Sequence
atgc intronic sequence ATGC exonic sequence...accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57870.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 6
accatacctgcaattgactagaatttgtcataa-acaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatg-tgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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acttcaattat--ttattttaaaaccgtgatcatgcatgtacttacagactgaaattcactaagttttgatggtactaataaggtcttccttcgcactgtagGTTAACCCACATACACACCAGCTCAAAATATGTGATTTTGGCAGTGCAAAAGTTTTG
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 5
------accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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tggcttaacctaactgaaagatgatacaatttgt----agcaaatatacctgtgatgccatttgttactatttggttggctcaaatgcatgt-tactcatgt-cagGTGAACCCACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 6
accatacctgcaattgactagaatttgtcataaacaaatgttgcct-tgtttttattaaacaatcttttatttttttct----ttacacctattgtgat-gtg-cagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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----tgacttaacctaactgaaagatgatacaat---atgtagcaaatatacctgtgatgccatctgttactatttgttgggctcaaatgtatgttactcatgtcagGTGAACCCGCACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 5
----accatacctgcaattgactagaatttgtcataaacaaatgttg--ccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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tttggacagacttatca--ggcta-actccatggtga-cgacttttaaattttgatcttgttatcttactttgtaagactgatttgttaa--attgttatgttcagGTGAACCCACACACGCATCAGCTGAAACTTTGTGATTTTGGGAGTGCGAAAGTTTTG
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------------------------------------------------------------accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatc----ttttatttttttctttaca--cctat---tgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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gtacgtgtgtccgacgaatcttgtcatgtgttcaagtatcttgaaaacacgatgctgactgtttaagcactcgtatttgttgctcggcatgggtggaagctggttactgagatgtttggtatgagtcacgggaaagtacaggagttgccgtggtgtcgtaacaaacttgtgtttgcatggcacagGTGAATCCTCATACGCACCAGCTGAAACTGTGTGATTTTGGAAGTGCGAAAGTGCTG
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 6
accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
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-----------------------------gtaaaccctccttg--tgctttcgagtcctggaattcttatgcttttcttt-tgctggatttcat---cagGTAAATCCACACACACACCAGCTCAAGCTCTGTGACTTTGGGAGTGCTAAAGTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
tttattaaacaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatacctgcaattgactagaatttgtcataaacaaatgttgccttgtttttattaaacaatcttttatttttttctttacacctattgtgatgtgcagGTGAATCCACACACACATCAGCTGAAAATTTGTGATTTTGGGAGTGCAAAAGTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA