Sequence
atgc intronic sequence ATGC exonic sequencegtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 9
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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gtatgatttgcctttgttaatctcagtagttg---gctaactgctctcagctaataatttgggtatgaaattt-tgtggctttcagCTGAAATATCATGATACTGGGAAGGAAAAGGAGTGCTTGCCACAAGTTGGTCAGTGGAACATGGTGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 9
gtaatattcacc--atcctaaatttat---atatgtgaaagatgat-aggtattacacattgt-gcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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gtaatgtgcatctcaaccaagaggtgtaagatacttaaagtatgattacttttttttcactattgattgatatgcagtac---ttgtctgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAATTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 10
---------------gtaatattc-accatcctaaatttatatatgtgaaag----atgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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gtaatgtgcttcttcatcttcttctaaagatctggtttgtcatatactgaaaccttaagttaccttttccctgccattcattaatttaaagcacttctgagcgcagCTTAAATATCATGAAAGTGGGAAAGAAAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 1
gtaatat--tcaccatcctaaa---tttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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gtaatatgcttctcaaccaaaggatttaagatacttaaagtatgattactttttctgtctctatacattgatacgtagtacttgtctgcagCTTAAATATAACGAAAGTGGGAAAGAAAAGAATTGTTTACCCCAAGTTGGCCAGTGGAATATGATGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 10
gtaatat---tcaccatcctaaatttatatatgtgaaagatgataggtattac--acattgtgcctgat-----ctgactt----ctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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gtaatgtgcttctccttctaaagatctgatttgtcatatactgaaactttaatttaccttttccctgtcattcattaatttaaagcacttctgaatgcagCTTAAATATCACGAAAGTGGGAAAGAGAAGAACTGTTTACCCCAAGTTGGTCAGTGGAATATGATGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA----------------------------
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gtaaaaaacctaaacagatctctgaatgctcatactatgagaa-tactg----ttatgttaattcgtctctctttgcttgctacagCTTAAGTATCACGAGAACGGGAAAGAAAAAGATTGTCTCCCGCAAGTTGGTCAGTGGAATATGATGAACAAGAAAATGATCAACGGGATGACTGTGAGCA
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ19862 (Selaginella moellendorffii), 3'ss of exon 9
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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-------------------gtttgtgtttcttct---cttttgttgtcatacaatgttctttaa--aaatgcgg----gtttgcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGAATATGATGAACAAG
upper sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EFJ19863 (Selaginella moellendorffii), 3'ss of exon 9
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
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-------------------gtttgtgtttcttct---cttttgttgtcatacaatgt-tctgaaaaaatgcgggttt-----gcagCTGAAATATCATGAAACGGGTAGAGAAAAGGATTGCTTGCCTCAAGACGGGACCTGGCATATGATGAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
atctgac putative branch site (score: 3)
cttctattttatct CT-rich tract
ttctattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatattcaccatcctaaatttatatatgtgaaagatgataggtattacacattgtgcctgatctgacttctattttatctgcagCTGAAATATCATGAAACTGGGAAGGAAAAGGATTGTTTGCCTCAAGTCGGTCAGTGGAATATGATGAACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA