCTGGAATCAGTAACTGAACAATCCCATCGGGTATCCACTATTAGTCAATAGTATTACTCCATTTCTGTGAAA
AGTCCTCCTCAGAATCTCTTTGAACAAATTCTCCAAACATTATTCTTTCCCTATCGAATACCCACATGTATGGAAGTGCGATATTCTCAAATCAGTTGGTGGCTGGCCTTCACACGATTTTCAGAGCCCGCGTGCCTTCCATAGGGAGCTTCTCAACAGCAGTACAAGCTTGTGGGCTTTCTCGTACTCGGGCCTTTTCA
AGACCAATGACAGGAGCAGTCTCACCATGCTTTCCTGAATTTATTCCTGTGGATGATAAAGAATGGGCTGTCAAAAACATATCAGAGGGGTCCATTATCCGCGTTGTCTCATACAATATTCTTGCTCAGGCATACGTAAAGAGCACATTATTTCCACACTCTCCATCACATTCCCTGAAATGGAAGGCTCGTTCACAATC
TCTCCTATCACTACTAAAAAGTTTGGAGGCTAACTTCTTATGTCTACAGGAATTAGATGAATTTGAAACATTTTACAAAGGAAACATGGACATGCAAGGGTACTCAAGTGTATATATCCAACGAGGTGGACGCAAGCGTGATGGCTGTGGCATCTTTTACAAGCGTGAGCGAGCAGAGCTAATTTTAGAAGAGGATATTG
ATTACAATGACCTTGTACCTGCTGATGAAGATCCAGAAAATTCAGACAAGGTGAAAGATGAAGAAAACTTAAGTTCTAATAACAGCAGAGGATCCCCACAAACTGATTTACTGGATGACAGAGGAGATCCAGACGACCCTAGGGTGAGATTGAAGCGAGATTGTGTTGGACTGTTAACAGCATTCAAACTTCTAGATCCC
CCACACCACGTGATTGTTCTCGCAAACACACATATTTACTGGGATCCTGAATGGGCAGATGTAAAGCTTGCACAAGCAAAGTATCTTCTATTACGTCTTACCCAATTTAAGAACACAGTCTCAGAAAGATTCAGTTGTAACCCTCTAGTCATTGTTGCAGGTGTATCAATACCTTACATCAGGGATTTCACAATCGAGTA
AAGGATATTCTTCCATTGGCAATGAGCCAGAAGCATCTGAACAGAGCCCAATAGCATTACATAGTCTTTATTCATTTATTGGAGGAGAACCTCCATTTACAAATTACACACCTGGATTCACTGGAACACTTGATTATATTTTGTTCTCAAGCTCTGAGCACATGCAGCCTGTCAGCTTTCTCAAACTGCCATCTGTGGAA
TCCCCTGACATTCTTGGTGGATTGCCAAATGAAAATCATCCCAGTGATCACTTGCCCATTGGAGCAGATTTTGAAATTCGTTAGAACACAATAGCTTCTTATGATGAACAGTAAATTTTAAAGAACTTTAAACTTTCTTGATGTTATTCTCTGCTTCTTTATTTATTATAGAGAATAAACGTTGCTCTTTTA

>TRINITY_DN105118_c0_g1_i3 from sample A2 / Example unspliced isoform:

AACGCGTCCGAATACCCCGCCATTTGATTCCAAATATGTATAATACTGCATTTAAATCTACCGGATGCCATTATTCAATATTCTCGGAGGCCCAAAACAAGTGACAATATAGGACACTGGGCAAATTGCTGGAATCAGTAACTGAACAATCCCATCGGGTATCCACTATTAGTCAATAGTATTACTCCATTTCTGTGAAA
AGTCCTCCTCAGAATCTCTTTGAACAAATTCTCCAAACATTATTCTTTCCCTATCGAATACCCACATGTATGGAAGTGCGATATTCTCAAATCAGTTGGTGGCTGGCCTTCACACGATTTTCAGAGCCCGCGTGCCTTCCATAGGGAGCTTCTCAACAGCAGTACAAGCTTGTGGGCTTTCTCGTACTCGGGCCTTTTCA
AGACCAATGACAGGAGCAGTCTCACCATGCTTTCCTGAATTTATTCCTGTGGATGATAAAGAATGGGCTGTCAAAAACATATCAGAGGGGTCCATTATCCGCGTTGTCTCATACAATATTCTTGCTCAGGCATACGTAAAGAGCACATTATTTCCACACTCTCCATCACATTCCCTGAAATGGAAGGCTCGTTCACAATC
TCTCCTATCACTACTAAAAAGTTTGGAGGCTAACTTCTTATGTCTACAGGAATTAGATGAATTTGAAACATTTTACAAAGGAAACATGGACATGCAAGGGTACTCAAGTGTATATATCCAACGAGGTGGACGCAAGCGTGATGGCTGTGGCATCTTTTACAAGCGTGAGCGAGCAGAGCTAATTTTAGAAGAGGATATTG
ATTACAATGACCTTGTACCTGCTGATGAAGATCCAGAAAATTCAGACAAGGTGAAAGATGAAGAAAACTTAAGTTCTAATAACAGCAGAGGATCCCCACAAACTGATTTACTGGATGACAGAGGAGATCCAGACGACCCTAGGGTGAGATTGAAGCGAGATTGTGTTGGACTGTTAACAGCATTCAAACTTCTAGATCCC
CCACACCACGTGATTGTTCTCGCAAACACACATATTTACTGGGATCCTGAATGGGCAGATGTAAAGCTTGCACAAGCAAAGTATCTTCTATTACGTCTTACCCAATTTAAGAACACAGTCTCAGAAAGATTCAGTTGTAACCCTCTAGTCATTGTTGCAGgtgacttcaattctactcctggagatgagGTGTATCAATA
CCTTACATCAGGGATTTCACAATCGAGTAAAGGATATTCTTCCATTGGCAATGAGCCAGAAGCATCTGAACAGAGCCCAATAGCATTACATAGTCTTTATTCATTTATTGGAGGAGAACCTCCATTTACAAATTACACACCTGGATTCACTGGAACACTTGATTATATTTTGTTCTCAAGCTCTGAGCACATGCAGCCTG
TCAGCTTTCTCAAACTGCCATCTGTGGAATCCCCTGACATTCTTGGTGGATTGCCAAATGAAAATCATCCCAGTGATCACTTGCCCATTGGAGCAGATTTTGAAATTCGTTAGAACACAATAGCTTCTTATGATGAACAGTAAATTTTAAAGAACTTTAAACTTTCTTGATGTTATTCTCTGCTTCTTTATTTATTATAG
AGAATAAACGTTGCTCTTTTA