Sequence
atgc intronic sequence ATGC exonic sequencegtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g49430.1 (Oryza sativa), 3'ss of exon 7
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaac-atctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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---------------------------------------------gtaagacacaatattctctttgccacctaaccatggtaactttgcttgaaaaatttccatcatattcgctttattcctcccagTTGTGTGGAATCCGTGGGAAAAGAAATCGAAAAACATCGTGGACTTCGGCGATGAGGAGTACAAACAGATGCTGTGCGTTGATGCGGCTGCAGCGGAGAG
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G02160.1 (Glycine max), 3'ss of exon 7
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacac-cattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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----------------gtaagtttatttgtaaacaatacttacaactcaaaatcaaatactgttcttagatt--gtttctctcttacacaaactaaaaattcatttctgatttgacattgca---tagTTGTTTGGAATCCTTGGGAAAGAAAATCCAAGTCCATATTAGATTTAGGGGATGAAGAGTACAAACAGATGCTATGTGTTGATGGTGCAGCAGTTGAAAA
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G43330.1 (Glycine max), 3'ss of exon 6
gtaagttccatttttcatga-attcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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gtaagtttctttgtaaacaatgcttccaactcaaaatcag-aaactattgttagattgtttctctcatttccttacac----aaactaaaaaatcattttttgatt-tggcattgcat--------agTTGTTTGGAATCCTTGGGAAAGAAAATCCAAGTCCATAGTAGATTTAGGGGATGAAGAGTACAAACAGATGCTATGTGTTGATGGTGCAGCAGTTGAAAA
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G23730.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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-------------------------------gtaagatccaaataccgaaaaccttaaccgccctttttaccaagaatccagtttttaac----agtattagattctcgg-------tttgttgcagTGGTATGGAATCCATGGGAGAAGAAAGCGAGAGCATTGACGGATTTGGGAGATGATGAGTATAGACACATGTTGTGTGTGGATGGAGCAGCCATTGAGAA
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ11392 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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---------------------------------------------------------------gtaagacttgcttttagtgctgg-actggtcggtaaccattgctggtgctgttct-----acagTCGTGTGGAATCCATGGGACAAGAAAGCCAAAGCCATGGCAGACTTTGGAGACGACGAGTATTTACACATGGTGTGCGTGGAGCCAGCAGTGATCGAGAC
upper sequence: Vv02s0025g01030.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: EFJ06112 (Selaginella moellendorffii), 3'ss of exon 7
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
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---------------------------------------------------------------gtaagacttgctttaagtgctgg-actggtcggtaaccattgctggtgctgttct-----acagTCGTGTGGAATCCATGGGACAAGAAAGCCAAAGCCATGGCAGACTTTGGAGACGACGAGTATTTACACATGGTGTGCGTGGAGCCAGCAGTGATCGAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
ttttaat putative branch site (score: 3)
ctgcttttt CT-rich tract
ttttatttttattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttccatttttcatgaattcaatatagagaagcagcaaacaatgaacaacaccattgtctcaacatctagtatttttatttttattttttattttttgtttcttgtgctgctttttaatgcagTGGTGTGGAATCCATGGGACAAGAAAGCCAAGGCCTTGGTTGATTTTGGGGATGATGAGTACAAACAGATGCTGTGTGTTGATGGGGCAGCAATCGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG