sp|Q8LL04|CPL3_ARATH ----> RNA polymerase II C-terminal domain phosphatase-like 3

Intron 1 GTGAGGGTTT ... TATGTTATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	52.94	4	6	3
A2	35	13	3	11
A3	44	7	3	8
A4	36.84	6	4	3
A5	33.33	6	1	5
A6	45.45	3	1	4
A7	22.22	7	0	4
A8	11.11	4	0	1
A9	33.33	3	1	2
A10	20	8	0	4

>TRINITY_DN109248_c8_g1_i5 from sample A3 / Example spliced isoform

ATTCAGAATCTCTTCTCCAGTAGCAGTCATGTTTTGCTTGCTGCAGAGCCACTAGAAGGAAGCTTCTTTGTTGGAGATGTGGGTATCAATTCGATTTCACATTACAGGCCATGGCAGCATCCTGAAAAACCTAGTCAGTTACAACTACATATCCCAACCAAAGAGCAGTTTACTCGTTCTGATTCTCTGAGCTCATTCGA
CCAAGGAAAGGGAAAATGGGATACCAGTAGAAGCACTATAGTAACTTCTGAACCTGTTAAATGCTGGTCTAAGGTAGCTATGCCTTATACTGGCCTGCCAATATCCATGTCTGACCATGCTTGTTGGCCTGAAAACAGTATTTTTGCTTCACTATCTAGTGATGTGGTTGAAATATCGAAAATAGGTATTTATGAAGATT
CAACAAAATTCAAGAAATACAACAATAATTCTGAGGGAAGGGACGCCACACTCAAAAGAAATCAGAATGATATGGGCTCTAATAAAAGACAGAAAACTGTGTCATGTTATATGCCAAGCATGTGGCATAGTCCTGTCGCTGAAATTGATAAAGGGATGGTTGATAATCAATGTTTCGAGATGCGGTTTTCAGATGTGGAA
CAAAGAAGACAGAGAAGAGAGGTTCCTAATGGCACCAAGATTGAAAATTTTGAGATCTCAGTAAAACACAGTTCAATGGAGCAAGGAAGTAATGTATCCTGTCCTCCAGTTAGCAGAGATATCTGCATGACTCTTGGCGAATTGACCACAACCTCAGTAGTGCCAACAGTCCAAGAGCAGTCCTTGTCTAATACTGCTCC
ATACTTTACAGAAAAGAGTCTGAGCATGGCAAAAGGGTTGGGATACTCTCATTTCAACTTGCCCATACTGACTCCTGAGTTTGGGAGAGCAAAGGAGGATCCCCAACTTTTGGTTGGCCAGTCAAACAGAGACAGCAAAACAATTGAAGGATCCCAAATTTTATTTAGGAATAAAAGGGATGGTAATCTGGCAGTAAATG
ATCCTGGCATTATTAATCTCCCTTCCGTGCAGTGCTTGCCAGATCCATATACAATGAATTGTACAACAGATTTGGATAGTTCTTTTGTTACCAAGGACCATTTATTTGAAGGATTGAATGAGAAACAAAGAACTGCTATTCAGCAAGAAACAAGGAGAATCAAAGAACGGAACAAAATGTTCAATGCAAGAAAGCTCAGC
CTTGTGCTGGATCTTGATCATACTCTTCTCAATTCAGCTATGTTCTCAGATATTGAGCCAGTTCATGAAGAAATGTTAAAGATAAAAGAGGAGAAAGATCAAGAGAGTCCTCATCGTCATCTTTTTCACTTACCAAACATCAGAATGTGGACAAAATTGCGGCCAGGGATTTGGCAGTTTTTGGATAGGGCAAGCAAGTT
GTATGAATTACATGTTTACACAATGGGTAGCAGAGTCTATGCCACAGAGATGACGAAAATTCTCGATCCTACAGGAAAACTATTTGCAGGACGTGTTATTTCTAAGGGTGATGAGGCTGATGTAGGTGGATTTGGAATATCTTCCAAAAGCAAAGACTTGGATGGGGTAATGGGTATGGAGTCTTCAGCAATTGTTATTG
ATGATACCGAGAAGATGTGGCCTCATCACAGGCCCAATTTGATTGTGGTTGAGAGGTATACATACTTCCCATGTAGTAGACGCCAATTTGGACTGGCAGGGCCCTCTCTGTTTGAGATTGATCATGATGAGGGGCCAGAAGATGGAATGTTGGCATCTACTTTACGGGTTATTGAAGAAATACACAATGATTTTTTCTCA
AAGAAACTGTTATTTGAAGTAGATGTCCGTGATCTTTTGGCAACTAAACAACACAGGGTTCTTATGGGTTGCAGAATAGTTTTCAGTAGGGTTTTTCCTATGGAAGAAGCCCAACCCCATCT

>TRINITY_DN109248_c8_g1_i2 from sample A3 / Example unspliced isoform:

ATTCAGAATCTCTTCTCCAGTAGCAGTCATGTTTTGCTTGCTGCAGAGCCACTAGAAGGAAGCTTCTTTGTTGGAGATGTGGGTATCAATTCGATTTCACATTACAGGCCATGGCAGCATCCTGAAAAACCTAGTCAGTTACAACTACATATCCCAACCAAAGAGCAGTTTACTCGTTCTGATTCTCTGAGCTCATTCGA
CCAAGGAAAGGGAAAATGGGATACCAGTAGAAGCACTATAGTAACTTCTGAACCTGTTAAATGCTGGTCTAAGGTAGCTATGCCTTATACTGGCCTGCCAATATCCATGTCTGACCATGCTTGTTGGCCTGAAAACAGTATTTTTGCTTCACTATCTAGTGATGTGGTTGAAATATCGAAAATAGGTATTTATGAAGATT
CAACAAAATTCAAGAAATACAACAATAATTCTGAGGGAAGGGACGCCACACTCAAAAGAAATCAGAATGATATGGGCTCTAATAAAAGACAGAAAACTGTGTCATGTTATATGCCAAGCATGTGGCATAGTCCTGTCGCTGAAATTGATAAAGGGATGGTTGATAATCAATGTTTCGAGATGCGGTTTTCAGATGTGGAA
CAAAGAAGACAGAGAAGAGAGGTTCCTAATGGCACCAAGATTGAAAATTTTGAGATCTCAGTAAAACACAGTTCAATGGAGCAAGGAAGTAATGTATCCTGTCCTCCAGTTAGCAGAGATATCTGCATGACTCTTGGCGAATTGACCACAACCTCAGTAGTGCCAACAGTCCAAGAGCAGTCCTTGTCTAATACTGCTCC
ATACTTTACAGAAAAGAGTCTGAGCATGGCAAAAGGGTTGGGATACTCTCATTTCAACTTGCCCATACTGACTCCTGAGTTTGGGAGAGCAAAGGAGGATCCCCAACTTTTGGTTGGCCAGTCAAACAGAGACAGCAAAACAATTGAAGGATCCCAAATTTTATTTAGGAATAAAAGGGATGGTAATCTGGCAGTAAATG
ATCCTGGCATTATTAATCTCCCTTCCGTGCAGTGCTTGCCAGATCCATATACAATGAATTGTACAACAGATTTGGATAGTTCTTTTGTTACCAAGGACCATTTATTTGAAGGATTGAATGAGAAACAAAGAACTGCTATTCAGCAAGAAACAAGGAGAATCAAAGAACGGAACAAAATGTTCAATGCAAGAAAGCTCAGC
CTTGTGCTGGATCTTGATCATACTCTTCTCAATTCAGCTATGTTCTCAGATATTGAGCCAGTTCATGAAGAAATGTTAAAGATAAAAGAGGAGAAAGATCAAGAGAGTCCTCATCGTCATCTTTTTCACTTACCAAACATCAGAATGTGGACAAAATTGCGGCCAGGGATTTGGCAGTTTTTGGATAGGgtgagggtttt
gttgattaaaaaataaactagaaagaaccaaaggctccagcagcatgctactatagtttctttctattcctgttatattttcaacgagacattttaaattttctagatagggttggcatttgctggattggaactctttggaatcaagcaacaggttgtctgtcatcttgcagtgtgaacatgttttgcttacagtcttt
ttattattgttgtgtatgttatagGCAAGCAAGTTGTATGAATTACATGTTTACACAATGGGTAGCAGAGTCTATGCCACAGAGATGACGAAAATTCTCGATCCTACAGGAAAACTATTTGCAGGACGTGTTATTTCTAAGGGTGATGAGGCTGATGTAGGTGGATTTGGAATATCTTCCAAAAGCAAAGACTTGGATGG
GGTAATGGGTATGGAGTCTTCAGCAATTGTTATTGATGATACCGAGAAGATGTGGCCTCATCACAGGCCCAATTTGATTGTGGTTGAGAGGTAGAAGTTGAGCTCAAAATATTTATGGTTCATTTTTGCTCTCAAGGTCCTTGGCAATACTGTTTTTGATTCTTACAAATGAGAAGCTGTGATGTACAGGTATACATACT
TCCC

Intron 2 GTAGAAGTTG ... TGATGTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	50	4	4	1
A2	14.29	12	2	0
A3	37.5	10	6	3
A4	0	7	0	0
A5	33.33	12	6	0
A6	-1	0	0	0
A7	12.5	7	1	0
A8	26.67	11	4	0
A9	20	8	2	0
A10	40	3	2	0

>TRINITY_DN109248_c8_g1_i5 from sample A3 / Example spliced isoform

ATTCAGAATCTCTTCTCCAGTAGCAGTCATGTTTTGCTTGCTGCAGAGCCACTAGAAGGAAGCTTCTTTGTTGGAGATGTGGGTATCAATTCGATTTCACATTACAGGCCATGGCAGCATCCTGAAAAACCTAGTCAGTTACAACTACATATCCCAACCAAAGAGCAGTTTACTCGTTCTGATTCTCTGAGCTCATTCGA
CCAAGGAAAGGGAAAATGGGATACCAGTAGAAGCACTATAGTAACTTCTGAACCTGTTAAATGCTGGTCTAAGGTAGCTATGCCTTATACTGGCCTGCCAATATCCATGTCTGACCATGCTTGTTGGCCTGAAAACAGTATTTTTGCTTCACTATCTAGTGATGTGGTTGAAATATCGAAAATAGGTATTTATGAAGATT
CAACAAAATTCAAGAAATACAACAATAATTCTGAGGGAAGGGACGCCACACTCAAAAGAAATCAGAATGATATGGGCTCTAATAAAAGACAGAAAACTGTGTCATGTTATATGCCAAGCATGTGGCATAGTCCTGTCGCTGAAATTGATAAAGGGATGGTTGATAATCAATGTTTCGAGATGCGGTTTTCAGATGTGGAA
CAAAGAAGACAGAGAAGAGAGGTTCCTAATGGCACCAAGATTGAAAATTTTGAGATCTCAGTAAAACACAGTTCAATGGAGCAAGGAAGTAATGTATCCTGTCCTCCAGTTAGCAGAGATATCTGCATGACTCTTGGCGAATTGACCACAACCTCAGTAGTGCCAACAGTCCAAGAGCAGTCCTTGTCTAATACTGCTCC
ATACTTTACAGAAAAGAGTCTGAGCATGGCAAAAGGGTTGGGATACTCTCATTTCAACTTGCCCATACTGACTCCTGAGTTTGGGAGAGCAAAGGAGGATCCCCAACTTTTGGTTGGCCAGTCAAACAGAGACAGCAAAACAATTGAAGGATCCCAAATTTTATTTAGGAATAAAAGGGATGGTAATCTGGCAGTAAATG
ATCCTGGCATTATTAATCTCCCTTCCGTGCAGTGCTTGCCAGATCCATATACAATGAATTGTACAACAGATTTGGATAGTTCTTTTGTTACCAAGGACCATTTATTTGAAGGATTGAATGAGAAACAAAGAACTGCTATTCAGCAAGAAACAAGGAGAATCAAAGAACGGAACAAAATGTTCAATGCAAGAAAGCTCAGC
CTTGTGCTGGATCTTGATCATACTCTTCTCAATTCAGCTATGTTCTCAGATATTGAGCCAGTTCATGAAGAAATGTTAAAGATAAAAGAGGAGAAAGATCAAGAGAGTCCTCATCGTCATCTTTTTCACTTACCAAACATCAGAATGTGGACAAAATTGCGGCCAGGGATTTGGCAGTTTTTGGATAGGGCAAGCAAGTT
GTATGAATTACATGTTTACACAATGGGTAGCAGAGTCTATGCCACAGAGATGACGAAAATTCTCGATCCTACAGGAAAACTATTTGCAGGACGTGTTATTTCTAAGGGTGATGAGGCTGATGTAGGTGGATTTGGAATATCTTCCAAAAGCAAAGACTTGGATGGGGTAATGGGTATGGAGTCTTCAGCAATTGTTATTG
ATGATACCGAGAAGATGTGGCCTCATCACAGGCCCAATTTGATTGTGGTTGAGAGGTATACATACTTCCCATGTAGTAGACGCCAATTTGGACTGGCAGGGCCCTCTCTGTTTGAGATTGATCATGATGAGGGGCCAGAAGATGGAATGTTGGCATCTACTTTACGGGTTATTGAAGAAATACACAATGATTTTTTCTCA
AAGAAACTGTTATTTGAAGTAGATGTCCGTGATCTTTTGGCAACTAAACAACACAGGGTTCTTATGGGTTGCAGAATAGTTTTCAGTAGGGTTTTTCCTATGGAAGAAGCCCAACCCCATCT

>TRINITY_DN109248_c8_g1_i2 from sample A3 / Example unspliced isoform:

ATTCAGAATCTCTTCTCCAGTAGCAGTCATGTTTTGCTTGCTGCAGAGCCACTAGAAGGAAGCTTCTTTGTTGGAGATGTGGGTATCAATTCGATTTCACATTACAGGCCATGGCAGCATCCTGAAAAACCTAGTCAGTTACAACTACATATCCCAACCAAAGAGCAGTTTACTCGTTCTGATTCTCTGAGCTCATTCGA
CCAAGGAAAGGGAAAATGGGATACCAGTAGAAGCACTATAGTAACTTCTGAACCTGTTAAATGCTGGTCTAAGGTAGCTATGCCTTATACTGGCCTGCCAATATCCATGTCTGACCATGCTTGTTGGCCTGAAAACAGTATTTTTGCTTCACTATCTAGTGATGTGGTTGAAATATCGAAAATAGGTATTTATGAAGATT
CAACAAAATTCAAGAAATACAACAATAATTCTGAGGGAAGGGACGCCACACTCAAAAGAAATCAGAATGATATGGGCTCTAATAAAAGACAGAAAACTGTGTCATGTTATATGCCAAGCATGTGGCATAGTCCTGTCGCTGAAATTGATAAAGGGATGGTTGATAATCAATGTTTCGAGATGCGGTTTTCAGATGTGGAA
CAAAGAAGACAGAGAAGAGAGGTTCCTAATGGCACCAAGATTGAAAATTTTGAGATCTCAGTAAAACACAGTTCAATGGAGCAAGGAAGTAATGTATCCTGTCCTCCAGTTAGCAGAGATATCTGCATGACTCTTGGCGAATTGACCACAACCTCAGTAGTGCCAACAGTCCAAGAGCAGTCCTTGTCTAATACTGCTCC
ATACTTTACAGAAAAGAGTCTGAGCATGGCAAAAGGGTTGGGATACTCTCATTTCAACTTGCCCATACTGACTCCTGAGTTTGGGAGAGCAAAGGAGGATCCCCAACTTTTGGTTGGCCAGTCAAACAGAGACAGCAAAACAATTGAAGGATCCCAAATTTTATTTAGGAATAAAAGGGATGGTAATCTGGCAGTAAATG
ATCCTGGCATTATTAATCTCCCTTCCGTGCAGTGCTTGCCAGATCCATATACAATGAATTGTACAACAGATTTGGATAGTTCTTTTGTTACCAAGGACCATTTATTTGAAGGATTGAATGAGAAACAAAGAACTGCTATTCAGCAAGAAACAAGGAGAATCAAAGAACGGAACAAAATGTTCAATGCAAGAAAGCTCAGC
CTTGTGCTGGATCTTGATCATACTCTTCTCAATTCAGCTATGTTCTCAGATATTGAGCCAGTTCATGAAGAAATGTTAAAGATAAAAGAGGAGAAAGATCAAGAGAGTCCTCATCGTCATCTTTTTCACTTACCAAACATCAGAATGTGGACAAAATTGCGGCCAGGGATTTGGCAGTTTTTGGATAGGGTGAGGGTTTT
GTTGATTAAAAAATAAACTAGAAAGAACCAAAGGCTCCAGCAGCATGCTACTATAGTTTCTTTCTATTCCTGTTATATTTTCAACGAGACATTTTAAATTTTCTAGATAGGGTTGGCATTTGCTGGATTGGAACTCTTTGGAATCAAGCAACAGGTTGTCTGTCATCTTGCAGTGTGAACATGTTTTGCTTACAGTCTTT
TTATTATTGTTGTGTATGTTATAGGCAAGCAAGTTGTATGAATTACATGTTTACACAATGGGTAGCAGAGTCTATGCCACAGAGATGACGAAAATTCTCGATCCTACAGGAAAACTATTTGCAGGACGTGTTATTTCTAAGGGTGATGAGGCTGATGTAGGTGGATTTGGAATATCTTCCAAAAGCAAAGACTTGGATGG
GGTAATGGGTATGGAGTCTTCAGCAATTGTTATTGATGATACCGAGAAGATGTGGCCTCATCACAGGCCCAATTTGATTGTGGTTGAGAGgtagaagttgagctcaaaatatttatggttcatttttgctctcaaggtccttggcaatactgtttttgattcttacaaatgagaagctgtgatgtacagGTATACATACT
TCCC