Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgtgtgtggcttacttctttcagaattgaaatttgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G061515_T01 (Zea mays), 3'ss of exon 1
----------------------------gtgagtgtgtgtggcttacttctttcagaattgaaatttgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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gtagtatattcatccctcacgtacgatcacaacgctgtgatgcatgcggctgt-ggaatcaaaatttaacggacatgggaacatgtactgatttataactgaggatgtttgtgtgtgaac-cagCTCTGGAACATCCGGAGGGGAGAGGAAGCTGATGCCGACCATCGCCGACGAGCTGGACAGGAGGTCGTTGCTGTATAGCCTGCAGATGCCGGTGATGAGC
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G38000.1 (Glycine max), 3'ss of exon 1
----gtgagtgtgtgtggcttacttctttcag--aattgaaatttgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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tttgctaaaatcttgacatcaattttcttcatacaatttgtccttcttcctttttaaattaagtatagctgaa--attagatatatttattgaatgaaatagCTCTGGGACTTCTGGTGGGGAGAGAAAATTGATGCCAACCATAGAAGAGGAGCTAGAGAGGAGATCAATGCTTTATAGCCTCTTGATGCCAGTGATGGAT
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G32410.1 (Glycine max), 3'ss of exon 1
gtgagtgtgtgtggcttacttctttcaga--attgaaatttgatccgttttgagttctgtgtt-ttggaattg---tgagttgt---tttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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----atattgacaataaattttcttcatataacttgtccttcttccttttcaaataaagtgcaactgaaattaatctgagatatatgtttcttgaatgaat-tagCTCTGGGACTTCTGGTGGGGAGAGAAAATTGATGCCAACCATAGAAGAGGAGCTAGAGAGGAGATCAATGCTTTATAGCCTCTTGATGCCGGTGATGGAT
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G11200.1 (Glycine max), 3'ss of exon 2
----gtgagtgtgtgtggcttacttctttcagaattg-aaatttgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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agaaacaagagaatgtgaattataataaagaaaattatgaaaaaagtgcatgttgtaaaaagagtgagtaaaataaca-ttattctgttgatttaatatagCTCTGGAACATCTGGTGGGGAGAGAAAACTGATGCCAACCATAGAAGAGGAGCTAGAGCGAAGATCATTACTCTACAGCCTCCTGATGCCAGTGATGGAG
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
---gtgagtgtgtgtggcttacttctttcagaattgaaatt--tgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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aagaagagaaacaagaggatgtgaattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataaca-ttattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
upper sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G54510.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagtgtgtgtggcttacttctttcagaattgaaatttgatccgttttgagttctgtgttttgga-att---gtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
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tccattcactgttaaaacctttatccaaaaagaaaatttttaatgggtctacttttatctttcatatattcacaaaagaattattgatatatgtcaacagTTCTGGGACTTCTGGTGGAGAGAGGAAACTGATGCCAACAATCGAAGAGGAACTAGACAGAAGATCACTTCTCTACAGTCTCTTGATGCCTGTGATGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
ttttgat putative branch site (score: 4)
ttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgtgtgtggcttacttctttcagaattgaaatttgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT