Sequence
atgc intronic sequence ATGC exonic sequence...tggtctagtgttgggttcttaattcaacaaatctctatggctcttatacttgtaatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g08230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 7
tggtctagtgttgggttcttaattcaacaaatctctatggctctta-tacttgtaatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
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-----tatcactcgaaggtt--ttcaaactctttctaccattttaaatatgctaggtgtccatggtacgaagaacaggtaaactcattgtttttcttttc---cttatagACCATCATGCACACGATCACACCCATGATCCTGGTGTTTCTTCTGTAAGCATTGTTTGTGAAGGGGAGATGGATCTTGAAAAG
upper sequence: Vv09s0002g08230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G180418_T01 (Zea mays), 3'ss of exon 12
tggtctagtgttgggttcttaattcaacaaatctctatggctcttatacttgtaatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
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----cttgtctttaattttgtatatgtaaattctctcttatcact-tatttataa--atcccaa-gtatgaagtaagtaaactctgtgctgccc-tctttttcttgtagATCATCATGCACATGACCACACTCATGATCCTGGTGTTTCTTCTGTGAGCATTGTTTGCGAAGGGGAGATGGATCTTGAAAAG
upper sequence: Vv09s0002g08230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 7
----------------------------------tggtctagtgttgggttc-ttaattcaacaaatctctatggctcttatacttgt-aatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
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gtacctattattttgccttgagtcatagctttttaaatgccattttgattttgtttgtagcactagtcacaatgcactggttgcttctcaattcattctgtcgttggcaataaaaatcattttgttttgtgtacagAACACCATGATCACCACTCTCATGATCATAGTCACGATCCTGGTGTTTCATCTGTCAGCATAGTTTGTGAAGGAAGCTTAGACCTTGAGAAG
upper sequence: Vv09s0002g08230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 7
--------------------------------tggtctagtgttgggttcttaattcaa---caaatctctatggctcttatacttgt--aatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
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gtacctattattttgcctcgagtcagagctgtttgaatgccattttgttcttgtttgtagcacgagtcacaatgcactggttgcttctcaattcattctgttgttgggaataaaaattattg---ttttgtgtacagAACACCATGATCATCACTCTCATGATCATAGTCACGATCCTGGTGTTTCATCTGTCAGCATAGTTTGTGAAGGAAGCTTAGACCTTGAGAAG
upper sequence: Vv09s0002g08230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G80480.1 (Arabidopsis thaliana), 3'ss of exon 7
-tggtctagtgttgggttcttaattcaacaaatctctatggctcttatacttgtaatgatagtaatgagtgatattgatgttt---------------tcaacattgggcatgcagAACACA----ATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
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gtaagtttattaggaaaccttgatttagttatattgattgcatgctccagctttacgaacatggattgttggttctggtctctctcatcacaacctaatcagtctctgattcttaaacctcagATCATCATCATCATTCTCATGATCACACCCATGATCCCGGTGTTTCTTCAGTCAGTATAGTTTGCGAAGGAAGCTTAGACCTTGAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacttgtaatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
tattgat putative branch site (score: 3)
taatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtctagtgttgggttcttaattcaacaaatctctatggctcttatacttgtaatgatagtaatgagtgatattgatgttttcaacattgggcatgcagAACACAATGATCACCATTCCTATGATCACACTCATGACCCAGGTGTTTCTTCAGTCAGCATAGTTTGTGAAGGGAGCTTGGACCTTGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - -gtgttgg
- - - - - - - - - - - - -aacaaat
- - - - - - - - - - - - - - - - ctctatg