Sequence
atgc intronic sequence ATGC exonic sequence...tcttcatgtaccacttggaatgttatagctattattcatattggatttagcatcatatagcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 13
tcttcatgtaccacttgga-atgttatagctattattcatattggatttagcatcatatagcttggagaacattttt--tattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
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---gtttgtgctgcatgcatacaatatagctata---catct---attta----catcttccatgaaagtcatttcaagcatttaattgttctttca--acagGAGGCCGTCCTCCAAACTGTTAGTGTTATTTTTGAAGACCCAGGTGTGCAGGATCTACTCGTGAAGCTTTACCAGAAAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 19
tcttcatgtaccacttggaatgttatagctattattcatattggatttagcatcatat-agcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
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-attactttggtatgttcaatgaaatcaccattttgatgaatatctcttgctttggaagagatttgacttctgatacattgaattttcttcttggtgatagGAAGCTGTGCATCAAACTGTCAGTGTGATATTTGAAGATCCTGGTGTCCAGGAGTTACTGGTGAAGCTATATCAGAAAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT1G71820.2 (Arabidopsis thaliana), 3'ss of exon 19
-----------------------------------------------------------------------------tcttcatgtaccacttggaatgttatagcta-ttattcatattggatttagcatcatatagcttggagaacatttttta----ttaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
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gttcgtcaaagattcctttttctccctggtcttcaatccaaatatagtttttgcatctcgatttatggccttacagttgcccagatggctgttgaaatgaaatttcaacttgatcttgcgatctttaaagttaaaatttatgttggattttacacaagtcccatctggtcctttgatttcagGAAGCAGTGCATCAAACAGTTCGCGTTATCTTTGAGGATCCAGGAGTTCAGGAATTACTTGTCAAGCTTTACCAGAAAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ08885 (Selaginella moellendorffii), 3'ss of exon 17
tcttcatgtaccacttggaatgttatagctattattcatattggatttagcatcatatagcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
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---------------------------------------gtgaggagggaggtgatgtagaatgaggcga------tgacaaagtgcattc---tcgtagGAAGCCGTCCAACAAACCGTGAGGGTGATTTTTGAAGATCCTGGAGTAAAGGAGCTACTTGTCAAACTTTATCAGAAAG
upper sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: EFJ12004 (Selaginella moellendorffii), 3'ss of exon 17
tcttcatgtaccacttggaatgttatagctattattcatattggatttagcatcatatagcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
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---------------------------------------gtgaggagggagatgatgtagaatgaggcga------tgacaaagtgcattc---tcgtagGAAGCTGTCCAACAAACCGTGAGGGTGATTTTTGAAGATCCTGGAGTAAAGGAGCTACTTGTCAAACTTTATCAGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagcatcatatagcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
tattgat putative branch site (score: 3)
aacattttttattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcatgtaccacttggaatgttatagctattattcatattggatttagcatcatatagcttggagaacattttttattaaattgcttattgatggtagGAAGCTGTGCATCAAACTGTGAGTGTTATATTTGAAGACCCAGGAGTGCAAGAGTTACTTGTCAAGCTTTATCAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- -tcatgta
- - - - - ccacttg
- - - - - - - - - - - - - - - - - - - - - - - - agcatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - agcttgg