Sequence
atgc intronic sequence ATGC exonic sequence...ctcacatttggtgggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os07g08400.1 (Oryza sativa), 3'ss of exon 6
ctcacatttggtgggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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----------------gtgtgtttctctggctcatgac----atgctcacctccattctctcat-ttgatagctattaacttgacttatcttgatcatagATTCGTGAAGCTGATATATCTAGACTCTCATTTGCTGTTGAAATTGCTGAAGAATTCTATGGAAG
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 3'ss of exon 6
ctcacatttggtgggttctttttattttaattttta-atttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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----------gtaatctatctctctactcatatacacgcataaactcacttgtctgtttgtgtgtgcttagact--tttacttgttatgtcat---tgcagGTGCGTGAAGCTGATATATCTAGGCTCTCATTTGCTGTTGAGATTGCAGAAGAATTCTATGGAAG
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G030138_T01 (Zea mays), 3'ss of exon 6
ctcacatttggtgggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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----------gtgagttcctatcttatgatgcctcagggcttcaccacctcttgtttatttgataggagttaaaatttacttactt--ttggcga--cagATTCGTGAAGCCGATATATCGAGACTTTCATTTGCCGTCGAAATTGCTGAAGAATTCTATGGAAG
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G16130.1 (Glycine max), 3'ss of exon 8
ctcacatttggtgggttctttttatttt---aatttttaatttttgtgtgtgtgtgtgttc-ttggatat-taatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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--tttacttggtaaagactgaataatcttgaactcttcaatcagcatatttcattttatttgttttataggttagactgaaatg-ttatct--ttgtgcattcagATACGTGAAGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAG
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G03660.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------------------------------------ctca---catttggtgggttctttttatttt---aatttttaatttttgtgtgtgtgtgtgttc-ttggatat-taatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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gttctctcacttaacaactagcttttaaggcagggtttcccaagtggttgaatgattatcagaattttacttatatctagtttcaatttacttggtaaagacttaataatcttgaacccttcaaccagcatatttcattttatttgttttataggttagactgaaatg-ttatct--ttgtgtattcagATACGTGAGGCTGACATCTCTCGACTCTCTTTTGCGGTTGAGCTTGCTGAAGAATTTTATGGGAG
upper sequence: Vv07s0141g00110.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G38840.1 (Arabidopsis thaliana), 3'ss of exon 6
ctcacatttggt--gggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggt-tgggtgtt---cagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
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----tgtttagttagaagtatacaaatatggatgtgtaacaga-gtagcta-gtatttaaaagaacttcatctacaatttctctctctgatatgagctctcatcagATCCGTGAAGCTGATATTTCTCGGCTCTCCTTTGCTGTTGAGCTTGCGGAAGAATTTTATGGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
tattaat putative branch site (score: 2)
ttcttggatattaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcacatttggtgggttctttttattttaatttttaatttttgtgtgtgtgtgtgttcttggatattaatattaatatgcttgtctggttgggtgttcagATTCGTGAAGCCGACATTTCTCGATTATCATTTGCTGTTGAGCTTGCTGAAGAATTCTATGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
ctcacat
- - - - tggtggg
- - - - - - - - - - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgtc