Sequence
atgc intronic sequence ATGC exonic sequence...ttacatagatcatgtaatttggacaaggaaacctaagcatttataccttgcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os03g40260.1 (Oryza sativa), 3'ss of exon 5
-ttacatagatcatgtaatttggacaaggaaacctaagcatttataccttgcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
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cttgca-acaccacacaaacaagaggatataccccccaacttttttagttgttttatttctagctattaacaagatacatgcaacttttcttactaaccagGCTATAATGAGTATGGTCAGCTTGGCAGAGGTTGTACTTCTGAAGGGCTACAGGGAGCTCGTGTATTAAATGCTTATGCAAGGTTCCTTGACGAAGCCCC
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G074024_T02 (Zea mays), 3'ss of exon 5
ttacatagatcatgtaatttggacaaggaaacctaagcattt-ataccttgcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
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cttcttttttaaaaaaaccaacaacaggatgcacggccacttgatttcaaaatttatatt-tctgactattgatgggacgtgctattttcttactaaccagGCTACAATGAGTATGGTCAGCTTGGCAGAGGTCGCACTTCTCAAGGACTTCAGGGAGCTCGTGTGTTAAATGCTTATGCAAGGTTCCTTGATGACGCCCC
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G50920.1 (Glycine max), 3'ss of exon 4
ttacatagatcatgtaatttggacaaggaaacctaagcatttatacctt---gcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
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ttatacag--cattaaatgtaggaaagaaaacttgagcacttacaaaggggggtttcttgcca-cctactaatcagggttttctcactgtttccataaaccagGCTACAATGAATATGGTCAACTTGGCCGAGGTGTTACTTGTGAAGGACTACAGGGGGCTTGTATTATAAGTTCTTATGCTAAATTCCTTGATGAAGCCCC
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G27700.1 (Glycine max), 3'ss of exon 5
-ttacatagatcatgtaatttggacaaggaaacctaagcatttatacctt--gcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
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tttacacag--catttaatctagggaagtaaactttagcacttacaaagtgggtttcacgcca-cctactaatgagggttatctcactgttttcataaaccagGCTACAATGAATGTGGTCAACTTGGCCGAGGTGTTACTTGTGAAGGACTACAGGGGGCTCATATTATAAGTTCTTATGCTAAATTCCTTGATGAAGCCCC
upper sequence: Vv14s0083g01020.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G02300.1 (Arabidopsis thaliana), 3'ss of exon 5
ttacatagatcatgtaatttggacaaggaaacctaagcatttataccttgcttcctgtcatcctattaatcagaattttaataatgttctgataa-atcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
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gtaagaatgctttgagatcttgttatgca--ttagaatctgtttgtttggtatttatttataatgattttgaggtttctg-tgttccatggatattataagGCTATAATGAACAAGGCCAACTTGGTAGAGGAGTCACTTGTGAAGGACTACAAGCACCTCGTGTGATAAATGCTTATGCGAAGTTCCTTGATGAAGCACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttgcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
tattaatcagaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacatagatcatgtaatttggacaaggaaacctaagcatttataccttgcttcctgtcatcctattaatcagaattttaataatgttctgataaatcagGTTACAATGAGTATGGTCAGCTTGGTAGGGGTATTACTTGTGAAGGACTACAGGGGGCTCGTGTTATAAATGCTTATTCAAAGTTCTTTAATGAAGCCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - -tcatgta
- - - - - - - - - - ggacaagg
- - - - - - - - - - - - - - aaaccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaga