Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 5
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggc-----------tcaatg---ttcatgc---tctatctg-atatggtctctaagaaagttggtcgat-tttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
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gtaagctgaatctgcacaattcatgtatttgcataaatttcattattaattcttatttcaatgaaatttatgcaaatacgtgtacacctgatgtctaa--aagctggcccccattcttgttgcctgcagTCCGATGATGAGCGTGAGATGTGTGCAAGGACTATTTACTGCACAAACATTGACAAGAAG
upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G32790.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
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---------------------------------gtgagattttcctctactatgcaaagtttctgatggttagcgactgaggaaaatgatttagtct-tgt-ctatgcagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGTACTAACATAGACAAGAAG
upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 5
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
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-----------gtaaggttttttcttgtgtttcatcacattctgactgcaaagttatggttttttagactcaagaggtttgatt-ttagtc--ctgtctttgttct-tagACTGAAGATGAGCGTGAGATGTGTGCAAGAACTATCTACTGCACTAACATTGACAAGAAG
upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 6
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttc--tgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
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--------acatgttggtgctagaaa--tgggtatagcttagaaacgtgccgatcaaacattgtttactat--ttcttgtgcttgttaattaaatgttatcgtgtcatccagTCTGAAGATGAACGTGAAATGTGCGCCAGGACTATTTACTGTACAAATATTGATAAGAAG
upper sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S62_224V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
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----ggaattgtttcatacttgcaacgattg--ttagtgatatgccatagttcttgaatacggctcgg-atgaattctggct---ctaacttagttactctccattacagTCTGAAGATGAGCGTGAAATGTGTGCACGGACCATCTACTGTACAAATATTGACAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
atctgat putative branch site (score: 4)
ttttctgt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaaaccttccggaaccaacatgcttgtcttaagttcatggctcaatgttcatgctctatctgatatggtctctaagaaagttggtcgattttctgtgctctgcagTCTGACGATGAACGTGAAATGTGTGCAAGGACTATCTACTGCACAAACATAGACAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG