Sequence
atgc intronic sequence ATGC exonic sequence...ctcatattaattttatattccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g47940.1 (Oryza sativa), 3'ss of exon 6
----ctcatattaattt-tatattccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
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gttactagcatggctttgtctagctgattcattgaaggcatttttgccacacaattatgaaccaa---aaatgacacct--cattacaaattattgataatgcagGTTTAGCTGGACTTCGTGTGGGTTACGGAGCATTTCCTCTAAGCATAATCGAGTATTTATGGAGGGCTAAGCAGCCCTATAATGTTTCTGTAGCAGCAGA
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G170595_T01 (Zea mays), 3'ss of exon 6
ctcatattaattttatatt-ccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaa-tgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
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atcatctattgttcaaatcacttgccttgaaaaaaatcaaagacattttctacaaaattaca--aactgaaaggtcaagcttaaaagttattaacaatgcagGTTTAGCTGGTCTTCGTGTGGGTTATGGTGCATTTCCTCTGAGCATTATCGAGTATTTGTGGCGGGCCAAGCAGCCCTATAATGTTTCTGTGGCCGCAGA
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G27220.1 (Glycine max), 3'ss of exon 7
ctcatattaattttatattccacttttggaaacaacttcttttgttagcttt----cctttcatgttaaa-tagcttcttacatttcaaatgaac--actgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
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------ctgatttgttatattgagtg-ggaagctactttataacttgggcttggagttgcttgtcctaatctgaaccattaaatgcataattttctaattgtctcagGTTTAGCTGGACTTCGAGTGGGATATGGAGCTTTTCCTTTGAGTATAATTGAGTATCTTTGGAGAGCAAAGCAGCCGTATAATGTATCTGTTGCTGCTGA
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G71920.1 (Arabidopsis thaliana), 3'ss of exon 7
ctcatattaattttatattccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
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------------gtaaattttggtttatcactctatataatcta--aacattacagatataa-agtctgcatctaagaattctgatga----tatttcagGTTTAGCCGGGCTTCGAGTTGGATATGGAGCGTTTCCGTTGAGTATAATCGAATACCTGTGGAGAGCAAAGCAACCATACAATGTCTCTGTTGCAGGGGA
upper sequence: Vv18s0072g00940.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G10330.1 (Arabidopsis thaliana), 3'ss of exon 7
ctcatattaattttatattccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
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------------gtaaattttggtttatcactctatataatcta--aacattacagatataa-agtctgcatctaagaattctgatga----tatttcagGTTTAGCCGGGCTTCGAGTTGGATATGGAGCGTTTCCGTTGAGTATAATCGAATACCTGTGGAGAGCAAAGCAACCGTACAATGTCTCTGTTGCAGGGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
tttcatgttaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcatattaattttatattccacttttggaaacaacttcttttgttagctttcctttcatgttaaatagcttcttacatttcaaatgaacactgatgcagGATTAGCTGGACTCCGTGTGGGGTATGGAGCATTTCCTTTGAGCATTATTGAGTATCTTTGGAGAGCAAAGCAACCATATAATGTTTCTGTTGCTGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - -ggaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa