Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G03190.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 1
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
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-------------------------gttggtcc---accttattattttgcgttctgaaagcaaccttccaaaatttatatt-tgatcatg---tcaaataatcagtaatgtgactgactatgtgatatagataaaaatgttgtcgccattgtaagctatagtttcacttttgctaacacttaact---aatgcagGGGCAAAGTTGCTGAAGGTATTGATTTTGATCGGCACTATGGCAGATTAGTTATCATGTTTGGTGTTCCTTTCCAGTACACATTGAGTCG
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 7
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
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-------------------------------------------------------------------------ttct-catt-tactaattgagcta-ctagttgctgcggttgcttactactttacc--tatctattaagtt---catctgag-----cctaagaatatgtcta---cttgt-------ttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 7
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
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-------------------------------------------------------------------------------------------aggttgattttt-tatacaacaactagttgct--gtaattgcttattaccttacctatctattaagttcatccgatcctaagaatatatc-tacttgt-ttgcagGGGAAAGGTTGCTGAAGGTATAGATTTTGATCGACATTATGGCCGACTAGTAATCATGTTTGGTGTTCCTTTTCAATACACATTAAGCAA
upper sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 7
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
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------------------------------------------------------------------------------------------ggggaatcccctgatcccctggtatgaactgcataa-agggatgggggtgattgagggtccatcaagatgagattaaaa--gtttatttctgcact---gttgcagGGGGAAAGTAGCTGAAGGTATTGATTTTGATCGACATTATGGAAGATTAGTGATCATGTTTGGTGTTCCTTTCCAATACACATTAAGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
atcaaattttgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttttatttttgaatggtagatggtttgggaattcattgcaatgcgtctttggttctgcttctttgtttctgtattataatactggaattgtctcttctctcctattcttggttggttaacaaatattaaagaggtttcacttttgagaaatttcaaagaaagtgatcaaattttgtatttgaactgcagGGGGAAAGTTGCTGAAGGTATCGATTTTGATCGTCATTATGGAAGACTGGTTGTAATGTACGGAGTACCATTCCAGTATACATTAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA