Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagagcgttacattgattttaggaatgactattttgtgactgaaacataagtttaccctctttgttgctttgttgatcaatagttgtggcaatatcatcactaaatttaaacatccaaatttaatatcctcctgattaatgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G29380.1 (Glycine max), 3'ss of exon 5
gtaagtagagcgttacattgattttaggaatgactattttgtgactgaaacataagtttaccctctttgttgctttgttgatcaatagttgtggcaatatcatcactaaatttaaacatccaaatttaatatcctcctgattaatgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
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---------------------------------------------------gtaagttagacatgattttcttttagtatat--agagctttaatttggttttgtttgatgctcatcatgc---tttaattgtatgtca--caatcttattttatttactcaatttacat-cccttgtt-----attctgttaaactagGTCACTTGGTCAGGCAGCTCCGTGCGTAAATGCATTTGCAGCAGGCCAAGCAGCAGCATATAAGATGTTTGAGACAATTAAACGAAAGCCAAAAATTGAT
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 3
gtaagtagagcgttacattgattttaggaatgactattttgtgactgaaacataagtttaccctctttgttgctttgttgatcaatagttgtggcaatatcatcactaaatttaaacatccaaatttaatatcct-cctgattaatgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
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--------------------------------------------gtaagtgataaaatgaccct--tgattgaataactggc--attggcatgacattgtttaggcatataaagaatttttctatgttgtactttgtctaacgtttctaatggagtactgcaacctgattaatcttt-ctaacacat-----------agGTCACTTGGTCAAACATCTCCAAGCCTAAATGCATTCGCAGCAGGCCAAGCAGCAGCTTATAAGATGTTTGAGACAATTGCACGAAAGCCAAAAATTGAT
upper sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G46540.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtagagcgttacattgattttaggaatgactattttgtgactgaaacataagtttaccctctttgttgctttgttgatcaatagttgtggcaatatcatcactaaatttaaacatccaaatttaatatcctcctgattaatgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
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---------------------------------------------------------------------------------------------------------------gtgagtaaaacgattacttgtccttg-aagaaatcttgtgatac-tgatagccctaattttttacacatgcaattcacttcg---tagGGCGTTGGGGCAGACATTGCCTTCTCTTAACTCTTTTGCGGCCGGAACAGCTGCAGCTTACAAAATGTTTGAGACTATCAAAAGAAAACCAAAGATCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
ctcttac putative branch site (score: 3)
tgttctt putative PPT
tttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagagcgttacattgattttaggaatgactattttgtgactgaaacataagtttaccctctttgttgctttgttgatcaatagttgtggcaatatcatcactaaatttaaacatccaaatttaatatcctcctgattaatgtattgatgcgtgaccacctctcttacctttgtttgcaaatgttcttggactagGTCGTTGGGCCAAACATCCCCATGCTTGAATGCATTTGCAGCAGGACAAGCTGCAGCATATAAGATGTTTGAGACTATCAAACGAAAACCACAAATTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG