Sequence
atgc intronic sequence ATGC exonic sequencegtacccattatactatatccatacttatttgtagtcatcttatgtttttgtctggctaaacctcattttcttacacttctttctctcaatgtaattcatttttcagGTTGTTGCTTTCGTTGCTCCAAAAATTATCGGTGGGAGTAAAGCACCTTCCCCTGTGGGTGACCTTGGGATGGTAGAGATGACACAAGCATTGAATTTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G47390.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G47390.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA18G47790.1 (Glycine max), 3'ss of exon 5
gtacccattatactatatccatacttatttgtagtcatcttatgtttttgtctggctaaacctcattttcttacacttctttctctcaatgtaattcat--ttttcagGTTGTTGCTTTCGTTGCTCCAAAAATTATCGGTGGGAGTAAAGCACCTTCCCCTGTGGGTGACCTTGGGATGGTAGAGATGACACAAGCATTGAATTTAA
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-----agacaaattccaattagaattattttggcttatttg--gctttatcttattttgattttatttttatgatatgttggataacggtgatatttatgcccttcaGGTTTATGCTTTTGTTGCTCCTAAAATTATTGGTGGAAAGAATGCACCTTCTCCTGTGGGTGATCTTGGGATGGTTGAGATGTCACAGGCTTTAAATCTA-
upper sequence: AT3G47390.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G38520.1 (Glycine max), 3'ss of exon 5
gtacccattatactatatccatacttatttgtagtcatcttatgtttttgtctggctaaacctcattttcttacacttctttctctcaatgtaattcatttttcagGTTGTTGCTTTCGTTGCTCCAAAAATTATCGGTGGGAGTAAAGCACCTTCCCCTGTGGGTGACCTTGGGATGGTAGAGATGACACAAGCATTGAATTTAA
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--tccaatgagaattaatttg-gcttagttggctttatcttgtttgatttttttattat-tattattattatatgttggataatggtgatattatgcattc--cagGTTTATGCTTTTGTTGCTCCTAAAATTATTGGTGGAAAGAATGCACCATCTCCTGTGGGTGATCTTGGGATGGTTGCGATGTCACAGGCTTTAAATCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggctaaacctcattttcttacacttctttctctcaatgtaattcatttttcagGTTGTTGCTTTCGTTGCTCCAAAAATTATCGGTGGGAGTAAAGCACCTTCCCCTGTGGGTGACCTTGGGATGGTAGAGATGACACAAGCATTGAATTTAA
ttcttac putative branch site (score: 2)
ttcatttttc putative PPT
aatgtaattcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacccattatactatatccatacttatttgtagtcatcttatgtttttgtctggctaaacctcattttcttacacttctttctctcaatgtaattcatttttcagGTTGTTGCTTTCGTTGCTCCAAAAATTATCGGTGGGAGTAAAGCACCTTCCCCTGTGGGTGACCTTGGGATGGTAGAGATGACACAAGCATTGAATTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG