Sequence
atgc intronic sequence ATGC exonic sequencegtaagattgtagtggaaacatcaaaatatgcagctttcggttttggtgaaaggaaagtgtttcgttacaaattctcaatgcttgtgcttttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------gtaa--gattgtagtggaaacatcaaaatatgcagctttcggttttggtga---aaggaaagtgtttcgttacaaattctcaatgcttgtgcttttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
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gtgagtttttccccctttttagttttcacccttgttacatctttaatactgactaatttcagaattttgaagtctgtagctgcttgtatttcttattttaatgttttcccatttgaatcttctttctttatgcaactaatttccctccccctctgcaatgcttgcaa----agGTGGTGCCATGACATTGGCCGTGAGCAAGCTGCAAATAAGCCACTTTTGAAAACTGTCTTTCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------------------gtaagattgtagtggaaacatcaaaatatgcagctttcggttttggtga---aaggaaagtgtttcgttacaaattctcaatgcttgtgcttttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
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gtgagttttttttcctcttttttagttttcacccttgttccatcttaaatactgactaatttcagaatttttaagtctgtggctgcttgtatttcttattttaatgcttttccattttaatcttctttctttatgcaactaatttccctccccctctgcgatgcttgtaa----agGTGGTGCCATGACATTGGCCGTGAGCAAGCTGCAAATAAGCCACTTTTGAAAACTGTTTTTCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------gtaagattgtagtggaaacatcaaaatat-gcagctttcggttttggtg---------aaaggaaag--tgtttcgttacaaa------ttctcaatgcttgtgctttt-----agGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
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gtgagttcttttacgcttccttccttttaattatttttaatatagacttatgctaaaaaatttaaagttagtgtaagcgtgtaactgttgtacttctttgttttaatgtttttttttaagtcaaatcttctttctttgcgcaattgatctttcctcccctttattatttgtaaagGTGGTGTCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTTTTAAAAACTGTGTTTCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gtaagattgtagtggaaacatcaaaat--atgcagctttcgg----ttttggtgaaaggaaagtgtttcgttacaaattctcaatgcttgtgctttt----------------------------agGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
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gtgagttcttttaccccttcttcctttcaattatttttaatatagacttgtgctagaaattttcaagttagtgtaactgttgtacttctttgttttaatgttttttttttaagtcaaatcttctttctttgtgcgtttgatttttcctcccctttaatatttgtaaagGTGGTGCCATGACATTGGTCGCGAACAAGCTGCAAATAAGCCGCTGTTAAAAACTGTGTTTCAG
upper sequence: AT1G72960.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 5
-----------------gtaagat-tgtag--tggaaacatcaaaatatgcagctttcggttttggtgaaaggaaagtgtttcgt------tacaaat----tctcaatgcttgtgct-tttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
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gtaagttttattacaaaacaaggcatataacttggattctacagattatgtttcagttaaacatgttttgaggtatctctttaatggtttatgcgagtaatatcttgaagcgaattttgtttagGTGGTGTCATGATATTGGTCGTGAGCAGGCTGCAAATAAGCCTCTTCTGAAAACTGTATTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttggtgaaaggaaagtgtttcgttacaaattctcaatgcttgtgcttttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
tgctttt CT-rich tract
ttacaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagattgtagtggaaacatcaaaatatgcagctttcggttttggtgaaaggaaagtgtttcgttacaaattctcaatgcttgtgcttttagGTGGTGTCACGACATTGGCCGTGAACAAGCTGCTAATAAACCTCTCTTGAAAACTGTCTTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT