Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgaaaattttatgagaagtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g09230.2 (Oryza sativa), 3'ss of exon 3
gtaagtgaaaatt--ttatgagaagtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
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gtgagctgagctcgatcacgccattgccaccacctcgatcattgctcatgacatgttcgacgaattgcttgcgcgcagGACGACGTGGAGACGGAGATGAAGAGGCTTCGGCTGGAGCTGAAGCAGACCATGGACATGTACAGCACGGCGTGCAAGGAGGCGCTGAACGCGAAGCAGA
upper sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g54590.1 (Oryza sativa), 3'ss of exon 5
--------------------------------gtaagtgaaaattttatgagaagt-gaggaaattcagt----gaagttatctgatttgatca------tgtgttgattcatttac-agAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
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gtacacacaataatgcaagctagctagctagtacaggctagatttttgtttgcatcagatgagatttcgtcgccatgatcgatcgttgtgatcgatctctcacgtacgtacatataccagGAGGACATGGAGGCCGAGATGAAGCGGCTGCGGCTTGAGCTCAAGCAGACCATGGACATGTACAGCACCGCGTGCAAGGAGGCGCTCACGGCTAAACAGA
upper sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G05600.1 (Glycine max), 3'ss of exon 8
gtaagtgaaaattttatgagaagtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
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-------------------------gtgagattaagag------cctaactatagagtctttttacttcatttcagAAAGAGCTTGAAGCCGAGATGAAAAGATTGAGGCTTGAACTGAAGCAAACTATGGACATGTACAGCTCAGCTTGCAAGCAAGCAATCTCAGCCAAAAATC
upper sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G12000.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gtaagtgaaaattttatgagaagtgaggaaattcagtgaagtta-tctg-atttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
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gtatgtaaacaagtagagcaatagactttatgatgatatcgagtttgataagattagtatgcactaaattggttggatttttatttgcagAGGGATATTGAAGCTGAGATGAAAAGGTTAAAGATTGAACTCAAGCAAACCATGGACATGTATAGCTCAGCCTGCAAAGAAGCACTTAATGCAAAAAAGA
upper sequence: Vv04s0008g01360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G26150.1 (Arabidopsis thaliana), 3'ss of exon 4
----------gtaagtgaaaattttatgagaagtgagga--aattcagtgaagttatctgatttgatcatg--tgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
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gtacgttttcttgaacgaatttctttttaggttcaagaattaagtttgaaaggctcta-aatgtaaatatggttgttgctttatttgcagAAAGATATTGAAGCTGAGATGAGAAGGCTAAAGCTTGAACTTAAGCAAACTATGGACATGTATAGCTCAGCTTGTAAAGAAGCACTTACGGCAAAAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
tgttgat putative branch site (score: 4)
ttcattt CT-rich tract
attcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgaaaattttatgagaagtgaggaaattcagtgaagttatctgatttgatcatgtgttgattcatttacagAAAGAATTAGCTGCTGAGATGAAAAGATTAAAGCTTGAACTGAAGCAAACCATGGACATGTACAGCACAGCTTGCAAAGAAGCAATAACAGCTAAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA