Sequence
atgc intronic sequence ATGC exonic sequencegtattttattactttgaagttctgccgtgctattttattgatatcgcctttagatttttctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 3
gtattttattactttgaagtt-ctgc-cgtgctattttattgatatcgcctttagatttttctcc---tattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
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----gtgaatgttgcaaagacactgcataagctgctgcattgtttatccatgtgtgtttttgacgaagtgccctttttttactttttgtgcagAGTTACACACAATATATTCCGCTTCCCATTACTGATCTTGATTCATGGCTGAAAACACCTTCTATATATGTTTTTGACTGCTCAGCAGCTGGAATGATTG
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 4
-----gtattttattactttgaagttctgccgt----gctattttattgatatcgcctttaga----tttttctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
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gatatgggttccaattgagtataattccctcatttacaatattatgatgaaaagagcttcatgacattcttattctcattctgcatcacatcttgttca-gAGTTATACACAGTATATTCCCTTACCTATCAATGAACTTGATTCCTGGCTGAAGACCCCATCAATTTATGTTTTTGATTGCTCTGCGGCTGGGATGATTG
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G44210.1 (Glycine max), 3'ss of exon 4
----------gtattttattactttgaagt--tctgccgtgctattttattgatatcgcctttagattttt-ctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
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gatatgggttccaattgagtataatgccctcatttacaatatcatgatgaaaatagcttcatgacattcttattctcattcttcatcatatcatgttca-gAGTTATACACAGTATATTCCCTTACCTATCAGTGAACTTGATTCCTGGCTGAAGACCCCATCAATTTACGTCATTGATTGCTCTGCGGCTGGGATGATTG
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattttattactttgaagttctgccgtgctattttattgatatcgcctttagatttttctcctattctgactggtg---tattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
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gtctgttttttactagcgttttcttttctctaccatgttcttgttccttctcgtctgttaccacgagctgattgattctctgtttgagcagAGTTATACACAGTACATTCCCTTGCCAATCAGTGAACTTGATTCCTGGTTGAAGACACCCTCCATCTATGTTTTCGACTGCTCTGCTGCTAGGATGATTC
upper sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattttattactttgaagttctgccgtgctattttattgatatcgcctttagatttttctcctattctgactggtgtattg-gtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
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-------gtcagttttctttcctttctctctacattgtccatgttcttagaagtctgttatcagccacctattcatcttgtgtgtgcagAATTTTACGCAGTACATTCCCTTGCCAGTCAGCGAGCTTGATTCCTGGTTGAAAACACCCACCATTTACGTTTTTGACTGCTCTGCTGCTAGGGTGATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttattgatatcgcctttagatttttctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
ttctgac putative branch site (score: 2)
tttagattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttattactttgaagttctgccgtgctattttattgatatcgcctttagatttttctcctattctgactggtgtattggtgaagAGCTATACTCAGTATATCCCCTTGCCAATCAGCGACCTGGATTCCTGGTTGAAGACACCGTCAATATATGTTTTTGATTGCTCTGCTGCTGGGATGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT