sp|Q9C950|VIP5_ARATH ----> Protein RTF1 homolog

Intron 1 GTTTTATAAT ... TCCTGTGTAG

Found issues: Low number of reads

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	16.67	5	1	1
A2	100	0	1	0
A3	60	1	1	2
A4	33.33	1	1	0
A5	-1	0	0	0
A6	25	3	2	0
A7	17.65	7	3	0
A8	20	8	4	0
A9	20	6	3	0
A10	75	2	7	5

>TRINITY_DN47890_c0_g2_i9 from sample A7 / Example spliced isoform

AGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAAGTCGGGTATGATCCTTTC
ACTTAGCAGTGGACTCAATCTCAAAATTATTACACTACAAAGGGAAATGTTGCGGAAGACAACATGGGTGCTAACAAAGAGGCAAATGCAGCCAAGGTAGAGGGAGCTACGGCATTGGAAACGACCGAGGATGATGGAAAGCTTGTGGACACTAATGCTCCTATATCTGAAGATGCAGTGGTGTTTTATTTGCATGATTT
TGAACTTCCAATTTCACTTGCTGGACTGTAGAAGTATGGGGGTGCTCAAGGGGCCCATTTAGCTTTTATGGCTAGAA

>TRINITY_DN47890_c0_g2_i8 from sample A7 / Example unspliced isoform:

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGGTATAATCGATATGGTTGGGAGAAATGATCTTTGTTTATGGATCAAAATAACTGCTTACTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGgt
tttataatacctggagggcatggcacctttgagtgaattgcatcctctgatcctgtgtagATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGA

Intron 2 GTAATTCAAA ... CTATTTCTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	80	1	4	4
A2	83.33	1	5	1
A3	80	1	4	0
A4	80	1	4	1
A5	100	0	5	1
A6	83.33	2	10	0
A7	66.67	3	6	1
A8	73.33	4	11	0
A9	50	3	3	1
A10	36.36	7	4	5

>TRINITY_DN47890_c0_g2_i8 from sample A7 / Example spliced isoform

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGGTATAATCGATATGGTTGGGAGAAATGATCTTTGTTTATGGATCAAAATAACTGCTTACTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGGT
TTTATAATACCTGGAGGGCATGGCACCTTTGAGTGAATTGCATCCTCTGATCCTGTGTAGATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGA

>TRINITY_DN47890_c0_g2_i3 from sample A7 / Example unspliced isoform:

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGGTATAATCGATATGGTTGGGAGAAATGATCTTTGTTTATGGATCAAAATAACTGCTTACTACAGAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTC
AGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGgtaattcaaaggtgtattatttatttttatgtgtagtattttagtcagaagtgacagaacagatttgatctccggagtagtaggatgagggatgcatgtagttgtgatcttgtggtactgctcattgattaaatgttgaatttcgatttagt
taatactagcagtagtatcatttattttatgcaacaaagaacctttgtatgtaatactttggaagctttgttaacttgtcttgtgttaggaagagatttaatttatacattccagtaaatactatttctagGTTTTATAATACCTGGAGGGCATGGCACCTTTGAGTGAATTGCATCCTCTGATCCTGTGTAGATATTTT
TTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAGATAACCTTAGATTATTCTCACTGTATGCCATTATTTAGAGGATGCAAATTCAGTATTTATAAAGATCCTTGACATTACTAG

Intron 3 GTAATTCAAA ... TCCTGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	44.44	5	4	4
A2	100	0	5	1
A3	75	1	4	2
A4	71.43	1	4	1
A5	100	0	5	4
A6	66.67	3	10	2
A7	44	7	6	5
A8	44.83	8	11	2
A9	20	6	3	0
A10	77.78	2	4	10

>TRINITY_DN47890_c0_g2_i9 from sample A7 / Example spliced isoform

AGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAAGTCGGGTATGATCCTTTC
ACTTAGCAGTGGACTCAATCTCAAAATTATTACACTACAAAGGGAAATGTTGCGGAAGACAACATGGGTGCTAACAAAGAGGCAAATGCAGCCAAGGTAGAGGGAGCTACGGCATTGGAAACGACCGAGGATGATGGAAAGCTTGTGGACACTAATGCTCCTATATCTGAAGATGCAGTGGTGTTTTATTTGCATGATTT
TGAACTTCCAATTTCACTTGCTGGACTGTAGAAGTATGGGGGTGCTCAAGGGGCCCATTTAGCTTTTATGGCTAGAA

>TRINITY_DN47890_c0_g2_i3 from sample A7 / Example unspliced isoform:

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGGTATAATCGATATGGTTGGGAGAAATGATCTTTGTTTATGGATCAAAATAACTGCTTACTACAGAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTC
AGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGgtaattcaaaggtgtattatttatttttatgtgtagtattttagtcagaagtgacagaacagatttgatctccggagtagtaggatgagggatgcatgtagttgtgatcttgtggtactgctcattgattaaatgttgaatttcgatttagt
taatactagcagtagtatcatttattttatgcaacaaagaacctttgtatgtaatactttggaagctttgttaacttgtcttgtgttaggaagagatttaatttatacattccagtaaatactatttctaggttttataatacctggagggcatggcacctttgagtgaattgcatcctctgatcctgtgtagATATTTT
TTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAGATAACCTTAGATTATTCTCACTGTATGCCATTATTTAGAGGATGCAAATTCAGTATTTATAAAGATCCTTGACATTACTAG

Intron 4 GTGTATTATT ... TCCTGTGTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	36.36	7	4	4
A2	100	0	5	1
A3	80	1	6	2
A4	71.43	1	4	1
A5	83.33	1	6	4
A6	54.55	5	10	2
A7	40.74	8	6	5
A8	42.86	6	7	2
A9	0	6	0	0
A10	63.64	4	4	10

>TRINITY_DN47890_c0_g2_i4 from sample A7 / Example spliced isoform

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGGTATAATCGATATGGTTGGGAGAAATGATCTTTGTTTATGGATCAAAATAACTGCTTACTACAGAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTC
AGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGGTAATTCAAAGATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAAGTCGGGTATGATCCTTTCACTTAGCAGTGGACTCAATCTCAAAATTATTACACTACAAAGGGAAAT
GTTGCGGAAGACAACATGGGTGCTAACAAAGAGGCAAATGCAGCCAAGGTAGAGGGAGCTACGGCATTGGAAACGACCGAGGATGATGGAAAGCTTGTGGACACTAATGCTCCTATATCTGAAGATGCAGTGGTGTTTTATTTGCATGATTTTGAACTTCCAATTTCACTTGCTGGACTGTAGAAGTATGGGGGTGCTCA
AGGGGCCCATTTAGCTTTTATGGCTAGAA

>TRINITY_DN47890_c0_g2_i1 from sample A7 / Example unspliced isoform:

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGGTAATTCAAAGgtgta
ttatttatttttatgtgtagtattttagtcagaagtgacagaacagatttgatctccggagtagtaggatgagggatgcatgtagttgtgatcttgtggtactgctcattgattaaatgttgaatttcgatttagttaatactagcagtagtatcatttattttatgcaacaaagaacctttgtatgtaatactttggaa
gctttgttaacttgtcttgtgttaggaagagatttaatttatacattccagtaaatactatttctaggttttataatacctggagggcatggcacctttgagtgaattgcatcctctgatcctgtgtagATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGG
TGAGATAACCTTAGATTATTCTCACTGTATGCCATTATTTAGAGGATGCAAATTCAGTATTTATAAAGATCCTTGACATTACTAG

Intron 5 GTATAATCGA ... CTTACTACAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	45.45	3	3	2
A2	100	0	11	8
A3	73.33	2	7	4
A4	100	0	0	2
A5	50	2	2	2
A6	51.72	7	4	11
A7	73.33	2	3	8
A8	41.94	9	7	6
A9	62.79	8	10	17
A10	80	2	8	8

>TRINITY_DN47890_c0_g2_i1 from sample A7 / Example spliced isoform

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTCAGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGGTAATTCAAAGGTGTA
TTATTTATTTTTATGTGTAGTATTTTAGTCAGAAGTGACAGAACAGATTTGATCTCCGGAGTAGTAGGATGAGGGATGCATGTAGTTGTGATCTTGTGGTACTGCTCATTGATTAAATGTTGAATTTCGATTTAGTTAATACTAGCAGTAGTATCATTTATTTTATGCAACAAAGAACCTTTGTATGTAATACTTTGGAA
GCTTTGTTAACTTGTCTTGTGTTAGGAAGAGATTTAATTTATACATTCCAGTAAATACTATTTCTAGGTTTTATAATACCTGGAGGGCATGGCACCTTTGAGTGAATTGCATCCTCTGATCCTGTGTAGATATTTTTTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGG
TGAGATAACCTTAGATTATTCTCACTGTATGCCATTATTTAGAGGATGCAAATTCAGTATTTATAAAGATCCTTGACATTACTAG

>TRINITY_DN47890_c0_g2_i3 from sample A7 / Example unspliced isoform:

CGACTCTTTTAAAATTAATTCCATTCCAAGTCTATCAGGAAACTCCACGACATCAGCCTATGGGTTCAAGGCTGCGCTAGGGTTGAGGCAAGCTTCTTTAGGCTTGCTATAATGAACATCACTCCAATCTCCAGCTCGAGGTCCTTAAGGGATGAGACGGCCTCCACAAAATTGTGCAGCAGCAACCTAAAAAGATCTCC
CCAGGCATCATTCTCATGAATAATGACCTAGGGCACAAAATGATAAAGGGCGGATTTGCCTTTGTGGCTGGGCATTCTTACAAGCATTAACACCTTACGAATCGGATGAAACTCATGCCCAAACTTGATGGCTGTCACATAGAGTTGAACATGGATCAGACATCCCTGAGGCCTACAAACCGTTCTCACACTTTTCCCTT
GAAGTGCCACTTCCATACTACTGAGgtataatcgatatggttgggagaaatgatctttgtttatggatcaaaataactgcttactacagAAGATAAAGGATTCCCTCCTCTAAAATAGGTGGTTGTCCTTGATCTACAGAAAGATATAGGATGTCCTCCTCTTGGCTCTGGAATTCAATCATGCAGAAGATTGTCGTTTC
AGATTGGCAAGAACATACTGCTACAGATAGAAGAAGTTATGAGCAGCGGTAATTCAAAGGTGTATTATTTATTTTTATGTGTAGTATTTTAGTCAGAAGTGACAGAACAGATTTGATCTCCGGAGTAGTAGGATGAGGGATGCATGTAGTTGTGATCTTGTGGTACTGCTCATTGATTAAATGTTGAATTTCGATTTAGT
TAATACTAGCAGTAGTATCATTTATTTTATGCAACAAAGAACCTTTGTATGTAATACTTTGGAAGCTTTGTTAACTTGTCTTGTGTTAGGAAGAGATTTAATTTATACATTCCAGTAAATACTATTTCTAGGTTTTATAATACCTGGAGGGCATGGCACCTTTGAGTGAATTGCATCCTCTGATCCTGTGTAGATATTTT
TTCAACAAGAAGATAAGGTAGTCAAGTTGGGAGAAGCATCTAGAATTGATGACACCAATTGAGGTGAGATAACCTTAGATTATTCTCACTGTATGCCATTATTTAGAGGATGCAAATTCAGTATTTATAAAGATCCTTGACATTACTAG