Sequence
atgc intronic sequence ATGC exonic sequencegtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgttttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g27960.1 (Oryza sativa), 3'ss of exon 9
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctg-ttttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
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gtgtgtttagagaacttattagcatcct-ctgtattgttcatactttatacaattacaagagatcttacttttatgatctagtgcacattctaattct-----------gaataaatgtttccagGAAGGAACATCGAACTATTTTAAAGGCCTTATGCTTATCTTATGCTATCTCATAGTTGCTGCGAGCTTCTTCGTACATGTTGATCCCGATTCAA
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G00380.1 (Glycine max), 3'ss of exon 9
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgtt-ttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
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----------------------tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgacaaccatctttaatttgtgttat---tccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 9
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgttttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
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---------------------ttgatttgtgtgtgataggtttatatatagagttttttttttgttgccactattacttatgtttgtgacaaccattttaaatttgcgttat---tccatgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATTCTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTG
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 9
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgtt-ttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA----
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----------------------tgatttgtgtgtgataggtttatatgtagagtatttttttttgttgccactattatttatgtttgtgacaaccatctttaatttgtgttat---tccttgcagGAAGGAACCTCAAATTATTTTAAAGGGTTGATGCTTATACTATGCTATCTAATAGTTGCTGCCAGTTTTTTCGTACATGTAGACCCTAAAAGTGGTGA
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 10
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgttttgtagcctatttttagttctaatgttttcattt-tattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
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-----------------atgtacatagagctttatcttccta-----atcaatttattttccgtg-tataaattatttctttttta--cctgatgaattcattaattttggctttgtatttgcagGAAGGGACATCAAACTATTTTAAAGGTTTGATGCTTATTCTATGCTATCTCATAGTTGCAGCCAGCTTTTTTGTACATGTTGACCCTACAAAGG
upper sequence: GRMZM2G053004_T03 (Zea mays), 3'ss of exon 9
lower sequence: PP1S336_18V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgttttgtagcctatttttagttct----aatgttttcattttattatatatgtttttc-cagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTG-ATGCAA-----
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gtgagctgtcactgctgttcc-cttctttctttagaaattgatagaaatgca--tagttctcggttaaattataagcacattcgtgattgtttaaaacactaatgtttttttgtgtaaacttttgacagGAGGGTACTGCAAATTATTTCAAGGGTTTAATGTTAATATTATGCTACCTAATAGTTGGAGCAAGCTTCTTTGTCCATGTCGACATTCCAGACAAGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
ttctaat putative branch site (score: 2)
tgtttttcc putative PPT
tatttttagttctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcttacagaacaaagcaacatcctattctattttcctctgtatatgaagttactacacgggctgttttgtagcctatttttagttctaatgttttcattttattatatatgtttttccagGAAGGCACATCAAACTATTTTAAAGGTCTTATGCTCATCTTATGCTACCTCATAGTTGCTGCAAGCTTTTTTGTCCATGTCGACCCTGATGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT