Sequence
atgc intronic sequence ATGC exonic sequencegtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGATGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43430.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g10400.1 (Oryza sativa), 3'ss of exon 3
gtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgtt-ttgtttgtaacagCTCTTGATGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA--------------------
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---------------------gtatgttccatgaaacattt--attttctttcttttagtttaatttaacaaggcta-gtacttcgattc-ttcat---aagcattgcga---tcatttagtgatctct------gtcacatagctggatctttgtattgcattgtggttttgagccaatttcagaaattgcctaaactattgtttgatttt-tgtgacagCACGGATTTGAGACTGAACCAACCAAGGTATGCAACATTGCCAAACATAATGAAGGCAAAATCAAAAGTCATCAAGAAAGTCACCCCCGAAGATCTGGAT
upper sequence: AT5G43430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
gtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGA---TGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA--------------------
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-----------------------------------------------------------------------------------------------------------------tttctatgtaat-------agtaattagtgatttaacaagtgtgtttttctccctccttttaa-aaccctttcttgatatgtga--attttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
upper sequence: AT5G43430.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaa-attattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGATGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA--------------------
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-----------------------------------------------------------------------------------------------------------cagaaagctgactgcaattatttgccataggctagcataaatgcaacttggctct---------gtgtttcatctca----ttacttgacctgatattttgtacctca-tgcagCACTGATTTGAGACTGAACCAGCCTCGGTATGCAACACTCCCCAACATTATGAAAGCAAAATCGAAGGTAATAAAGAAGTTCACTCCACAGGAATTGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGATGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA
ctttaat putative branch site (score: 4)
ctcttgttttgttt putative PPT
aattaagctttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttctagattcttagatgattgtgtcatgatctctctcgagttgaggtttatatatatgcatcaactaacctgcatatgtcaatttgttcactgcattctttgtggaactttttttgtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagCTCTTGATGTTACAATGCAGAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAA
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