Sequence
atgc intronic sequence ATGC exonic sequencegtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 8
gtattgtt--cactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagc-agAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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gtaataatactacttctgccaggggaaagtagggctggatgatttgt---agctttatttttctagag-acatcc------aacaaagttttcttgacattttggattctgttaatgccagAGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 3
-----gtattgtt-cactgcactctgtgtcatttagtgcaatatgcattgtttggc-ctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggag-cagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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gtaattcattattactttgaggaaaaaataactccttttgattgacacctcttatctccttatgttgtcgagatatttgtaacacaatttct-cgaaataaatt--tgaaatctcattaatgtcagAGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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-----gtttgactctctctctctctctctgtctctctctctatctctatctctta--taattactgcagat---aatttgat--catcagattcctaaacttttatgc--ttaagcagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttca--ttaatgagaatgt--aatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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-------------------------------------------gtttgactctctctctctcatataaattactgct--gataatttgatcatcagattcctaaacttttctgcttaagcagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 9
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgctt--aaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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-------------------gtatgattct-tattttatgatcttattagattttggtgtgcaactcttttacctgtttgtgactgttgttaactcttttt----ggctttaaca---cagAGGCAAGCAGCTCAATGTGTAGGGCGAGTAATCCGGTCAAAGGCTGATTATGGGATGATGATATTTGCAGACAAAAG
upper sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
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gtatgtttcgctactggactggtttatggattcggttcatgaaattct-caacgagttcatgacattactttctccttttgcta-atgaggtgcatttgtatactcgtg-tgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
cattaat putative branch site (score: 3)
ttgcttaaataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT