Sequence
atgc intronic sequence ATGC exonic sequencegtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 6
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtt-tagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
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--------------------------------------gtagcaat--ttctttggttttctctcttttctttggtttgtttgtatcggtggaattatggtgtaattataagtcctgttcatcacaattttgcagGGATATTAAAGGTGCAAATATACTAGTAGATCCTAGTGGTCGTGTTAAGCTTGCAGATTTTGGAATGGCAAAACAT
upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA01G42960.1 (Glycine max), 3'ss of exon 5
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
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-------------gtgagtcttgttgatcattataacccacatgactatcttcaagttctgtttcaattatcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCAGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G01880.1 (Glycine max), 3'ss of exon 5
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
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------------------------------catgaatttctgtaattttttaaagtttatgcatagtataaattata-gtttgtgatttgtgaaacaatctctcctagtctgatca---ctacattctgatcagGGACATTAAAGGAGCAAACATATTGGTGGACCCTAGTGGGCGGATAAAATTGGCAGATTTTGGGATGGCAAAGCAT
upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G02520.1 (Glycine max), 3'ss of exon 8
gtaagttagatcatcttacattgttggtt-tggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
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-------------gtgagtcttgttgatcattataaccacatgcctatcttcaa-gttctgtttcaatca-tcaactttactattaatgttcttaaacttattttcctcttgtccaattactggattttactcagAGACATTAAAGCCGCAAACATATTGGTGGATCCTAATGGGAGGGTAAAATTGGCAGATTTTGGCATGGCAAAGCAT
upper sequence: Vv02s0025g03370.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G63700.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggta-agttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
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------------------------------------gtgaggcagtgaattct-atccattcttctgatacctcgttttccttcatccttcattagttggagaattagatgaacatggattttaattttattcagGGACATCAAAGGAGCAAATATATTGGTGGATCCTCATGGACGAGTAAAAGTTGCTGATTTTGGGATGGCAAAACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
tgctaat putative branch site (score: 2)
tcctgttt putative PPT
taagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttagatcatcttacattgttggtttggttatcctaggctatcattcatcactcacccccaatgaatctcatctgtttttgtcatcttagaacatctgtgctaattaggtaagttttgtatcctgtttagGGACATCAAAGGAGCAAATATACTGGTGGATCCCAATGGCCGTGTGAAATTGGCAGATTTTGGAATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG