Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtaaaacagtttgatttgatggatgaagtaaattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 3'ss of exon 3
----gtaatgtaaaacagtttgatttgatggatgaagtaaattgctgtttttctgttgagatgact-tatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gttagtaatg-acaagacattcatgtgcttagttaactcaa--gcggtgattctgtggaagccattgctcacttctgctctttcatgtttt-cagCGTACTTCAATGACGCGCAGAGGCAGGCAACCAAGGATGCCGGTGTCATTGCTGGCCTGAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G415007_T01 (Zea mays), 3'ss of exon 3
gtaatgtaaaacagtttgatttgatggatgaagtaaattgctgtttttctgt--tgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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--gttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttt-tgttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G114793_T01 (Zea mays), 3'ss of exon 3
-gtaatg-taaaacagtttgatttgatggatgaagtaaattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gttagtaactgaacaattctgctggttacctctagtag-ttgttatgtaaaaac-gtggcggctcacttccttgtgttgtgtttttttgcagCGTACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G36600.1 (Glycine max), 3'ss of exon 3
-------gtaatgtaaaacagtt--tgatttgatggatgaagtaaattg-ctgtttttctgttgagatgacttatgtttctatt-cttacaacttc----------tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgccaatttctcacattttcctttcaactgtacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G36620.1 (Glycine max), 3'ss of exon 3
-------gtaatgtaaaacagttt--gatttgatggatgaagtaaattg-ctgtttttctgttgagatgacttatgtttctat-tcttacaacttc----------tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gtaactggaagtctggaacaattcacgacttatttca-actgcaatttgattgttttcctcctgcttttgcctttatttcaatatctcacattttcctttaaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAATGAACCCACTGCTGCTGCCAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G02960.1 (Glycine max), 3'ss of exon 3
gtaatgtaaaacagtttgatttgatggatgaagtaa-attgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gtaactggaa---gtctggaacaattcatgactttctgattttgcttttatgccaatat--ctcacattt---tcctttcaactg-tacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAAGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATTAATGAACCTACTGCTGCTGCCAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G02940.1 (Glycine max), 3'ss of exon 3
-------gtaatgtaaaacagtttga--tttgatggatgaagtaaatt--gctgtttttctgttgagatgacttatgtttctatt-cttacaacttc----------tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttgattgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacagCTTACTTCAATGATGCTCAGAGGCAGGCCACCAAGGATGCTGGTGTCATTGCTGGTCTCAATGTTGCTAGAATTATCAACGAACCCACTGCCGCTGCCAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 3'ss of exon 3
------------gtaatgtaaa---acagtttgatttgatg-gatgaagtaaattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcagCTTACTTCAATGATGCTCAAAGGCAAGCTACCAAGGATGCCGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATCAACGAACCTACTGCTGCTGCTAT
upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 3'ss of exon 3
-gtaatgtaaaacagtttgatttgatggatgaagtaaatt-gctgtttttctgttgagatgacttatgtttcta-ttcttacaacttc-tacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
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gttagtttgttgttatat-atgtggtgga-gaggtatctttattatctgtatttggtgattgattgtttatttggtgtttttgactttgcgtagCTTACTTCAATGATGCTCAAAGGCAAGCTACTAAGGATGCTGGTGTTATTGCTGGGCTCAATGTTGCTAGAATCATTAATGAACCTACTGCTGCTGCTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
ttcttac putative branch site (score: 2)
cttctac putative PPT
ttatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtaaaacagtttgatttgatggatgaagtaaattgctgtttttctgttgagatgacttatgtttctattcttacaacttctacagCTTACTTCAATGATGCCCAGAGGCAGGCCACCAAGGATGCAGGGATTATTGCTGGACTGAATGTTGCAAGAATCATCAATGAACCTACAGCAGCAGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA