Sequence
atgc intronic sequence ATGC exonic sequence...ttttatttgtcatatcttactctattttcttcttatgatatttttttcccatgtgcatccagttctccttccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g46894.1 (Oryza sativa), 3'ss of exon 9
---ttttatttgtcatatcttactctattttcttcttatga----tatttttttcccatgtgcatccagttctccttccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
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tagttttaatagatttctggtcacgtattgactatatatagagtccactgttccttcatatgaatgtagtt-tcattcttgtttac--tgtgtga----tcaagcagGTGCTTACTTCAATGGCTGATTCAAACGGACAAATCTCTGCTGCTGTGATGGAGCGTCTTACATCAGCAGCAGCAGCTGAACCTTATGAATCTGTCAAAC
upper sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g44380.2 (Oryza sativa), 3'ss of exon 4
-----ttttatttgtcatatcttactctattttcttcttatgatatttttttcccatgtgcatccagttctccttccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
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tccaaaaggatatttcatagcctgaacttaacttgctttgaactacttttcacaccatcgttttgaattctatctttattgt-tggtgtacaaaac----atcagGTTCTTGCTTCTATGGCTGATGCGAACGGGCAAATTTCTTCTGAGGTGATGGAACGTGTCACTGCAGCAGCAGCAGCGGAGCCATATGGATCTGTTAGGC
upper sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT2G45540.2 (Arabidopsis thaliana), 3'ss of exon 11
ttttatttgtcatatcttactctattttcttcttatgatatttttttc----ccatgtgcatccagttctcct--tccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
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---catttttaatatcagatttgaatttgttatt-tgggattcttgtaaacaccatgttctttatgctaagaaaattcaagtaattttttctttcttttt--tcagATACTCGCATCAATGGCTGATTCAAGTGGACAGATTTCTGCAGTCGCAATGGAGCGCCTTACTGCTGCTTCTGCAGCTGAGCCTTATGAATCTGTTTCAT
upper sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G60920.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------------------------ttttatttgtcatatcttactctattttcttcttatgatatttttttccca---------tgtgcatccagttctccttcca--acttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
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gtaagtggaaattactctcaatttctttcttccggatcaatatctccccttatttattggcttttttcct-ttttgtttttataacatcatttaagaaagatagttctgatcatctgattaactttctgctattttcctgcttttactttttcttcagATACTTGCTTCAATGGCCGATGCAAGTGGCCAGATATCTACAGCCGTAATGGAGCGTCTTGCTGCTGCTGCTGCAGCTGAGCCCTATGAATCTGTTTCTT
upper sequence: Vv15s0048g01650.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S88_98V6.1 (Physcomitrella patens), 3'ss of exon 9
ttttatttgtcatatcttactctattttcttcttatgatatttttttcccatgtgcatccagttctc-cttccaac--ttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
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cttgaatgg--atggtttagcgttgcaactaagtatg-catctcattgaaacattgctcttgttatgactaagaaccgtaacattgtttcatttctgtgacagATTTTGGCCACATTGGCTGATGAAAACGGGCAGATTTCTGCCACAGCTATGGAACGCCTGACTGCATCTGCAGCAGCTGAGCCCTATGAATCCGTTCGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcccatgtgcatccagttctccttccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
aacttac putative branch site (score: 2)
tatttaagatttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttatttgtcatatcttactctattttcttcttatgatatttttttcccatgtgcatccagttctccttccaacttacactatttaagatttcaatcagGTTCTTGCTTCAATGGCTGATGCAAACGGGCAAATTTCTGCATCAGTGATGGAGCGCCTTACTGCTGCTGCTGCAGCAGAACCTTATGAATCCGTTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - -cccatgt