sp|P93735|ELIP1_ARATH ----> Early light-induced protein 1, chloroplastic

Intron 1 GTTTGTAGTA ... GGATCCATAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	22.73	102	30	13
A2	26.85	158	58	7
A3	20.57	112	29	9
A4	28.57	90	36	12
A5	28.38	53	21	9
A6	17.97	817	179	16
A7	17.96	201	44	3
A8	21.12	183	49	4
A9	15.79	288	54	10
A10	18.75	130	30	5

>TRINITY_DN40920_c1_g1_i7 from sample A6 / Example spliced isoform

GCGGTGAATGGATGAGTAGTCGCTACCCTTCTTTATTTCTTACTTGTTACTTGTTACTTGCAGCTTGATCTGTCCACTGTATCGTTACTTTGCAAATAGAAATTAGTCATTCAGTTGAGATGGCCACTGTGATGAATGCATCATTAATGGCGGTGAATGGAGCATCCCTCCTGCAGCGCAGGCCAGCGGCGATTAATATT
GGAGCATCCCTCCAGCAGCGCAGGCCAGCGGAGATGTCAACCGCCTCCAGGGCTCTTCGAGTGAGATGCATGGCAGAGCCCTTAAAGGAGTCAAAGCAATCGCCTCCTACCCCTCCTAAGATGGTGAGCACCAGGTTTGAGGACGTGTTTGCCTTCGCGGGGCCAGCACCGGAGACCATAAATGGGAGACTGGCCATGCT
CGGATTCGTCTCAGCTGTTGGGGTGGAGATTGTGAGCGGGAGAGGCCTCTTTTCTCAGCTCGCCAATGAAGGATTTCCATTGTTTGTTGGAAGCGCGGTTCTGCTGACAGTTGCTTCGGTGATACCCATGTTCAAGGGAATCTCCAAAGAGAGCAAATCAGAAGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCC
GTTATGCCATGCTTGGCCTAGTTGCGTTGGCACTCACTGAATACCTCAAGGGAGGTCCTCTCATCTCATGATCATCATCTGAGAATACACAGGGAGGTCCTCTGTCTGAGAGTAGGATGTAATCATACACAGCTTGTATTTACTCTGCTATCAGGAGATATAATACTGTAACAAATTTTTTTCGCAATGTATATAATGTT
TGAGACGTATATCCGTAATTTCTCTCTCTTTGATTCACATATTTACGTAATAAACATTGAAATG

>TRINITY_DN40920_c1_g1_i12 from sample A6 / Example unspliced isoform:

GCGGTGAATGGATGAGTAGTCGCTACCCTTCTTTATTTCTTACTTGTTACTTGTTACTTGCAGCTTGATCTGTCCACTGTATCGTTACTTTGCAAATAGAAATTAGTCATTCAGTTGAGATGGCCACTGTGATGAATGCATCATTAATGGCGGTGAATGGAGCATCCCTCCTGCAGCGCAGGCCAGCGGCGATTAATATT
GGAGCATCCCTCCAGCAGCGCAGGCCAGCGGAGATGTCAACCGCCTCCAGGGCTCTTCGAGTGAGATGCATGGCAGAGgtttgtagtattgttgctgtttctgtgtatatgtttaaatatattgttgttgtttctgtgcatatgtgtatatgttgctgtttctgtgttagtaatatataaggatcaaatatatttacgac
ttgtgtttgcatgtggatccatagCCCTTAAAGGAGTCAAAGCAATCGCCTCCTACCCCTCCTAAGATGGTAAGCGATTAAGTGCCAATTTTTACCAGAACAACAGAGCAATATGCACTGCCCATTCATTGAAATAATTTGAGCGGACACCATTAATGCAGGTGAGCACCAGGTTTGAGGACGTGTTTGCCTTCGCGGGG
CCAGCACCGGAGACCATAAATGGGAGACTGGCCATGCTCGGATTCGTCTCAGCTGTTGGGGTGGAGATTGTGAGCGGGAGAGGCCTCTTTTCTCAGCTCGCCAATGAAGGATTTCCATTGTTTGTTGGAAGCGCGGTTCTGCTGACAGTTGCTTCGGTGATACCCATGTTCAAGGGAATCTCCAAAGAGAGCAAATCAGA
AGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCCGTTATGCCATGCTTGGCCTAGTTGCGTTGGCACTCACTGAATACCTCAAGGGAGGTCCTCTCATCTCATGATCATCATCTGAGAATACACAGGGAGGTCCTCTGTCTGAGAGTAGGATGTAATCATACACAGCTTGTATTTACTCTGCTATCAGGAGATATA
ATACTGTAACAAATTTTTTTCGCAATGTATATAATGTTTGAGACGTATATCCGTAATTTCTCTCTCTTTGATTCACATATTTACGTAATAAACATTGAAATG

Intron 2 GTAAGCGAAT ... ATTAACTCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.44	5	0	4
A2	0	3	0	0
A3	30	7	0	3
A4	0	1	0	0
A5	36.36	7	0	4
A6	33.33	40	0	20
A7	26.32	14	0	5
A8	15.38	11	0	2
A9	24.39	31	2	10
A10	13.33	13	0	2

>TRINITY_DN39321_c0_g2_i3 from sample A9 / Example spliced isoform

CGCACGATTTCTTCTACTCCTCCTCCTCCTGCCCCTAAAAAGGTTAGCACCAAGTTTGGCGACGTTTTTGCTTTCGGTGGGCCAGCGCCAGAGACCATAAATGGAAGACTGGCCATGCTTGGATTCGTCTCAGCTCTGGCAGTGGAGATTGCTAGTGGGAGGGATATCTTCTCTCAGCTGGCCAGCGGAGGAATTCCACT
GTTTCTTGGAAGTGCGGTTCTGCTGTCAGTTGCTTCGGTGATACCCATGTTGAAGGGAGTCTCCAGAGAGAGCAAATCAAAGGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCCGTTTCGCCATGCTTGGCCTCGTTGCGTTGGCCTTAACTGAATACTTGAAGGGAGGTCCTCTCATCTCATGATGACCAACAA
TTCATACCTCCCTCACAGTATGATGTAATGATAACCAAATTGTATTTACTCTGCTTTCAAGAGAAACACTCTAACAAAAATTTTTGAACATTAACATCATATTTGAGACGTATATTCATAATCTCTGTCACTTTGATTCAGATGTGTGCATAGTAAACATTTAATATATAAGACTGTCTACATTTTTGACAGGCTGATCT
TGA

>TRINITY_DN39321_c0_g2_i8 from sample A9 / Example unspliced isoform:

GCCACAGCCGAAGGACTCTTCCACGCCCTCCACTCACACGATTTCTTCTACTCCTCCCCCTCCTGCCCCTAAAAAGgtaagcgaattggtgcttatctttacatgcggtaagcgaagaagtattcatatgttcatgcactgaaaaataattgctgcattaactcagGTTAGCACCAAGTTTGGCGACGTTTTTGCTTTCG
GTGGGCCAGCGCCAGAGACCATAAATGGAAGACTGGCCATGCTTGGATTCGTCTCAGCTCTGGCAGTGGAGATTGCTAGTGGGAGGGATATCTTCTCTCAGCTGGCCAGCGGAGGAATTCCACTGTTTCTTGGAAGTGCGGTTCTGCTGTCAGTTGCTTCGGTGATACCCATGTTGAAGGGAGTCTCCAGAGAGAGCAAA
TCAAAGGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCCGTTTCGCCATGCTTGGCCTCGTTGCGTTGGCCTTAACTGAATACTTGAAGGGAGGTCCTCTCATCTCATGATGACCAACAATTCATACCTCCCTCACAGTATGATGTAATGATAACCAAATTGTATTTACTCTGCTTTCAAGAGAAACACTCTAACA
AAAATTTTTGAACATTAACATCATATTTGAGACGTATATTCATAATCTCTGTCACTTTGATTCAGATGTGTGCATAGTAAACATTTAATATATAAGACTGTCTACATTTTTGACAGGCTGATCTTGA

Intron 3 GTAAGCGATT ... ATTAATGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	28.41	81	5	31.3
A2	23.4	106.7	5	31.3
A3	22.58	78.3	4	21.3
A4	12.14	60.7	0	8.7
A5	24.03	30.7	5	9
A6	17.14	629.3	10	134.3
A7	18.9	150.7	0	34.7
A8	21.9	131	8	35.7
A9	18.25	233.7	6	51.7
A10	16.32	96.7	8	18.3

>TRINITY_DN40920_c1_g1_i7 from sample A6 / Example spliced isoform

GCGGTGAATGGATGAGTAGTCGCTACCCTTCTTTATTTCTTACTTGTTACTTGTTACTTGCAGCTTGATCTGTCCACTGTATCGTTACTTTGCAAATAGAAATTAGTCATTCAGTTGAGATGGCCACTGTGATGAATGCATCATTAATGGCGGTGAATGGAGCATCCCTCCTGCAGCGCAGGCCAGCGGCGATTAATATT
GGAGCATCCCTCCAGCAGCGCAGGCCAGCGGAGATGTCAACCGCCTCCAGGGCTCTTCGAGTGAGATGCATGGCAGAGCCCTTAAAGGAGTCAAAGCAATCGCCTCCTACCCCTCCTAAGATGGTGAGCACCAGGTTTGAGGACGTGTTTGCCTTCGCGGGGCCAGCACCGGAGACCATAAATGGGAGACTGGCCATGCT
CGGATTCGTCTCAGCTGTTGGGGTGGAGATTGTGAGCGGGAGAGGCCTCTTTTCTCAGCTCGCCAATGAAGGATTTCCATTGTTTGTTGGAAGCGCGGTTCTGCTGACAGTTGCTTCGGTGATACCCATGTTCAAGGGAATCTCCAAAGAGAGCAAATCAGAAGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCC
GTTATGCCATGCTTGGCCTAGTTGCGTTGGCACTCACTGAATACCTCAAGGGAGGTCCTCTCATCTCATGATCATCATCTGAGAATACACAGGGAGGTCCTCTGTCTGAGAGTAGGATGTAATCATACACAGCTTGTATTTACTCTGCTATCAGGAGATATAATACTGTAACAAATTTTTTTCGCAATGTATATAATGTT
TGAGACGTATATCCGTAATTTCTCTCTCTTTGATTCACATATTTACGTAATAAACATTGAAATG

>TRINITY_DN40920_c1_g1_i12 from sample A6 / Example unspliced isoform:

GCGGTGAATGGATGAGTAGTCGCTACCCTTCTTTATTTCTTACTTGTTACTTGTTACTTGCAGCTTGATCTGTCCACTGTATCGTTACTTTGCAAATAGAAATTAGTCATTCAGTTGAGATGGCCACTGTGATGAATGCATCATTAATGGCGGTGAATGGAGCATCCCTCCTGCAGCGCAGGCCAGCGGCGATTAATATT
GGAGCATCCCTCCAGCAGCGCAGGCCAGCGGAGATGTCAACCGCCTCCAGGGCTCTTCGAGTGAGATGCATGGCAGAGGTTTGTAGTATTGTTGCTGTTTCTGTGTATATGTTTAAATATATTGTTGTTGTTTCTGTGCATATGTGTATATGTTGCTGTTTCTGTGTTAGTAATATATAAGGATCAAATATATTTACGAC
TTGTGTTTGCATGTGGATCCATAGCCCTTAAAGGAGTCAAAGCAATCGCCTCCTACCCCTCCTAAGATGgtaagcgattaagtgccaatttttaccagaacaacagagcaatatgcactgcccattcattgaaataatttgagcggacaccattaatgcagGTGAGCACCAGGTTTGAGGACGTGTTTGCCTTCGCGGGG
CCAGCACCGGAGACCATAAATGGGAGACTGGCCATGCTCGGATTCGTCTCAGCTGTTGGGGTGGAGATTGTGAGCGGGAGAGGCCTCTTTTCTCAGCTCGCCAATGAAGGATTTCCATTGTTTGTTGGAAGCGCGGTTCTGCTGACAGTTGCTTCGGTGATACCCATGTTCAAGGGAATCTCCAAAGAGAGCAAATCAGA
AGCAATATGGTCTTCTGGAGCAGAGATGTTGAATGGCCGTTATGCCATGCTTGGCCTAGTTGCGTTGGCACTCACTGAATACCTCAAGGGAGGTCCTCTCATCTCATGATCATCATCTGAGAATACACAGGGAGGTCCTCTGTCTGAGAGTAGGATGTAATCATACACAGCTTGTATTTACTCTGCTATCAGGAGATATA
ATACTGTAACAAATTTTTTTCGCAATGTATATAATGTTTGAGACGTATATCCGTAATTTCTCTCTCTTTGATTCACATATTTACGTAATAAACATTGAAATG