Sequence
atgc intronic sequence ATGC exonic sequencegtcggtctcttgtttcctattacaatttcttgattcttttcaagaatgtctctccacttcttggaaacttttatgaagctttttgtcctgctttggattgatttgatcattgatatcactttactgttgagtagggtagaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35840.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08540.1 (Glycine max), 3'ss of exon 1
gtcggtctcttgtttcctattacaatttcttgattcttttcaagaatgtctctccacttcttggaaacttttatgaagctttttgtcctgctttggattgatttgatcattgatatcactttactgttgagtagggtagaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
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-------------------------------------------------------------------------------------tccaaagtttggttaatgtttttctt-atatccctaccctagtgtttt------aaccattaaggtgtggtgtgtgctttgt-ttaaggttgtttttgtcttctgcagTTGGCACTTTGTTGGGGGCTTTGACTGGAGCTTTGATAGGACAAGAAACTGAGAGTGGCTTCATTCGAGGGGCTGCTGTTGGTGCCATATCAGGAGCTGT
upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G36760.1 (Glycine max), 3'ss of exon 2
gtcggtctcttgtttcctattacaatttcttgattcttttcaagaatgtctctccacttcttggaaacttttatgaagctttttgtcctgctttggattgatttgatcattgatatcactttactgttgagtagggtagaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
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---------------------------------------------------------------------------aatgcttttcttctattacctagtgttttaaacattaa---------agtgtggtgtgtgctttttttaaggacaatgagttctaatgt---gtt------gtttttgtctgctgcagTTGGCACTTTGTTGGGGGCTTTGACTGGAGCTTTGATAGGACAAGAAACTGAGAGTGGCTTCATTCGAGGGGCTGCTGTTGGTGCCATATCAGGAGCCGT
upper sequence: AT4G35840.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0264g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtcggtctcttgtttcctattacaatttcttgattcttttcaagaatgtctctccacttcttggaaacttttatgaagctttttgtcctgctttggattgatttgatcattgatatcactttactgttgagtagggtagaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
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-------------------------------------------------------------------------------------tataaatcaccagttcccccaaaaggaagaacaccttaattccaggaaccatatatttt----cttagaactgtca---ataattgaattggcc-tttgtgtttgcagTGGGTACCATGTTGGGAGCCATGACTGGAGCTTTGATAGGCCAAGAGACAGAGAGCGGGTTTGTTAGAGGGGCTGCTGTTGGAGCAATATCAGGAGCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
ttgtttccttcttc CT-rich tract
tttttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcggtctcttgtttcctattacaatttcttgattcttttcaagaatgtctctccacttcttggaaacttttatgaagctttttgtcctgctttggattgatttgatcattgatatcactttactgttgagtagggtagaatctgcaactttgggtttttatgtagagctaagaaagttgtttccttcttcagTGGGCACATTGCTTGGAGCACTTACTGGAGCTTTGATAGGCCAAGAAACCGAAAGTGGGTTTATCCGAGGAGCGGCGGTTGGAGCCATTTCGGGAGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT