Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G14000.1 (Glycine max), 3'ss of exon 3
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
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--gtactgtggatcatgtagtctagtcttttaacatatttaagtattcaat--gttttacttgttagtcattgtcaggattggttgtgtgcttgaactttct-gcat-tggcagATGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGTTTGACCAAAATGACACAGATGCGGATACGTATGAGGAAACTTGCTTTGAAGACAAG
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G43930.1 (Glycine max), 3'ss of exon 3
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
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--gtactgtggatctacgttgtcttttgacatgtttatgtattcaatgttttac--atgttagtg----attatcaagatcagttgtg-tgcttgaccattctgcat-tggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 13
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
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--------gtattctacttctccttgcaatttcatagggtttttgtttcct---ctttatcgaagtttttggaggacaccggttgcttaatctatatttatttggttttaacagATGTTTTGGCCGAAGTTGCTTGTTCACAAAACAAAGCAGCGTCTCACTAAAATGACTCAGATGCGAATTCGCATGAGGAAGCTTGCATTGAAAACAAG
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 4
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
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--------gtattctact-tctccttgcaatttcatatggtttttgtttact--cttcatcgaagtttttggaggacaccagttgcttaatctatatttatttggttttaacagATGTTTTGGCCGAAGTTGCTTGTTCACAAAACAAAGCAGCGTCTCACTAAAATGACTCAGATGCGAATTCGCATGAGGAAGCTTGCATTGAAAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
ttcttac putative branch site (score: 2)
ttattttctttcttac CT-rich tract
ttttaattattttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG