Sequence
atgc intronic sequence ATGC exonic sequencegtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08960.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G18530.1 (Glycine max), 3'ss of exon 12
----gtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatat-gtattgg-tgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
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gtatgttacatagacatgtataatgtat-ttattcttgttatcattacttatgtttctctgctagttcaacatatccttctttatcttgtttcgaactaaccatgtgaatatatattt-----tttagCTGGCAGCATGTCGATCCCTATGCTTGCATATTGAAGATGCAAACTTTTCAGAGAGGGAGTTTGTTGATCTTCTTCCTATTTGTTGGGATTCATGTTTTA
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA18G43420.1 (Glycine max), 3'ss of exon 12
gtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
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gta-tgttacatagacatgtatactgttttcttattattattacttatgtttctctgctagttcaacgtgtatatcctttatcttgttttggactaaccatgtgaa-tatttttttct-tagCTGGCAGCATGTCGATCCCTATGTTTGCATATCGAAGATGCAAACTTTTCGGAAAGGGAGTTTGTTGATCTTCTTCCTATTTGTTGGGATTCATGTTTTA
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA16G19490.1 (Glycine max), 3'ss of exon 14
----gtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
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gtatgttacatagacatgtataatgtattcttgttatcattacttatgtttctctgctagttcaacatatccttctttatcttgtttcga---actaaccatgtgaatatatattt-----tttagCTGGCAGCATGTCGATCCCTATGCTTGCATATTGAAGATGCAAACTTTTCAGAGAGGGAGTATGTTGATCTTCTTCCTATTTGTTGGGATTCATGTTTTA
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0217g00040.t01 (Vitis vinifera), 3'ss of exon 3
gtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
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--------------------gtatgatgcataaattcacttttcttttgtatatgttatgccacctaaattt----gttatatggtt---caatcactgaagttgtacatctattgttttagCTGGCAGCCTGTCGGTCTCTATGTTTTCATATTGAAGATGCGAACTTTTCAGAGCAAGGTTTTACTGATCTTCTTCCAATCTGCTGGGATTTATGTTTCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
tttactt CT-rich tract
tttctttatatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtctcatcttatctcatctttgtttcttttatctttctgtcttgcattaagggcacattctctcatttttttctttatatgtattggtgacctctgagatcatctgtttacttatgtagCTGGCAGCTAGTAGGTCATTATGCTTACATGTCGAGGATGCAAATTTTTCGGAGCAAAGTTTTCTTGATCTTCTTCCAATCTGTTGGGATTCATGTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG