Sequence
atgc intronic sequence ATGC exonic sequence...tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
--------------------tcactgatgagggtaatatatccatatccaaccatgtttcagtttg-cttactctctgatatg-gtctctaa-----gaaagttggtcgat-tttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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gtaagctgaatctgcacaattcatgtatttgcataa-atttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaaaagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgata--tggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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-------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcgattttctgtgctc---tgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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------gtaaggtt--ttttcttgtgtttcatcacattctgactgcaaagttatggttttttagactcaagaggtttgattttagtcctgtctttgttcttagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
--tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcgattttc--tgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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acatgttggtgctagaaatgggt--atagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcg------attttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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------ggaattgtttcatacttgcaacgattgttagtgatatgccatagttcttgaatacggctcggatgaattctggctctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG
upper sequence: GRMZM2G123866_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S196_50V6.1 (Physcomitrella patens), 3'ss of exon 6
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctc--taagaaagttggtcgatt-----ttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
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-----aagaattttgataaatttttagtga--cgtagttgtatgtgaacaatcctggaaattgcttcaataaggtggttgttctaacacaacttctctatgtttcagTCTGAAGACGAGCGTGAAATGTGTGCACGTACCATCTACTGTACAAATATTGATAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttactctctgatatggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
ttttctgt CT-rich tract
taagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcactgatgagggtaatatatccatatccaaccatgtttcagtttgcttactctctgatatggtctctaagaaagttggtcgattttctgtgctctgtagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATTGACAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- -ctgatga
- - - - - - - - - - - - - -ccaacca
- - - - - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttctg