sp|A2Z1U1|HOX11_ORYSI ----> Homeobox-leucine zipper protein HOX11

Intron 1 GTAAGACTTG ... TCTTTTGCAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	13.37	175	14.3	27
A2	20.59	81	11	21
A3	16.88	128	8.7	26
A4	21.84	68	5	19
A5	15.25	50	3	9
A6	14	467	23.7	76
A7	13.89	533	34	86
A8	16.32	518	29	101
A9	14.78	444	26	77
A10	14.57	516	28.3	88

>TRINITY_DN48349_c2_g4_i1 from sample A7 / Example spliced isoform

GTTTTCATCATTGCTCTTCCACCACCCATGCTGACTTAATTATATTGCTCCCGACTCCTAATCATTCTTGCTAAGCTCAATTTGAACTTTCATATATTATATATTTTATGTATATATCCATCACAAATATATATGCACTAGTCAAGCCATCGAACTTTCAAGCGCGCGTGCATCTACAGCACCCCACATGATGAGAGGAT
ATGCCCATCAATGATGATCTTATTAACTTGCTCAGATTCTTGAGAGCCTCAGCCTCCTGCCTTCCTTATTTCTTGAGCTCTAAGCCGTGTTCTTCAAGTTGAGAGAGGGTTTCAGCCTTCAGGAGCTTGGACTGTTTGTTTGGCTTCTTGCGCTGGAATTAATTAGGTTTTGACTATTTTCCAGCGAAGTGTCTTCCACG
TTTATACGACTGGCCTGCTTGACTTTCATCATCCCTGACGTCTGGGAGCCAAGATAAATCTCCGGGTGCACTTGTGTGTGAAGAATCAGATTATTCATGGAAGAGATGAAGAACAAGCAGAGAGGTCTCGAGTGGCTGAAGACTATGGCTAACGATGAAGCGATGGGGTTGGCTCTTGGCGTTGGTGTGTCTATGGCGAT
GCCCGCCACAGCTTTGCGCGAAGACGATCAGAAAAACGCGCCGCTGCAGATCGAACCGCTGACCTTTCGCCCCATTGCTGCTCGCGTCGGGGCTGCTCCGGCTCCCTCGGCGCCGTTTCTTTGGTTCATGCCCAAGAACTGCCGGGAAGAGGTAACGGTCGCGGAGACGAATCCGTCCGAGGTTGTGCGTGGAGGGATAG
ACATGAATCAGGTTCCGTCGTCCAATGAATCTGAGTATTCGTCGGTTTTACAGGCTGATGGCTTGCGGGCTGTGGACAACGGTCCGATGGCGGTGAAGAGAGAACGAGAAAGAGCTTTTGATTTGGAGGCTGAGAGGGATCGAACCTGCGACGTGAGTTCGAGGACTAGCGACGAGGAAGAGATAGGTTCGACGAGGAAA
AAGCTGCGGCTTTCCAAAGAGCAATCTGCACTGCTGGAGGAAAGTTTCTTGGAGCACAGCACTCTGAATCCGCAGAAACAGAAAAACGCTCTGGCCAAGGCGTTGAACTTGCAACCCCGGCAGGTTGAAGTCTGGTTTCAGAACAGAAGAGCACGAACAAAGTTGAAGCAGACAGAAGTAGACTGCGAGGTTTTGAAGCG
GTGCTGCGAGAATCTAACGGAGGAGAACAGAAGGCTACAGAAAGAGTTGCAAGAGCTTAGGGCATTGAAGGCGGTTCCTCCTCAGTGCGTTATAGGACCGGATAATTACTACATGCCTCTGCCTGCCACCACACTCACCATGTGTCCTTCCTGTGAAAGGGTGGCTACCATGGAAAACGGCCGAAGCCTTCCATTTTCCA
AGTCCCGGATTTCACAGTTTGCCCAACAGTCTGCAGCCTGCTAACTTTTTGTTGGGTTCATTGGGCAAGACTGGGCTTGCAAGCTTGTCCATGTAATATCATTGCTCAGTGGTCGTTTTTTTTTAGATTTCTGAGAGATTTCGCTCCCTTTGAAAAGCCAAAAACACATATTACACACTACATATATCACCATCTAACCC
TTTGTGTTTTGCAAAGTAATTTCTCTGTTGTGCTAATTCACAGCGATATTGGGCAACCCAAGATGTGTAATCTGATCTTTGAAGGATCAAACGCCCTTTACTTTACTGATGTACTTCTCAGGGAAATGATATGGCGATTCATAAACGCCCATGGTAGTTTCTCTGCAAACAAGAACACCGGGTTGAATACATAATGTAAT
ATCTCTTGTTAAAGATAAAATTATAGCTCCTTGCCAGGAAAAGTAGCTCAACACGTTCAGGAACGACTGTGTCAGTTCTGAGTTCTGGTTGCTTTTATTTATTTCTCCATCTCAGATTTCAATTTCATTGTCAACTTTTCCAAAGCTGGTGTTAAATTGACAGGCTCTTTGTATGTACAATTTTTGTAACTTCAAAATTT
TGAACATGTTGACAGGTCTGTCATAAAACGTATTTAAAACATTTCTAAAACTGCACAATACCCCATTTTGAAAAATCCCTACAACGCTCTCAAGTACATGTCTATAATCATTCACCTCGAAACAGGTCAATAGATAGAAGTCTGAAGAAACTCTTGTACATTTATTATGCATAACAAATGGATAGATAGAAATCTGAAGA
AACTCTTGTACATGTATTATGCATGTTGATGTAAAAAAAGTTTATCACAGGAAACCTAACAATTGCTTTGATAAATGCCACGCTGATGTACGTCGGGTATCGATGTCCTTAACGCAACGGTGGTACATGTGAGCTTTTTTTATTTATTTATAAATGTACGTAGGGTATCGCTGTGCTTAACAACCGCGTATATTCTGTAT
ATTGTTCATCAGCGTATATTGCTCAAGGGTACTACCGGTGTATATTGCTTAAGGGTATCGCTGCCAGCTGGTAAAGTACCTAAATTCTTGGCAAAATGACATGAGAAAATAGCAAATTGTAACAGGAGTTCTTTAAATATGAG

>TRINITY_DN48349_c2_g4_i3 from sample A7 / Example unspliced isoform:

GTTTTCATCATTGCTCTTCCACCACCCATGCTGACTTAATTATATTGCTCCCGACTCCTAATCATTCTTGCTAAGCTCAATTTGAACTTTCATATATTATATATTTTATGTATATATCCATCACAAATATATATGCACTAGTCAAGCCATCGAACTTTCAAGCGCGCGTGCATCTACAGCACCCCACATGATGAGAGGAT
ATGCCCATCAATGATGATCTTATTAACTTGCTCAGATTCTTGAGAGCCTCAGCCTCCTGCCTTCCTTATTTCTTGAGCTCTAAGCCGTGTTCTTCAAGTTGAGAGAGGGTTTCAGCCTTCAGGAGCTTGGACTGTTTGTTTGGCTTCTTGCGCTGGAATTAATTAGGTTTTGACTATTTTCCAGCGAAGTGTCTTCCACG
TTTATACGACTGGCCTGCTTGACTTTCATCATCCCTGACGTCTGGGAGCCAAGATAAATCTCCGGGTGCACTTGTGTGTGAAGAATCAGATTATTCATGGAAGAGATGAAGAACAAGCAGAGAGGTCTCGAGTGGCTGAAGACTATGGCTAACGATGAAGCGATGGGGTTGGCTCTTGGCGTTGGTGTGTCTATGGCGAT
GCCCGCCACAGCTTTGCGCGAAGACGATCAGAAAAACGCGCCGCTGCAGATCGAACCGCTGACCTTTCGCCCCATTGCTGCTCGCGTCGGGGCTGCTCCGGCTCCCTCGGCGCCGTTTCTTTGGTTCATGCCCAAGAACTGCCGGGAAGAGGTAACGGTCGCGGAGACGAATCCGTCCGAGGTTGTGCGTGGAGGGATAG
ACATGAATCAGGTTCCGTCGTCCAATGAATCTGAGTATTCGTCGGTTTTACAGGCTGATGGCTTGCGGGCTGTGGACAACGGTCCGATGGCGGTGAAGAGAGAACGAGAAAGAGCTTTTGATTTGGAGGCTGAGAGGGATCGAACCTGCGACGTGAGTTCGAGGACTAGCGACGAGGAAGAGATAGGTTCGACGAGGAAA
AAGCTGCGGCTTTCCAAAGAGCAATCTGCACTGCTGGAGGAAAGTTTCTTGGAGCACAGCACTCTGAATCCGGTAACATATCCTTGAATCTCTAAATTTTTTATAGTTTGCTTATTTTTGAAACCCCAGCAATCCATGGCTTTTAAAGATTATAAGCTGATCCGGTTTTCAATCGTGATCCTAGCAGAAACAGAAAAACG
CTCTGGCCAAGGCGTTGAACTTGCAACCCCGGCAGGTTGAAGTCTGGTTTCAGAACAGAAGAGCACGgtaagacttgggagaaaaaaaacacacataaaagaactgctccatggttatgattttgcggccattaacgtaagttcttctttgtttcttttgcagAACAAAGTTGAAGCAGACAGAAGTAGACTGCGAGGTT
TTGAAGCGGTGCTGCGAGAATCTAACGGAGGAGAACAGAAGGCTACAGAAAGAGTTGCAAGAGCTTAGGGCATTGAAGGCGGTTCCTCCTCAGTGCGTTATAGGACCGGATAATTACTACATGCCTCTGCCTGCCACCACACTCACCATGTGTCCTTCCTGTGAAAGGGTGGCTACCATGGAAAACGGCCGAAGCCTTCC
ATTTTCCAAGTCCCGGATTTCACAGTTTGCCCAACAGTCTGCAGCCTGCTAACTTTTTGTTGGGTTCATTGGGCAAGACTGGGCTTGCAAGCTTGTCCATGTAATATCATTGCTCAGTGGTCGTTTTTTTTTAGATTTCTGAGAGATTTCGCTCCCTTTGAAAAGCCAAAAACACATATTACACACTACATATATCACCA
TCTAACCCTTTGTGTTTTGCAAAGTAATTTCTCTGTTGTGCTAATTCACAGCGATATTGGGCAACCCAAGATGTGTAATCTGATCTTTGAAGGATCAAACGCCCTTTACTTTACTGATGTACTTCTCAGGGAAATGATATGGCGATTCATAAACGCCCATGGTAGTTTCTCTGCAAACAAGAACACCGGGTTGAATACAT
AATGTAATATCTCTTGTTAAAGATAAAATTATAGCTCCTTGCCAGGAAAAGTAGCTCAACACGTTCAGGAACGACTGTGTCAGTTCTGAGTTCTGGTTGCTTTTATTTATTTCTCCATCTCAGATTTCAATTTCATTGTCAACTTTTCCAAAGCTGGTGTTAAATTGACAGGCTCTTTGTATGTACAATTTTTGTAACTT
CAAAATTTTGAACATGTTGACAGGTCTGTCATAAAACGTATTTAAAACATTTCTAAAACTGCACAATACCCCATTTTGAAAAATCCCTACAACGCTCTCAAGTACATGTCTATAATCATTCACCTCGAAACAGGTCAATAGATAGAAGTCTGAAGAAACTCTTGTACATTTATTATGCATAACAAATGGATAGATAGAAA
TCTGAAGAAACTCTTGTACATGTATTATGCATGTTGATGTAAAAAAAGTTTATCACAGGAAACCTAACAATTGCTTTGATAAATGCCACGCTGATGTACGTCGGGTATCGATGTCCTTAACGCAACGGTGGTACATGTGAGCTTTTTTTATTTATTTATAAATGTACGTAGGGTATCGCTGTGCTTAACAACCGCGTATA
TTCTGTATATTGTTCATCAGCGTATATTGCTCAAGGGTACTACCGGTGTATATTGCTTAAGGGTATCGCTGCCAGCTGGTAAAGTACCTAAATTCTTGGCAAAATGACATGAGAAAATAGCAAATTGTAACAGGAGTTCTTTAAATATGAG

Intron 2 GTAACATATC ... GTGATCCTAG

Sample	Retention score (%)	Exon junction reads	5'ss reads	3'ss reads
A1	13	194	29	8.8
A2	23.17	126	38	5.2
A3	18.44	146	33	4.6
A4	13.68	82	13	2.4
A5	16.67	60	12	3
A6	17.82	509	110.4	18.8
A7	18.77	639.4	147.8	25
A8	17.76	528	114	17.2
A9	17.18	567.8	117.8	20.2
A10	17.77	617	133.4	19

>TRINITY_DN118754_c0_g1_i1 from sample A1 / Example spliced isoform

CATCTACAGCACCCCACATGATGAGAGGATATGCCCATCAATGATGATCTTATTAACTTGCTCAGATTCTTGAGAGCCTCAGCCTCCTGCCTTCCTTATTTCTTGAGCTCTAAGCCGTGTTCTTCAAGTTGAGAGAGGGTTTCAGCCTTCAGGAGCTTGGACTGTTTGTTTGGCTTCTTGCGCTGGAATTATTAGGTTTT
GACTAGTTTCCAGCGAAGTGTCTTCCACGTTTATACGACTGGCCTGCTTGACTTTCATCATCCCTGACGTCTGGGAGCCAAGATAAATCTCCGGGTGCACTTGTGTGTGAAGAATCAGATTATTCATGGAAGAGATGAAGAACAAGCAGAGAGGTCTCGAGTGGCTGAAGACTATGGCTAACGATGAAGCGATGGGGTTG
GCTCTTGGCGTTGGTGTGTCTATGGCGATGCCCGCCACAGCTTTGCGCGAAGACGATCAGAAAAACGCGCCGCTGCAGATCGAACCCCTGACCTTTCGCCCTATTGCTGCTCGCGTCGGGGCTGCTCCGGCTCCCTCGGCGCCGTTTCTTTGGTTCATGCCCAAGAACTGCCGGGAAGAGGTAACGGTCGCGGAGACGAA
TCCGTCCGAGGTTGTGCGTGGAGGGATAGACATGAATCAGGTTCCGTCGTCCAATGAATCTGAGTATTCGTCGGTTTTACAGGCTGATGGCTTGCGGGCTGTGGACAACGGTCCGATGGCGGTGAAGAGAGAACGAGAAAGAGCTTTTGATTTGGAGGCTGAGAGGGATCGAACCTGCGACGTGAGTTCGAGGACTAGCG
ACGAGGAAGAGATAGGTTCGACGAGGAAAAAGCTGCGGCTTTCCAAAGAGCAATCTGCACTGCTGGAGGAAAGTTTCTTGGAGCACAGCACTCTGAATCCGCAGAAACAGAAAAACGCTCTGGCCAAGGCGTTGAACTTGCAACCCCGGCAGGTTGAAGTCTGGTTTCAGAACAGAAGAGCACGAACAAAGTTGAAGCAG
ACAGAAGTAGACTGCGAGGTTTTGAAGCGGTGCTGCGAGAATCTAACGGAGGAGAACAGAAGGCTACAGAAAGAGTTGCAAGAGCTTAGGGCATTGAAGGCGGTTCCTCCTCAGTGCGTTATAGGACCGGATAATTACTACATGCCTCTGCCTGCCACCACACTCACCATGTGTCCTTCCTGTGAAAGGGTGGCTACCAT
GGAAAATGGCCGAAGCCTTCCATTTTCCAAGTCCCGGATTTCACAGTTTGCCCAACAGTCTGCAGCCTGCTAACTTTTTGTTGGGTTCATTGGGCAAGACTGGGCTTGCAAGCTTGTCCATGTAATATCATTGCTCAGTGGTCGTTTTTTTTTAGATTTCTGAGAGATTTCGCTCCCTTTCAAAAGCCAAAAACACATAT
TACACACTACATATATCACCATCTAACCCTTTGTGTTTTGCAAAGTAATTTCTCTGTTGTGCTAATTCACAGCGATATTGGGCAACCCAAGATGTGTAATCTGATCTTTGAAGGATCAAACGCCCTTTACTTTACTGATGTACTTCTCAGGGAAATGATATGGCGATTCATAAACGCCCATGGTAGTTTCTCTGCAAACA
AGAACACCGGGTTGAATACATAATGTAATATCTCTTGTTAAAGATAAAATTATAGCTCCTTGCCAGGAAAAGTAGCTCAACACGTTCAGGAACGACTGTGTCAGTTCTGAGTTCTGGTGTAGCTCAGATTTCAATTTCATTGTCAACTTTTCCAAAGCTGGTGTTAAATTGACAGGCTCTTTGTATGTACAATTTTTGTA
ACTTCAA

>TRINITY_DN118754_c0_g1_i2 from sample A1 / Example unspliced isoform:

CATCTACAGCACCCCACATGATGAGAGGATATGCCCATCAATGATGATCTTATTAACTTGCTCAGATTCTTGAGAGCCTCAGCCTCCTGCCTTCCTTATTTCTTGAGCTCTAAGCCGTGTTCTTCAAGTTGAGAGAGGGTTTCAGCCTTCAGGAGCTTGGACTGTTTGTTTGGCTTCTTGCGCTGGAATTATTAGGTTTT
GACTAGTTTCCAGCGAAGTGTCTTCCACGTTTATACGACTGGCCTGCTTGACTTTCATCATCCCTGACGTCTGGGAGCCAAGATAAATCTCCGGGTGCACTTGTGTGTGAAGAATCAGATTATTCATGGAAGAGATGAAGAACAAGCAGAGAGGTCTCGAGTGGCTGAAGACTATGGCTAACGATGAAGCGATGGGGTTG
GCTCTTGGCGTTGGTGTGTCTATGGCGATGCCCGCCACAGCTTTGCGCGAAGACGATCAGAAAAACGCGCCGCTGCAGATCGAACCCCTGACCTTTCGCCCTATTGCTGCTCGCGTCGGGGCTGCTCCGGCTCCCTCGGCGCCGTTTCTTTGGTTCATGCCCAAGAACTGCCGGGAAGAGGTAACGGTCGCGGAGACGAA
TCCGTCCGAGGTTGTGCGTGGAGGGATAGACATGAATCAGGTTCCGTCGTCCAATGAATCTGAGTATTCGTCGGTTTTACAGGCTGATGGCTTGCGGGCTGTGGACAACGGTCCGATGGCGGTGAAGAGAGAACGAGAAAGAGCTTTTGATTTGGAGGCTGAGAGGGATCGAACCTGCGACGTGAGTTCGAGGACTAGCG
ACGAGGAAGAGATAGGTTCGACGAGGAAAAAGCTGCGGCTTTCCAAAGAGCAATCTGCACTGCTGGAGGAAAGTTTCTTGGAGCACAGCACTCTGAATCCGgtaacatatccttgaatctttaaattttttatagtttgcttatttttgaaaccccagcaatccatggcttttaaagattataagctgatccggttttca
atcgtgatcctagCAGAAACAGAAAAACGCTCTGGCCAAGGCGTTGAACTTGCAACCCCGGCAGGTTGAAGTCTGGTTTCAGAACAGAAGAGCACGAACAAAGTTGAAGCAGACAGAAGTAGACTGCGAGGTTTTGAAGCGGTGCTGCGAGAATCTAACGGAGGAGAACAGAAGGCTACAGAAAGAGTTGCAAGAGCTTA
GGGCATTGAAGGCGGTTCCTCCTCAGTGCGTTATAGGACCGGATAATTACTACATGCCTCTGCCTGCCACCACACTCACCATGTGTCCTTCCTGTGAAAGGGTGGCTACCATGGAAAATGGCCGAAGCCTTCCATTTTCCAAGTCCCGGATTTCACAGTTTGCCCAACAGTCTGCAGCCTGCTAACTTTTTGTTGGGTTC
ATTGGGCAAGACTGGGCTTGCAAGCTTGTCCATGTAATATCATTGCTCAGTGGTCGTTTTTTTTTAGATTTCTGAGAGATTTCGCTCCCTTTCAAAAGCCAAAAACACATATTACACACTACATATATCACCATCTAACCCTTTGTGTTTTGCAAAGTAATTTCTCTGTTGTGCTAATTCACAGCGATATTGGGCAACCC
AAGATGTGTAATCTGATCTTTGAAGGATCAAACGCCCTTTACTTTACTGATGTACTTCTCAGGGAAATGATATGGCGATTCATAAACGCCCATGGTAGTTTCTCTGCAAACAAGAACACCGGGTTGAATACATAATGTAATATCTCTTGTTAAAGATAAAATTATAGCTCCTTGCCAGGAAAAGTAGCTCAACACGTTCA
GGAACGACTGTGTCAGTTCTGAGTTCTGGTGTAGCTCAGATTTCAATTTCATTGTCAACTTTTCCAAAGCTGGTGTTAAATTGACAGGCTCTTTGTATGTACAATTTTTGTAACTTCAA