Sequence
atgc intronic sequence ATGC exonic sequencegtaagtaaagctcgacgctgtgtatatacacccaagtaattcaatatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G51590.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 9
-----gtaagtaaagctcgacgctgtgtatatacacccaagtaattcaa---tatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
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ttaaggcatttcaatttt--cctttcacataaatattgaataagtgtaagtgttttttaacttctttttttcatctatttctttctggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGCCTGTCAAGTTTGATTAGGAGATCAACACCATCTTCTTTTACTTATATATGTGAGAAGAATGGAGGATCTCTC
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 8
-------gtaagtaaagctcgacgctgtgtatatacacccaagtaattcaatatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
|| | | || ||| | | |||| | | | | | | | | | ||||| | | | || ||||||||||||||||||||||||||||||| | | ||| ||| | | || ||||||||| || |||||| | ||||||||||||||||| ||| | |
agacatttcaattttcctttcacataaaatat-tgaataagtgtaaatgttttttaaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 9
----gtaagtaaagctcgacgctgtgtatatacacccaa--gtaattcaatatcagcaataaaggataaggactaaatctttc-ttaatgtattg-aatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
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agattttcttttaaatatccaatgtctaaaaaatgtcaacagtctttccttcatagaatctattgatatcaa--aattcttttattggtttgttggaagcagAGAAATGTGGGAGACATCTATGAAAGGTCTGTTAAGCTTGGTCCGAAGAACAACACCATCATCTTTCACATATATATGTGAGAAAAATGGGGATTCTCTG
upper sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 4
-------gtaagtaaagctcgacgctgtgtatatacacccaagtaattcaatatcagcaataaaggataaggactaaatctttc-ttaatgtattg-aatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
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agattttcttttaaatatccaatgtctaaaaaatgt-cgacagtctttccttcatagaatctattgatatcaa--aattcttttattggtttgttggaagcagAGAAATGTGGGAGACATCTATGAAAGGTCTGTTAAGCTTGGTCCGAAGAACAACATCATCATCTTTCACATATATATGTGAGAAAAATGGGGATTCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
taaatctttcttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtaaagctcgacgctgtgtatatacacccaagtaattcaatatcagcaataaaggataaggactaaatctttcttaatgtattgaatcagAGATATGTGGGAGAAATCAATGAAAGGTTTGTTAAGCTTGGTCAAGAAATCAACACCTTCATCATTTACGTATATATGTGAGAAGAACGGAAATAATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC