Sequence
atgc intronic sequence ATGC exonic sequence...tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 4
tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtg---tgggctaaatctgttgaaa----tttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
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-------------gtaaactagtt-atagttagttctgtctttgtcaccaaagaaat-ttatcaaatatatatgcattggtttaaatataaagaaacatgtgtgcagGTGCTGTGGAAATGCGATGGGTTGACACATACTTCCCATTCACTAACCCGTCCTTTGAACTCGAGATATATTTTCAG------------
upper sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G078756_T01 (Zea mays), 3'ss of exon 4
tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtgtgggcta-aatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
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--gtaaatcatttgtagcttgt--------tccttatcatttgaggggatgacgaaattgatccttgtttcagataaactatagaaaaatgtcatctgcagGTGCTGTAGAGATGCGATGGGTTGACACATACTTCCCATTTACCAACCCATCCTTTGAGCTCGAAATATATTTTCAG------------
upper sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G52890.1 (Glycine max), 3'ss of exon 6
-----tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA-----------
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agcctcctccatctccctctaaccaaacattatgtaaatgattttcttt---ttttaaatagccttctctgcgcatttatagtttttcccttttgcgttt--cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCGTTTGAACTTGAAATATATTTCAAGGCATGCTATGCATACTTATCTCT
upper sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 4
tcttgaaatttctgaaatctatcagaaaggtagt--tttcatcttggggtttaccatatactgtataga---atctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
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----tatacacaaggcgtctagttatgaacttgtgatattcctttgaagtcaaatataatttgcaaagctacgtacttataaattttcccttttactgttt-cagGTGCTGTGGAAATGCGCTGGGTGGATACTTATTTCCCATTTACTAATCCATCATTTGAACTTGAAATTTATTTCAAG------------
upper sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------tcttgaaatttctgaaatctatcagaaaggtagttt--tcatcttggggtttacc-------atatactgtatagaatctg-tgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
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gtacattaagatccaataaacaatctatattcttcagcaagtgtaaataacttcaaagatggtttattaagagttgtttaggatgattatttcattaatttaagaagaagttggggaaatatacatgaaataatttgatctgagcttctttttttgg--ctgccagGTTCGGTGGAGATGAGATGGGTTGATACATATTTCCCATTTACCAATCCATCTTTTGAGCTTGAGATATATTTTAAG------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttaccatatactgtatagaatctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
ggctaaa putative branch site (score: 3)
ttgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttgaaatttctgaaatctatcagaaaggtagttttcatcttggggtttaccatatactgtatagaatctgtgtgggctaaatctgttgaaatttgcagGTAATGTGGAAATGCGCTGGATTGATACATATTTCCCTTTCACCAACCCATCATTTGAACTTGAGATATATTTTCAGGTATGCTTTTGA
- - - - - - - - - - - - -aaaggta
- - - - - - - - - - - - - - - - - - - - - -ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - - -ccatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg