Sequence
atgc intronic sequence ATGC exonic sequencegtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g48270.1 (Oryza sativa), 3'ss of exon 4
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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ccacaactccacttcaaactcggctctcggagttaaa---tttaggcgttag-agctctcccaaataaactctgaaa---ctgatcaatctctga--atttgcatg------------cagGATGGGCGGATCAGCTACGAGGAGTTCGTGGCGATGATGAAATCCGGGACGGATTGGAGGAAGGCGTCGCGGCAATACTCGAGGGAGCGGTTCAAGACGC
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G01470.1 (Glycine max), 3'ss of exon 6
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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------------------ataaaatgtgattgatataataatcatgtta---catctcatatacgccccacatgttttcctcaagtccttaaaacgattttctatttttctgtgttcacagGATGGTCGTATCAGTTATGAAGAGTTTGTGGCCATGATGAAAACTGGAACTGACTGGAGAAAAGCATCTAGGCAGTATTCAAGGGAGAGATTCAAGAGCT
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G10410.1 (Glycine max), 3'ss of exon 6
gtttgac--tctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaa----gatattgtatcatccctgtacctttcttgatga--tttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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gtttggcaatcttactcatgactcatttttttattttccatttagcaggttctttacttcttattaatactgccaatgcatagtttccacaagtccttaaaacaattttttatttttctgttttcccagGATGGTCGCATCAGTTATGAAGAGTTTGTGGCCATGATGAAAACTGGAACTGACTGGAGAAAAGCATCAAGGCAGTATTCAAGGGAGAGATTCAAGAGCT
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G34440.1 (Glycine max), 3'ss of exon 7
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtat-catccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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---------------------atttgctgcctctcatgttacttgcctttaccatcttatgtgcacgtcctgcttgcttctttacgtgttgttccaacgtttttct-gttttcacttcacagGATGGTTGCATCAGTTATGAGGAGTTTGTGGCAATGATGAAAACTGGAACTGACTGGAGAAAAGCATCCAGGCAATATTCAAGGGAGAGATTCAAGAGTT
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G20170.1 (Glycine max), 3'ss of exon 6
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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----gcctctcatg--ttacttgcctttaccatttt-atgttcatgtcctgcatgcttcttta-------cctgtcattccaat--ctttttcgattttctg-----ttttcacttcacagGATGGTCGCATCAGTTATGAGGAGTTTGTGGCGATGATGAAAACTGGAACTGACTGGAGGAAAGCATCTAGGCAATATTCAAGGGAGAGATTCAAGAGTT
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G18890.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtaccttt---cttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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-----gttctttcaaatatccaaaaaaatcctcctttaaggcctaacaataa-agcttgtcaagagaaaagatat-atccctctgcttctgagtcggattgttgggcttgtttgctttttacagGACGGACGTATAAACTATGATGAGTTTGTGACGATGATGAAAGCTGGAACTGACTGGAGAAAGGCATCGAGACAATATTCAAGAGAGAGGTTCAAAAGCT
upper sequence: Vv17s0000g05520.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G74740.1 (Arabidopsis thaliana), 3'ss of exon 6
gtttgactctcaaggcttgcca--gctgctggcatca-tgactttcaagccttgccagctctttcaa-agatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
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-------------gtttttctaaagctctatacatcagctcctttctcgctataaagactcttcctatagaaagtttatta-------aatacttaagaggagtcataatgtttgatt-ttgcagGACGGAAAAATAAACTATGATGAGTTTGTGGTGATGATGAAAGCTGGAACTGATTGGAGAAAGGCATCAAGACAATACTCAAGAGAGAGGTTTAAAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
tcttgat putative branch site (score: 4)
tttttttgtc putative PPT
atagttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgactctcaaggcttgccagctgctggcatcatgactttcaagccttgccagctctttcaaagatattgtatcatccctgtacctttcttgatgatttgcatagtttttttgtcacagGATGGGCGTATCAATTACGATGAGTTTGTGGCAATGATGAAAACTGGAACCGACTGGAGAAAGGCTTCTCGCCAGTACTCAAGGGAGAGGTTCAAAAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG