sp|Q9LW77|HRD1A_ARATH ----> ERAD-associated E3 ubiquitin-protein ligase HRD1A

Intron 1 GTAAGAATCT ... TAATGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	11.54	23	3	0
A2	13.89	31	5	1
A3	5.88	32	2	2
A4	17.39	19	4	0
A5	30.77	9	4	2
A6	14.29	96	16	0
A7	15.38	110	20	0
A8	8.67	158	15	0
A9	11.5	100	13	1
A10	10.75	83	10	0

>TRINITY_DN42790_c2_g1_i1 from sample A9 / Example spliced isoform

AGGGCGCAACTTCTTATATGAATGGAGATAAGAGCAAAGGTGCTAGAAGTCATCTGCTTCTTACAAGTGATACTGAGGCTCTGCATTGCTCTATTTGTATGGAGGAATGGACAACTGCAGGGGATCACCGCATATGCTCCCTTGCCTGTGGGCACATGTTTGGCATGTCCTGTATTAGAGAGTGGCTTCAACGACACAAG
AACAATATTGGCAAGTGTCCACAATGCAATATCAAGGCTGAGCTGGGTGACATCAGAATTCTTTATGTGCCAGTTATAGCTCTCACTGGTCAACAATACTGACAGATCAGTTATCTTGGTTGCAATACCCACAGTTTTCGTCATCCTTAGAGCTTCATTCTGCATCTTTGTATGAGTAGGTGATGGATTTAGTATGGCTG
AAGAATTATAAAACTATTGCCAACTGATATTAGTAGTCCTTAACATGCACCCACTAGACCAGTTTGACCAACTGCTATGATTGGCTAGGACTAATCCAAGATTGCAAAAGTCAGCCAAAGATAATTTTTTGAAGGTATTAAAAGGCCACTTCTCCACAGATTCTGTAAATATGTGTTTGGCAAAGAGTAATGGTTTGGTT
CTGACAGAAAAGGAAAACTTGCAAACTCTTTTAATTTCTGTGTTGCTCCATCTTATTTTCTTCTAAATTCTGTATCAGCAACATAATTTTTGTTTATTAATGTCTTGTTGCCAATCAGAAGTGACAGTTTGTTTGGAAAGTTGTTAGTAATATAGTTTTAGAATATGTACCTCAGACAGTCTTCTACATCAGCAGCAGTA
CTCACAGTGTCACAGCAGATCTGGGCACCTTCTTTACAGCAGCAGCAGATCCATACAGCATCCTAATGAGGGCACAGGATCCTAGATCCATTTTCTTTGTACATCCCTTTCCTAGATCGGCTCTCCATCCTTGGAGTTCGCCTTCTGCTATTTAGGTTAGAATCATACTTTTCTTTCTGGATCTCTCTTTTATAGGAGCC
TCCTTAGTGCTCCCACATTGTATTGACATCATGGTACCAAACAGTCCCATTGACCTACTTTTGTGGTCGTTCATTGGAC

>TRINITY_DN42790_c2_g1_i4 from sample A9 / Example unspliced isoform:

AGGGCGCAACTTCTTATATGAATGGAGATAAGAGCAAAGGTGCTAGAAGTCATCTGCTTCTTACAAGTGATACTGAGGCTCTGCATTGCTCTATTTGTATGGAGGAATGGACAACTGCAGGGGATCACCGCATATGCTCCCTTGCCTGTGGGCACATGTTTGGCATGTCCTGTATTAGAGAGTGGCTTCAACGACACAAG
AACAATATTGGCAAGgtaagaatctgcaagctcacaaattgttgttttccatggtgtcatattaattgaactggtaagactataaagttcatgaaaaagatgaaatatttttttatcatttttgttgtactaaatctttgagattataattttttatttctgtaaataatgtgtagTGTCCACAATGCAAT

Intron 2 GTATTAAAAG ... TGTACCTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	76.63	4	8.7	14
A2	77.07	3.7	7	5.3
A3	59.2	6.3	3	14.3
A4	68.04	3.7	6.7	4
A5	68.44	1.3	4.7	1
A6	79.22	9.7	33.3	31
A7	61.99	10.7	23.3	8
A8	78.52	14	51	27.3
A9	78.91	10.3	39.3	22.7
A10	80.04	4.7	17	7

>TRINITY_DN40773_c9_g4_i1 from sample A6 / Example spliced isoform

TGTACCCACTCGATCTGTTTGACCAACTGCCATGATTGGCTAGGACTAATCCAAGATTGCAAAAGTCATCCAAAGATAATTTCTTGAAGACAGTCTCTTACATCAGCAGCAGTACTCACAGTGTCACAGAAGATCTGGGCACCTTCATTACAGCAGCAGCAGATCCATACAACATCATAATGAGGGCACAGAATCCTAGA
TCCATTTTCTTTATACACCCCTTTCCTAAATCGGCTCTCCATCCATGGAGTTCACCTTCTGGTATTTGGGTTAGAATCATACTTTTCTTTCTGCATCTCTCTTTTATAGGAGCTGCCTTAGTGCTCCCACATTGTATTGAGATCATGGTACCAAACAGTCCCACTGACCTACTTTTGTGGTCATTCATTGGACATCAATA
TAATTAATAATTATCTTATCTCATCTTAACTGACAGTTTCTTCTCCTCTCTTGAAAGAA

>TRINITY_DN40773_c9_g4_i2 from sample A6 / Example unspliced isoform:

TGTACCCACTCGATCTGTTTGACCAACTGCCATGATTGGCTAGGACTAATCCAAGATTGCAAAAGTCATCCAAAGATAATTTCTTGAAGgtattaaaaggccactccttctccacagtttctgtaaatatttgtttggcaaagagtaatggttctgacagagaaggaaaacttgcaagctctttcaatttgtcttactcc
atcttatttacttctaaattctgtattagaaacatattttttgtttattaatttcgtgttgccaatcagaagtgacagtttgtttggaaaattcttagtaacacagtgttagaatatgtacctcagACAGTCTCTTACATCAGCAGCAGTACTCACAGTGTCACAGAAGATCTGGGCACCTTCATTACAGCAGCAGCAGA
TCCATACAACATCATAATGAGGGCACAGAATCCTAGATCCATTTTCTTTATACACCCCTTTCCTAAATCGGCTCTCCATCCATGGAGTTCACCTTCTGGTATTTGGGTTAGAATCATACTTTTCTTTCTGCATCTCTCTTTTATAGGAGCTGCCTTAGTGCTCCCACATTGTATTGAGATCATGGTACCAAACAGTCCCA
CTGACCTACTTTTGTGGTCATTCATTGGACATCAATATAATTAATAATTATCTTATCTCATCTTAACTGACAGTTTCTTCTCCTCTCTTGAAAGAA