sp|Q9LI74|CHUP1_ARATH ----> Protein CHUP1, chloroplastic
Intron 1 GTAACAATCT ... ATATTTTCAG
| Sample | Retention score (%) | Exon junction reads | 5'ss reads | 3'ss reads |
| A1 | 84.62 | 1 | 3 | 8 |
| A2 | 66.67 | 5 | 5 | 15 |
| A3 | 61.9 | 4 | 4 | 9 |
| A4 | 66.67 | 4 | 6 | 10 |
| A5 | 100 | 0 | 1 | 0 |
| A6 | -1 | 0 | 0 | 0 |
| A7 | 66.67 | 1 | 1 | 3 |
| A8 | 100 | 0 | 0 | 1 |
| A9 | 83.33 | 1 | 4 | 6 |
| A10 | 63.64 | 4 | 8 | 6 |
>TRINITY_DN33324_c0_g1_i1 from sample A9 / Example spliced isoformGGACTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGCATGAATTCA
TGCTGGCTTGTGTGCTGAGCAGTCAACTATACTGGTCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGACTCCGGTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTT
CGCGGTTTGTAAGCGTGTCAGGTGATCGAGGACGCCGTATTTCTGAGACTCAATGACACCTGAGCGCGATAGGCGGGCGATTAGCGGTGGAGAGTAAAAGACTTACATATATGTTAGTGAAGGTAGGCCTTGCTATCAGTCTCTCGGTTACAGCTTACATATTGACTCACCTGAGATTTAGGCCTGTCAACCGAAAGCTT
GTCAAAGGATCGGATGCTCGGGGAGAATTAGGAAATTCTAACGAGAAGGCTCAAGACAATGTGGAAATTGAGAAAGAAATCTGCTCGTACACAAAAGTGGACTCAACACAGGAAGTTGATGGGGGTGAGGTTAAAACAGTTGATAGCATTAGTCCATCACTGAGCTTGGCCAACGATGAACTTCTCTTGCCAGAGTTTAA
TGATCTTTTATCAGGAGAGATGGAGTTTCCTTTGGAAGAGGTTGTTCCATCTTCTAAACCTACACAGTCTGGCGGTGAGGAGAAGCAGGCTAGTACAGTAGATCCTGATATAATGTCTGAGGATTATAAACACATGTACGATGAGGCAATATCAGATAATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAAT
TGCAGAAAAGTGAAGAAAATCTTCAAGGGG
>TRINITY_DN33324_c0_g1_i2 from sample A9 / Example unspliced isoform:GGACTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGgtaacaatct
gatccatgcttcccacaattaaaaactgtgtgcttcccacaatatttagcagttatggaatatattccagttggagtaatatttaattggatggacggctgccggcaaaatttctcgggatgctgcttgaacttcccggtaccgcgtacagagtgatatggacatcgtgattcggaatttcgtgtattcttgaaaccctt
gcatgacgaatcttatattgaatttgcttatatcaactaaactctgagcatattttcagCATGAATTCATGCTGGCTTGTGTGCTGAGCAGTCAACTATACTGGTCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGACT
CCGGTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTTCGCGGTTTGTAAGGTTTGACTCGAATTTTCCGGTTATGATTTGATTTGTTAGAGGTATTATTAGATCAATCTTTGAATTCGTTGGCTGTTTAAACGAATAAGCCGTCGAAAATTTTGCTTAAACG
Intron 2 GTAACAATCT ... TATATTCCAG
Found issues: Low number of reads
| Sample | Retention score (%) | Exon junction reads | 5'ss reads | 3'ss reads |
| A1 | 100 | 0 | 3 | 4 |
| A2 | 69.23 | 2 | 5 | 4 |
| A3 | 40.74 | 8 | 4 | 7 |
| A4 | 52 | 6 | 6 | 7 |
| A5 | 100 | 0 | 1 | 1 |
| A6 | -1 | 0 | 0 | 0 |
| A7 | 100 | 0 | 1 | 1 |
| A8 | -1 | 0 | 0 | 0 |
| A9 | 80 | 1 | 4 | 4 |
| A10 | 88.24 | 1 | 8 | 7 |
>TRINITY_DN108663_c5_g3_i3 from sample A3 / Example spliced isoformGAGGACTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGTTGGAGTA
ATATTTAATTGGATGGACGGCTGCCGGCAAAATTTCTCGGGATGCTGCTTGAACTTCCCGGTACCGCGTACAGAGTGATATGGACATCGTGATTCGGAATTTCGTGTATTCTTGAAACCCTTGCATGACGAATCTTATATTGAGTTTGCTTATATCAACTAAACTCTGAGCATATTTTCAGCATGAATTCATGCTGGCTT
GTGTGCTGAGCAGTCAACTATACTGGTCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGACTCCGGTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTTCGCGGTTTG
TAAGGTGATCGAGGACGCCGTATTTCTGAGACTCAATGACACCTGAGCGCGATAGGCGGGCGATTAGCGGTGGAGAGTAAAAGACTTACATATATGTTAGTGAAGGTAGGCCTTGCTATCAGTCTCTCGGTTACAGCTTACATATTGACTCACCTGAGATTTAGGCCTGTCAACCGAAAGCTTGTCAAAGGATCGGATGC
TCGGGGAGAATTAGGAAATTCTAACGAGAAGGCTCAAGACAATGTGGAAATTGAGAAAGAAATCTGCTCGTACACAAAAGTGGACTCAACACAGGAAGTTGATGGGGGTGAGGTTAAAACAGTTGATAGCATTAGTCCATCACTGAGCTTGGCCAACGATGAACTTCTCTTGCCAGAGTTTAATGATCTTTTATCAGGAG
AGATGGAGTTTCCTTTGGAAGAGGTTGTTCCATCTTCTAAACCTACACAGTCTGGCGGTGAGGAGAAGCAGGCTAGTACAGTAGATCCTGATATAATGTCTGAGGATTATAAACACATGTACGATGAGGCAATATCAGATAATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGTGAAGAA
AATCTTCAAGGGGAATTGCTGGAATATAAACAC
>TRINITY_DN108663_c5_g3_i1 from sample A3 / Example unspliced isoform:GAGGACTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGgtaacaat
ctgatccatgcttcccacaattaaaaactgtgtgcttcccacaatatttagcagttatggaatatattccagTTGGAGTAATATTTAATTGGATGGACGGCTGCCGGCAAAATTTCTCGGGATGCTGCTTGAACTTCCCGGTACCGCGTACAGAGTGATATGGACATCGTGATTCGGAATTTCGTGTATTCTTGAAACCC
TTGCATGACGAATCTTATATTGAGTTTGCTTATATCAACTAAACTCTGAGCATATTTTCAGCATGAATTCATGCTGGCTTGTGTGCTGAGCAGTCAACTATACTGGTCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGA
CTCCGGTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTTCGCGGTTTGTAAGGTGATCGAGGACGCCGTATTTCTGAGACTCAATGACACCTGAGCGCGATAGGCGGGCGATTAGCGGTGGAGAGTAAAAGACTTACATATATGTTAGTGAAGGTAGGCCTTGCTATC
AGTCTCTCGGTTACAGCTTACATATTGACTCACCTGAGATTTAGGCCTGTCAACCGAAAGCTTGTCAAAGGATCGGATGCTCGGGGAGAATTAGGAAATTCTAACGAGAAGGCTCAAGACAATGTGGAAATTGAGAAAGAAATCTGCTCGTACACAAAAGTGGACTCAACACAGGAAGTTGATGGGGGTGAGGTTAAAAC
AGTTGATAGCATTAGTCCATCACTGAGCTTGGCCAACGATGAACTTCTCTTGCCAGAGTTTAATGATCTTTTATCAGGAGAGATGGAGTTTCCTTTGGAAGAGGTTGTTCCATCTTCTAAACCTACACAGTCTGGCGGTGAGGAGAAGCAGGCTAGTACAGTAGATCCTGATATAATGTCTGAGGATTATAAACACATGT
ACGATGAGGCAATATCAGATAATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGTGAAGAAAATCTTCAAGGGGAATTGCTGGAATATAAACAC
Intron 3 GTAACAATCT ... TGCTGAGCAG
| Sample | Retention score (%) | Exon junction reads | 5'ss reads | 3'ss reads |
| A1 | 100 | 0 | 3 | 8 |
| A2 | 70.37 | 4 | 5 | 14 |
| A3 | 76.47 | 2 | 4 | 9 |
| A4 | 73.91 | 3 | 6 | 11 |
| A5 | 50 | 1 | 1 | 1 |
| A6 | -1 | 0 | 0 | 0 |
| A7 | 100 | 0 | 1 | 3 |
| A8 | 100 | 0 | 0 | 1 |
| A9 | 73.33 | 2 | 4 | 7 |
| A10 | 56.52 | 5 | 8 | 5 |
>TRINITY_DN43156_c0_g3_i3 from sample A10 / Example spliced isoformCTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGTCAACTATACTGG
TCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGACTCCGGTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTTCGCGGTTTGTAAGGTGATCGAGGACGCCGTATTTC
TGAGACTCAATGACACCTGAGCGCGATAGGCGGGCGATTAGCGGTGGAGAGTAAAAGACTTACATATATGTTAGTGAAGGTAGGCCTTGCTATCAGTCTCTCGGTTACAGCTTACATATTGACTCACCTGAGATTTAGGCCTGTCAACCGAAAGCTTGTCAAAGGATCGGATGCTCGGGGAGAATTAGGAAATTCTAACG
AGAAGGCTCAAGACAATGTGGAAATTGAGAAAGAAATCTGCTCGTACACAAAAGTGGACTCAACACAGGAAGTTGATGGGGGTGAGGTTAAAACAGTTGATAGCATTAGTCCATCACTGAGCTTGGCCAACGATGAACTTCTCTTGCCAGAGTTTAATGATCTTTTATCAGGAGAGATGGAGTTTCCTTTGGAAGAGGTT
GTTCCATCTTCTAAACCTACACAGTCTGGCGGTGAGGAGAAGCAGGCTAGTACAGTAGATCCTGATATAATGTCTGAGGATTATAAACACATGTACGATGAGGCAATATCAGATAATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGTGAAGAAAATCTTCAAGGGGAATTGCTGGAATA
TAAACACGTGTACAACGAGGCAATATCAGATGATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGGAAAGAAAATCTTCAAGGGGAATTGCTGGAATATAAACACGTGTACAACGAGGCAATATCAGAT
>TRINITY_DN43156_c0_g3_i1 from sample A10 / Example unspliced isoform:CTCGTGGGTGGAAATTCCGAGACTCAACAAACTCGTTGAATGTGAAAAAACATCGATCTCGGGGATTGAATTCTCAGCTTCAACATTTAAGATTCGACGACCCCACAATTGTGTCGATTTGGTGTGCGATGCTCAGCAAAAAATGGAAGAGCAGAAGCCACCGCGGCGATCCAACATTATGTCAACGgtaacaatctgat
ccatgcttcccacaattaaaaactgtgtgcttcccacaatatttagcagttatggaatatattccagttggagtaatatttaattggatggacggctgccggcaaaatttctcgggatgctgcttgaacttcccggtaccgcgtacagagtgatatggacatcgtgattcggaatttcgtgtattcttgaaacccttgca
tgacgaatcttatattgaatttgcttatatcaactaaactctgagcatattttcagcatgaattcatgctggcttgtgtgctgagcagTCAACTATACTGGTCTATGCAAAATCTGGCCCGAACTTTGTCCAGCTTTTTGAAGGTTCGCTATTCTTCGTTCCGGGAAAAGAAGTTTCGTTGAAGAATTTGATAGACTCCG
GTACCGACGAGAAAACGACACGACACTGGCTTCATAGTTTGGTTTTGGTAATATTGGAACCAGTTTCGCGGTTTGTAAGGTGATCGAGGACGCCGTATTTCTGAGACTCAATGACACCTGAGCGCGATAGGCGGGCGATTAGCGGTGGAGAGTAAAAGACTTACATATATGTTAGTGAAGGTAGGCCTTGCTATCAGTCT
CTCGGTTACAGCTTACATATTGACTCACCTGAGATTTAGGCCTGTCAACCGAAAGCTTGTCAAAGGATCGGATGCTCGGGGAGAATTAGGAAATTCTAACGAGAAGGCTCAAGACAATGTGGAAATTGAGAAAGAAATCTGCTCGTACACAAAAGTGGACTCAACACAGGAAGTTGATGGGGGTGAGGTTAAAACAGTTG
ATAGCATTAGTCCATCACTGAGCTTGGCCAACGATGAACTTCTCTTGCCAGAGTTTAATGATCTTTTATCAGGAGAGATGGAGTTTCCTTTGGAAGAGGTTGTTCCATCTTCTAAACCTACACAGTCTGGCGGTGAGGAGAAGCAGGCTAGTACAGTAGATCCTGATATAATGTCTGAGGATTATAAACACATGTACGAT
GAGGCAATATCAGATAATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGTGAAGAAAATCTTCAAGGGGAATTGCTGGAATATAAACACGTGTACAACGAGGCAATATCAGATGATGCTGCCGAAATTGAGAGATTGAAGAATCTTGTCAACGAATTGCAGAAAAGGGAAGAAAATCTTCA
AGGGGAAATGCTGGAGTATTATGGTCTCATGGAACAGGAAACAAGCATAGTAGAATTACAAAAACAGCTTAAACTAAATGCAGTTGAGATTGAAATGCTCAATTTAAAAATAAATTCTTTGGAAACTCAAAAGAAGATAGTTGAAGAGGAATTAGAGGAATCTTCCCTAGTAAAGAAAGAGCTTGAATTTGCCAGAGCAA
AGATTAAAGAGCTTCAGAGACAGATGCAAATGGAATCTATGCAGACAGAAGAAGAATTTGTTATGCTTAGACAACAAGTTACAGTTCTTCAAGACTCTGAGAAAGTGTTTTCTGAAAATAAATTTGAGATCGAGAAGAAACTGCAGACTTTGAGAGAATTGGAAGTAGAAGTGGTGGAATTAAGAAGGGCCAACAAAGAG
TTGCAACATGAGAAACGGGAGCTGATGCTGAAACTAGACATTACAGAAACCCAAATTGCTTCCCTCTCTCAATTAACAGAGACAGAGACAATTGAAGAGGCAAGAGAAGAGGTGCACACTTTGAGGCATGCGAATGAAGATCTGTTAAAGCAAGTGGAAGGTCTGCAAAATAATCGATTTAGTGAAGTGGAAGAATTGGT
TTATTTGAGATGGGTGAATGCATGTCTACGCTATGAATTAAGGAACTACCAAGCCCCTCCAGGAAAACTGAAAGCACGAGATCTCAACAAAAGCTTGAGCCCAAGGTCACAGGAGAAGGCAAAGCAACTTATGCTAGAATATGCAGGACATGATTCTTTAGCATTGCAGGAGAAAGAGTATACAGATAATGACTCCAAGA
GTCCATCATCCCATACATCCACACCTTCCGAGAGTGGTGATTTTGATGAATTCTCTTTAGACAGTGCCTCTACCAGAATAACTAAATCAAAGAAACCAAGCTTAATTCACAAGCTAAAAAAATGGGGGAGAAGTAAGGAAGATTCTACAGTATCTTCAGTTGGGTCAGCTGGAGACAGAAAAGGAAACGAGGCTATTACA
GGGCACAGAAGTCCATGGCACAAGCATTCTATTTCAGGTAGCTCGTTAGAATTTATAATGCCAAGAAGTTCAAGCAGTGGTGCTTCTGTTGCCTCTTTAACAAGACATGATGGGCCCAAAACAAAGCCAAGGTCGAAATCAAGTAATTTTCTTGAGACACATAATCTTGCAGCAATGGTTGATTCTCCTGAAAAATATAA
GTTTCATACATCAAGAACAACTCTGGAAATGACTGACTCATTAATCAATGTAGCGACTTCATTTCAACTTATGTCAAAGTCTGTGGGAGGCATGAATTGGGGGGAGCATCCCGACTTTAAAGGCAGACATGATTTAGCAATACAGAGAGAGAGTGACATCAAAGAAAAAGCAGAGCAAGCAAGAACAGCAAAGTTTTCTG
AAAAAATGAAAACTGAGGCACTGACTGAAAGGGTTATACCAGAGAAGTTTATAGAAACTCTTCAAATGAGGGGATCTCAAACTGATTCACAAAATGGCAATGATCATCAAGGCAAGGAAACGGAAATTAGCAAAATGACATTTAAAGGAGTACAAAAGAGGGCTCTGAGGGTTGCAAAGAAACCTCCAAAGCCATCCACT
AGTTCTTTGACATGCATTAGTGCTTCATCAAATGCTTCCCATGCTTTACATATCTCCCCACCTCCTCCACCTCAACCCCCTAGTATGACTCCAACTCCACTGACACCGCCCACTGGCCGCCTACTTGAATCTCAAGGCAGAGCAGGAGATAAAGTGCAAAGCATGCCACCACAAGTAGTTGAGTTATATCAATCGCCAGT
GAAAAGAGAAGCACAGAAGGAAATTTCAAATGTGGCATCTACAGTATCAAGCAATATTTCAGATGCTGGTAGTAACATGATTGGAGAATTTGGAGACAAATCTGCATATCTTATATCTGTTAAAGCTGATGTGGAGACTCAAGGTGACTTTGTTCAATCACTGGCAACTGAAGTTAGGGCAGCTTCTTATACGAACATTA
AAGATGTTGTTGACTTTGTGCACTGGTTGGATGAAGAACTATCATTTTTGGTTGACGAGCGTGCTGTTCTTAAGCATTTTGATTGGCCTGAGGGTAAAGCTGATGCTTTGAGGGAAGCAGCATTCGAATATCGGGATTTGCAAAAGTTGGAGTCAGAAGTTGCTTCCTTTGTTGATGATCCCAGACTTTCTTGTGACACA
GCCCTTCATAGGATGTACTCCTTACTTGAATCAGTTGAGAAAAGTATGTATGCCCTTGTACGCACACGAGATATAGTAGTTGCTCGTTATAAAGAGTTCAATATTCCTGTTTACTGGCTTCTTGATTCCGGTCTTGTGGGCAAGATTAAATTTGCTTGTGTTCAACTAGCAAAAAAGTACATGGAACGTGTGGCGTTAGA
GCTAGATGATATTGCAAATATTTCGGAAAACGAACCAGTTAGAGAGTTTCTACTTCTGCAAGGAGTTCGTTTCGCCTTTCGCGTTCACCAGTTTGCTGGAGGTTTTGATGCAGAGAGCATGCGAACATTTGAGGATCTCAGAAGGCGTGCTCAAGAGCAAGCTAGAGAAGTAAACTAAGCAGCTATGACAGATTGAAGTT
TCAGATCCAATCCAATTTTCCTTAAAAATAATATTTGTATCATATTTCAGAAGTCGGTTAGGTTGATCAAAGTCAACCAACCTATTGTATTTAAAATTTTAGTAATTTCACAAAAGATGAAAATATTATGAATGGTAAAACCCTCTCTGATTTAGTATTGGCCG