Sequence
atgc intronic sequence ATGC exonic sequence...aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g64690.1 (Oryza sativa), 3'ss of exon 1
-aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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attctgcattgttgagagctgagatccatattataacataatatg-gctgggagttgggatggctgttgctgagatgtctttcttgtacctctttatccagGCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G28300.1 (Glycine max), 3'ss of exon 1
aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaacatatgtttcttctttgtgt------ggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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----agttcccttgg--tgattattttgatcttttaaaatatcgttggcttgataagtattttcctttttcttattttgcactgggttttcaatttgaatttgcagGCTTATGATCAGCATCTTAATATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G09090.1 (Glycine max), 3'ss of exon 1
aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcct--cattaacatatgtttcttctttgtg---tggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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-----aagtgcccttggtgattattttgatcttttaaaatttcgttggtttgatattgattttccttttcttattttgtactgggttttctatttgggtttgtagGCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGG
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G76860.1 (Arabidopsis thaliana), 3'ss of exon 1
aaccaaaaagtttggacttatttattacataaca-aagaagtttgcaatcct----cattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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---aatttaattttgacaaagttcttaaattttggaagatttctacactcttgagttactcacttaggtttgatgttgttgttgttgttaattct--ttgggcagGCGTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAAACTATCACTACAGTAGAAATCGATGACGAGACATATGAAGAGATTGTTCGG
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G21190.1 (Arabidopsis thaliana), 3'ss of exon 1
----aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaaca-tatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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tcagtttcgaaagcctcagcgagagctaattggcg-tagaaaacctcataatcttgttaaattctaagactctcacttttgttgtt----gtttttgtggtgtagGCTTTTGATCAGCATTTGAATATGATTCTGGGTGATGTTGAAGAGGTTATTACGACTATAGAAATCGACGACGAGACATATGAAGAGATTGTTCGG
upper sequence: Vv18s0072g00710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S16_329V6.1 (Physcomitrella patens), 3'ss of exon 1
aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaacatatgtttcttctttgtgtggt-ttggcaatc---tggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
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---tatgccggccgactttgcat-tttcattaaagtattgattgttgtagtatttgaagcagtttccctgctggcgggtccttattaattgaatgattgtgcagGCCTACGATCAGCACTTGAACATGATTCTTGGTGAGGTGGAGGAAGTTACCACTTCGGTAGAGATCGATGACGAGACTTATGAGGAGATTGTGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcctcattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
cattaac putative branch site (score: 2)
tttttc putative PPT
attaacatatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaccaaaaagtttggacttatttattacataacaaagaagtttgcaatcctcattaacatatgtttcttctttgtgtggtttggcaatctggtttttcagGCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
aaccaaa
- - - - - - - - - - - - - - - - caaagaa
- - - - - - - - - - - - - - - - - - - - - - caatcct
- - - - - - - - - - - - - - - - - - - - - - - - - -cattaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgg