sp|Q9FJG9|RUG3_ARATH ----> RCC1 domain-containing protein RUG3, mitochondrial

Intron 1 GTAAGACCAC ... TGTGACTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	78.08	8	21	36
A2	77.42	7	19	29
A3	85.19	4	14	32
A4	73.33	8	20	24
A5	72.97	5	8	19
A6	69.47	20	16	75
A7	69.78	21	34	63
A8	75	10	9	51
A9	74.71	22	41	89
A10	82.11	11	38	63

>TRINITY_DN45977_c0_g1_i2 from sample A7 / Example spliced isoform

CTCTCATCCTAAATCATCAACCTAAGGTAAGAAGTCGCTTCATTTATCAAAAAATCATCTGTTAACCTAATTCCCCGTCCTACCAAATGCCCATTCAACCTAGGTCTCTATAACGTGTTACTCTCTGCATCTTCCAAGAACAACCTGTATTGCAGTGCCAATGGCACAAACACCTCAACGCTCCGTAAATGTCTTAGCAA
AGGGAACTGGAAAAATATGAAACCACCCCACTAAATTTCACAATATCACCCAAAGCACGAGGCCACAAAAAAATCCATAAGATACTGATACTCGGAAATTGGAATGCATTGTTTAAGTTAGGTATTGGCGAGGGCTTTTCAAATGGTCCAGAGCGCACATGCCTTGTGCAAATTTGAATAATTCCCTGGCAGGGGGCATA
TGCGAATGGTTCCCTTATGTTACATGCTCTTATATACATATACTCCAAAGAGTTCAGGCAATACGAAGCAATCCCACGTTGAAATTTTGCAACAGATTGATCACAGGGAGCTTTACACGTGGGGAAGAGATGAGGGAGAAGGTAGACTGGGGCTTGGTAGTGAAGGTGGTCCCGATGAAGGTGCACTTGGCACTCCCACA
AGAGTGAAGGAATTACCTGTGCCTGTTGCTGCTATTAGCTGTGGAGGATTTTTTACCTTGGCTTTGACTTCAGAAGGACAGGT

>TRINITY_DN45977_c0_g1_i5 from sample A7 / Example unspliced isoform:

CTCTCATCCTAAATCATCAACCTAAGGTAAGAAGTCGCTTCATTTATCAAAAAATCATCTGTTAACCTAATTCCCCGTCCTACCAAATGCCCATTCAACCTAGGTCTCTATAACGTGTTACTCTCTGCATCTTCCAAGAACAACCTGTATTGCAGTGCCAATGGCACAAACACCTCAACGCTCCGTAAATGTCTTAGCAA
AGGGAACTGGAAAAATATGAAACCACCCCACTAAATTTCACAATATCACCCAAAGCACGAGGCCACAAAAAAATCCATAAGATACTGATACTCGGAAATTGGAATGCATTGTTTAAGTTAGGTATTGGCGAGGGCTTTTCAAATGGTCCAGAGCACACAAGCCTTGTGCAAATTTGAATAATTCCCTGGCAGGGGGCATA
TGCGAATGGTTCCCTTATGTTACATGCTCTTATATACATAGACTCCGAAGAGTTCAGGCAATACGAAGCAATCCCACGTTGAAATTTTGTAACAGATTGATCACAgtaagaccacccaacctgcattctttcgacaaacaaattacccattagagccactacaacatttctttcttttccctttttgcccctcatgttct
aagtgcagtatcagaaatgcagagttccgatgcattcatatttatcatcaatcgaatatattgaatcatagtaaaacaaaatgaacaagatgaagtggaagagcattgggtgttatagtactaggtattttagggcaccccacacagatgggtacccagcatatcgcgtatgtagccagaaaagaaacatttcatcatct
gaagtgtggagtatagtcgacgaggaagatggtcccagaacattggtagagcttctatcatggggaagaggaagtgcagggcagctgggtggtggcgtagaggagacaaggttttatccttgcagggttctgtcaatgactcttccttcaaatttcaggcttgcccccatgcagggccttcttagagaaaaaaatagaaa
cagtatgtcatcagcttctcatgttgtggaattgggtatatcatgtgggctgttccactcagctctgttggttgatggcaagttacatgtctggggaaagggagatggaggcaggcttggccttggcacggagaaaaatatgtatgagcctacactcaattcatatttggatccggtagagagcgttgcattgggaggcc
ttcattctgcagcacttactactcagggagagctctttacttggggatatggaggttttggagcacttggtcattctgtttatcacagggagctcatacctaagcaggttagaaaacattgggaggggaagattgtgtatcttgcaagcagtggagctcatacagctgctatctgtgactcagGGGAGCTTTACACGTGG
GGAAGAGATGAGGGAGAAGGTAGACTGGGGCTTGGTAGTGAAGGTGGTCCCGATGAAGGTGCACTTGGCACTCCCACAAGAGTGAAGGAATTACCTGTGCCTGTTGCTGCTATTAGCTGTGGAGGATTTTTTACCTTGGCTTTGACTTCAGAAGGACAGGTTTGGAGTTGGGGTGGGAACTCAAACTTTGAATTAGGGAG
AGGCACTAGTGGCAGTGACTGGAGACCAAGGCCTATACCTGATCTTGAAGGTGTTCGCATTGTTCAGATAGCATGTGGGGGCTTTCACTCTCTTGCTCTCACTGATGATGGCAAAGTCTTTACTTGGGGACATGGTGGACATGGGCAATTGGGTCATGGTTCTGTTCAATATGGACAGGTTCCACAAATTGTTCAGGCTT
TAGCAGATGAGCATATTGTTTATGTAGCATGTGGAAGTTTATCATCTGCTGTTGTTACTGATTCAGGGAAGTTGTATATGTGGGGGAAAGGTAGAGATCATCAGTTGGGTGTTCCTGGTCTGCCAGATGCACAACTGCTACCTGTCTTGGTAAACTTTCTGGTAGAGAACGAGGAGCTAGGCCCTGCTCATGTTCTTGCT
GTTGCGGCAGGAGCTTCACATGCAATGTGCCTTATCTCAAGGTCTCCTACATGATGTTTTTTTATTTCTGGATAAATGTTTTACATGTCAAGATGGCAGAAAGTGGAGTCACTGTTAGATGGTATGCCTATTTGCACAGAGAACATTTGATTATATGAATATTCCTTGTCCTGAACAAAATCATTATTTGCAATATGATG
GAATCAACTTGATAAAATTTGATGTTGCCTCTAGTAAGATGCAATGTACCAAGATTGGGTTGTATGCCTCACTTGATGTACATGCCGGGTCAGGCACCATAGTCAGCACCAATGGGCTTACACTAGGTACTATCCGCCAAAATGCAGGGAAGTGCCTGGGGTTGACCCTTGAGGTTTTCCTTGAAAATATTAAAAAAATG
TACTCATATTTGAAATTCAATATTGCCAACCAGACAGTTTGCATTAGATTAAAGAATACCCTCGTTGAATTTTAAATAGCCTTCGACTGTAGCCTGAAACCTTGATAATAAGAAACTGTGTTCTAGATCTTAACATGGG

Intron 2 GTTAGAAAAC ... TGTGACTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	73.17	11	24	36
A2	91.49	2	14	29
A3	76.12	8	19	32
A4	73.17	11	36	24
A5	66.04	9	16	19
A6	78.52	16	42	75
A7	62.79	32	45	63
A8	73.68	15	33	51
A9	74.75	25	59	89
A10	88.06	8	55	63

>TRINITY_DN47699_c0_g3_i1 from sample A10 / Example spliced isoform

TTAACCTAAGGTAAGAAGTCGCTTCATTTATCAAAAAATCATCTGTTAACCTAATTCCCCGTCCTACCAAATGCCCATTCAACCTAGGTCTCTATAACGTGTTACTCTCTGCATCTTCCAAGAACAACCTGTATTGCAGTGCCAATGGCACAAACACCTCAACGCTCCGTAAATGTCTTAGCAAAGGAAACTGGAAAAAT
ATGAAACCACCCCACTAAATTTCACAATATCACCCAAAGCACGAGGCCACAAAAAAATCCATAAGATACTGATACTCGGAAATTGGAATGCATTGTTTAAGTTAGGTATTGGCGAGGGCTTTTCAAATGGTCCAGAGCACACAAGCCTTGTGCAAATTTGAATAATTCCCTGGCAGGGGGCATATGCGAATGGTTCCCTT
ATGTTACATGCTCTTATATACATAGACTCCGAAGAGTTCAGGCAATACGAAGCAATCCCACGTTGAAATTTTGTAACAGATTGATCACAGTAAGACCACCCAACCTGCATTCTTTCGACAAACAAATTACCCATTAGAGCCACTACAACATTTCTTTCTTTTCCCTTTTTGCCCCTCATGTTCTAAGTGCAGTATCAGAA
ATGCAGAGTTCCGATGCATTCATATTTATCATCAATCGAATATATTGAATCATAGTAAAACAAAATGAACAAGATGAAGTGGAAGAGCATTGGGTGTTATAGTACTAGGTATTTTAGGGCACCCCACACAGATGGGTACCCAGCATATCGCGTATGTAGCCAGAAAAGAAACATTTCATCATCTGAAGTGTGGAGTATAG
TCGACGAGGAAGATGGTCCCAGAACATTGGTAGAGCTTCTATCATGGGGAAGAGGAAGTGCAGGGCAGCTGGGTGGTGGCGTAGAGGAGACAAGGTTTTATCCTTGCAGGGTTCTGTCAATGACTCTTCCTTCAAATTTCAGGCTTGCCCCCATGCAGGGCCTTCTTAGAGAAAAAAATAGAAACAGTATGTCATCAGCT
TCTCATGTTGTGGAATTGGGTATATCATGTGGGCTGTTCCACTCAGCTCTGTTGGTTGATGGCAAGTTACATGTCTGGGGAAAGGGAGATGGAGGCAGGCTTGGCCTTGGCACGGAGAAAACTATGTATGAGCCTACACTCAATTCATATTTGGATCCGGTAGAGAGCGTTGCATTGGGAGGCCTTCATTCTGCAGCACT
TACTACTCAGGGAGAGCTCTTTACTTGGGGATATGGAGGTTTTGGAGCACTTGGTCATTCTGTTTATCACAGGGAGCTCATACCTAAGCAGGGGAGCTTTACACGTGGGGAAGAGATGAGGGAGAAGGTAGACTGGGGCTTGGTAGTGAAGGTGGTCCCGATGAAGGTGCACTTGGCACTCCCACAAGAGTGAAGGAATT
ACCTGTGCCTGTTGCTGCTATTAGCTGTGGAGGATTTTTTACCTTGGCTTTGACTTCAGAAGGACAGGTGTGGAGTTGGGGTGGTAAGATGCTCAGCCTTCTGTAAGGCTCCCCTTATGAGCTAATCATTGTTGATTCAATGTCTGTTTTCTTGAAAGGATTTATAGTACTGTTTTGACAAAGATACTTTACTGTAATAA
GTTTACCTTTTCTAAGCAGGATATACAGTTCTGTTTTGTCCCCATCTATTTACCGTTTTCTTTGCTCTTCTGGGCATGGATTGTTTGCTTGATGTGTACTAAAGCAATGTAACTTGAAAGAAATGTGTTAGCTGCTTGAAGTGTT

>TRINITY_DN47699_c0_g3_i3 from sample A10 / Example unspliced isoform:

TTAACCTAAGGTAAGAAGTCGCTTCATTTATCAAAAAATCATCTGTTAACCTAATTCCCCGTCCTACCAAATGCCCATTCAACCTAGGTCTCTATAACGTGTTACTCTCTGCATCTTCCAAGAACAACCTGTATTGCAGTGCCAATGGCACAAACACCTCAACGCTCCGTAAATGTCTTAGCAAAGGAAACTGGAAAAAT
ATGAAACCACCCCACTAAATTTCACAATATCACCCAAAGCACGAGGCCACAAAAAAATCCATAAGATACTGATACTCGGAAATTGGAATGCATTGTTTAAGTTAGGTATTGGCGAGGGCTTTTCAAATGGTCCAGAGCACACAAGCCTTGTGCAAATTTGAATAATTCCCTGGCAGGGGGCATATGCGAATGGTTCCCTT
ATGTTACATGCTCTTATATACATAGACTCCGAAGAGTTCAGGCAATACGAAGCAATCCCACGTTGAAATTTTGTAACAGATTGATCACAGTAAGACCACCCAACCTGCATTCTTTCGACAAACAAATTACCCATTAGAGCCACTACAACATTTCTTTCTTTTCCCTTTTTGCCCCTCATGTTCTAAGTGCAGTATCAGAA
ATGCAGAGTTCCGATGCATTCATATTTATCATCAATCGAATATATTGAATCATAGTAAAACAAAATGAACAAGATGAAGTGGAAGAGCATTGGGTGTTATAGTACTAGGTATTTTAGGGCACCCCACACAGATGGGTACCCAGCATATCGCGTATGTAGCCAGAAAAGAAACATTTCATCATCTGAAGTGTGGAGTATAG
TCGACGAGGAAGATGGTCCCAGAACATTGGTAGAGCTTCTATCATGGGGAAGAGGAAGTGCAGGGCAGCTGGGTGGTGGCGTAGAGGAGACAAGGTTTTATCCTTGCAGGGTTCTGTCAATGACTCTTCCTTCAAATTTCAGGCTTGCCCCCATGCAGGGCCTTCTTAGAGAAAAAAATAGAAACAGTATGTCATCAGCT
TCTCATGTTGTGGAATTGGGTATATCATGTGGGCTGTTCCACTCAGCTCTGTTGGTTGATGGCAAGTTACATGTCTGGGGAAAGGGAGATGGAGGCAGGCTTGGCCTTGGCACGGAGAAAACTATGTATGAGCCTACACTCAATTCATATTTGGATCCGGTAGAGAGCGTTGCATTGGGAGGCCTTCATTCTGCAGCACT
TACTACTCAGGGAGAGCTCTTTACTTGGGGATATGGAGGTTTTGGAGCACTTGGTCATTCTGTTTATCACAGGGAGCTCATACCTAAGCAGgttagaaaacattgggaggggaagattgtgtatcttgcaagcagtggagctcatacagctgctatctgtgactcagGGGAGCTTTACACGTGGGGAAGAGATGAGGGAG
AAGGTAGACTGGGGCTTGGTAGTGAAGGTGGTCCCGATGAAGGTGCACTTGGCACTCCCACAAGAGTGAAGGAATTACCTGTGCCTGTTGCTGCTATTAGCTGTGGAGGATTTTTTACCTTGGCTTTGACTTCAGAAGGACAGGTTTGGAGTTGGGGTGGGAACTCAAACTTTGAATTAGGGAGAGGCACTAGTGGCAGT
GACTGGAGACCAAGGCCTATACCTGATCTTGAAGGTGTTCGCATTGTTCAGATAGCATGTGGGGGCTTTCACTCTCTTGCTCTCACTGATGATGGCAAAGTCTTTACTTGGGGACATGGTGGACATGGGCAATTGGGTCATGGTTCTGTTCAATATGGACAGGTTCCACAAATTGTTCAGGCTTTAGCAGATGAGCATAT
TGTTTATGTAGCATGTGGAAGTTTATCATCTGCTGTTGTTACTGATTCAGGGAAGTTGTATATGTGGGGGAAAGGTAGAGATCATCAGTTGGGCGTTCCTGGTCTGCCAGATGCACAACTGCTACCTGTCTTGGTAAACTTTCTGGTAGAGAACGAGGAGCTAGGCCCTGCACATGTTCTTGCTGTTGCGGCAGGAGCTT
CACATGCAATGTGCCTTATCTCAAGGTCTCCTACATGATGTTTTTTTATTTCTGGATAAATGTTTTACATGTCAAGATGGCAGAAAGTGGAGTCACTGTTAGATGGTATGCCTATTTGCACAGAGAACATTTGATTATATGAATATTCCTTGTCCTGAACAAAATCATTATTTGCAATATGATGGAATCAACTTGATAAA
ATTTGATGTTGCCTCTTGTAAGATGCAATGTACCAAGATTGGGTTGTATGCCTCACTTGATGTACATGCCGGGTCAGGCACCATAGTCAGCACCAATGGGCTTACACTAGGTACTATCCGCCAAAATGCAGGGAAGTGCCTGGGGTTGACCCTTGAGGTTTTCCTTGAAAATATTAAAAAAATGTACTCATATTTGAAAT
TCAATATTGCCAACCAGACAGTTTGCATTAGATTAAAGAATACCCTCGTTGAATTTTAAATAGCCTTCGACTGTAGCCTGAAACCTTGATAATAAGAAACTGTGTTCTAGATCTTAAC