Sequence
atgc intronic sequence ATGC exonic sequence...taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G41500.1 (Glycine max), 3'ss of exon 3
taaattttttatcttatcaatctgaaagt-atttttatgtgatgggattc----ttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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----ttgccaggattaagaagatgatctttatatttgaaccaaacatctcacagtcacattctattcttacctttgtt-cttctattcatactttggattttcagGCACCCCTTGTATCACAGACTGTGTGATGGCAGAACTTGAGAAGTTAGGCCAAAAATATCGTGTAGCTCTAAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G38690.2 (Glycine max), 3'ss of exon 5
taaattttttatcttatcaatctgaaagtatttttatgtgatgggat------tcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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--agaagctcgtctttgtaatgtggcattggcattgtatatttgaatcaaacatcccatattctattattacctttgtt----ctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAGTTAGGCCAAAAATATCGTGTAGCTCTAAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA12G31740.1 (Glycine max), 3'ss of exon 5
--taaattttttatcttatcaatctgaaa--gtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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tctagattaagaagcttgtctttgtaatgtggcattggcattaatcaaacatcccatattctattattacctctgtt----ctattgatattttggattttcagGCACCCCTTGTATTACGGACTGTGTGATGGCAGAACTCGAGAAATTAGGGCAAAAATATCGTGTAGCTCTAAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatc-ttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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----------------------gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S11_99V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------taaattttttatcttatcaatctgaa----agtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttct-atcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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gtaagtgaattgctagtgctagtgggttcgctgttcattctattgagtctcttttaagaagtattagttgctaaaaaactgggctacagaagtgtttcaaggttgttttagcatcctgtttgattgtattagtccatgactcatgaactgtttggcgtgcagGTACACCTTGTATCACAGATTGTGTAATGGCTGAGCTGGAGAAATTGGGTCAAAAATATCGAGTTGCTTTAAG
upper sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S153_101V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------taaattttttatcttatcaat--ctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttcctt------ctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
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gtaagtagcttgctttcgccagcggtttcattgttgtttttctgaatacctagtgtttattcgttgctagagaattggtccatagaagtttacggtatcaaggttgcttctgtatcctgtttgattgggcgagtacatgattaacgatttgtttggcctacagGTACACCTTGTATCACGGATTGTGTGATGGCCGAATTAGAGAAATTGGGTCAGAAGTATCGCGTCGCTTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
ttttaat putative branch site (score: 3)
cttccttctatctttt CT-rich tract
ttctatcttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - -gaaagta
- - - - - - - - - - - - - - - - - - -gtgatgg