Sequence
atgc intronic sequence ATGC exonic sequencegtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 11
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
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----------------------------------------------------------------------------caaagttggaatttgattatgtcg------taaaatatatgcaccc-tacatgttt-tagcttcatattgacttatattt-tcatatgtgctccttcaactgcacaaa--------------gCTGGAAGTTCCTGCATCTGAAGCCACTATTGATGCCACTGCGCAAGGCATTGCTTCCATGCTATGTGCTCATGGTCCCGATGTTGAGTGGAGAATATGTA
upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G36600.2 (Glycine max), 3'ss of exon 10
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctctt--gccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
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---------------------------------------------------------------------------------gttgtgttcacctttatcagttaacatttttattttctttatgttattctta-atttgtacagtcactcatgtagattctttccgtacacttgagatctaaaacatttgttgttgatcagATAGAAGTTCCTGCAGCTGAAGCCTCTATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA
upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 4
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
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------------------------------------------------------gttgtgtgcaactttatcagttaa-------catttttttttcttga----ttattcttattttttacagtcactcacgtagattctt-tccatacacttgaa--atctaaaacc-tttg--------------ttgttgatcagATAGAAGTTCCTGCAGCTGAAGCCTCAATTGAAGCTACTGCCCAAGGCATTGCATCAATGCTTTGTGCCCATGGTCCAGAGGTTGAATGGAGAATTTGCA
upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA09G07240.2 (Glycine max), 3'ss of exon 10
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctac-cttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
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--------------------------------------------------------------------------------------gttcggttactctttgcaagttacctcattttt-ctcattt-tgtatggtaatgtagagctaattctttatgcatgctgaagatctat-----aatatatatttgtct-atcagATTGAAGCTGCTTCAGCCGAAGCCACTATTGAAGCTACGGCCCAAGGCATTGCCTCAGTGCTTTGCGCTCATGGTCCAGAGGTAGAGTGGAGAATTTGTA
upper sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
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------------------------------------------------------------------------------------gcatggttcctctttatatttttctgctattccatctctgatatgc-----gattggcattctactaga----------aaattatattgaaactgactcatttcatctcaacagATAGAAGTTCCTGCAGCAGAAGCAACCATTGAAGCCACTGCCCAAGGAATTGCCTCAATGCTTTGTGCTCATGGTCCTGAAGTTGAGTGGAGAATTTGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
acctaac putative branch site (score: 2)
tccctcttgcc putative PPT
ttcgtttgaaaaaaaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagtgacttgctttcattgtttgtgtccaactaatttattctttgggatgaatgcctccagtttttggagtgcagatcatgcattcatctaccttaacctgttattttacacacacacacacacacacacagatgcatatgcaaacatatgtataacctaacttcgtttgaaaaaaaaaaaatccctcttgccagATAGAAGTGCCTGCAACTGAAGCAACTATTGAAGCCACTGCCCAAGGGATTGCATCAATGCTTTGTGCACATGGTCCCGAGGTTGAATGGAGAATTTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA