Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttttttgtgtggtggaaactctttttcatgcatatgacctgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctccatgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08960.1 |
intron # | 7 |
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 7
lower sequence: GLYMA18G43420.1 (Glycine max), 3'ss of exon 6
-gtgagtttttttgtgtggtggaaactctttttcatgcatatgacctgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctccatgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC
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taaaatattatttatctactttctgtgccttttcttgtgcataaaatgttactttttttttcttccttt-tattcttacaagacattttggttgtttgcagATTCGTCTTTTCAAAAGCAATATCCTAAATTTTGGGACTTTGTAAAGAGGGCATGTACCAAGTTGATGAAAATTTTAGTTGCCTTTCAGGGCAGACATCC
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA07G18530.1 (Glycine max), 3'ss of exon 6
gtgagtttttttgtgtggtggaaactctttttcatgcatatgacctgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctcca-------tgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC
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------caatctacaatgtctagttctcatatagtgcaaagaaaaagaaaacataaatat-tattttttttccttttattcttacaagacattttggttgtttgcagATTCGTCTTTTCAAAAACAATATCCTAAATTTTGGGACTTTGTAAAGAGGGCATGTACCAAATTGATGAAAATTTTAGTTGCCTTTCAGGGCAGACATCC
upper sequence: AT3G08960.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G19490.1 (Glycine max), 3'ss of exon 7
gtgagtttttttgtgtggtggaaactctttttcatgcatatgacctgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctccatgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC-----------------------------------
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-----------------------------------aaaaagaaaacataaatattattttttttccttttattcttacaagacattttggttgtttgcagattcgtcttttcaaaaacaatatcctaaattttagGACTTTGTAAAGAGGGCATGTACCAAATTGATGAAAATTTTAGTTGCCTTTCAGGGTAGACATCCATACTCATTTGGTGATAAATTTGTTCTTTCATCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctccatgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC
tgctaac putative branch site (score: 1)
cctccat putative PPT
atatatatgtatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttttttgtgtggtggaaactctttttcatgcatatgacctgtcagcacacatatatatgtatgtattgctaacttgtgtggagcctccatgcagATTCATCTTTTCAAAATCGAGATCCTAAATTCTGGGAGTTTGTAAAGAAGGCATGTGTCAAGCTGATGAAGGTGTTAGGTGCTATTCAAAGCAGGCATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT