Sequence
atgc intronic sequence ATGC exonic sequencegtacaagtcctcaactagcttttgttacagctgcgaaactaatgaagcggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggtgtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G17240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G17240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G39060.2 (Glycine max), 3'ss of exon 4
gtacaagtcctcaactagcttttgttacagctgcgaaactaatg-----aagcggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggtgtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
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------atttccaatagataggggtcacaagtacaatgcctgttttcactctcttcatcccattgtctagaaaatagagaattacta--attaccttgttttcaccagGTTCTATTATGCTATGGAACTTACACAAATTTGGAGCTTCTTGAACACTATGGGTTTCTCCTACAAGAAAATCCAAATGACAAAGTTTTTATCCCTTTGG
upper sequence: AT5G17240.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv04s0079g00650.t01 (Vitis vinifera), 3'ss of exon 1
gtacaagtcctcaactagcttttgttacagctgcgaaacta---atgaagcggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggt--gtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
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--------tcctacttagtgccaatggcatcatcatcattttgcatgtcttgttggcctttcatatatgaggcgacatgggtttgaaaataaagttacatgtttgcagGTTCTTTTAAGCTATGGAACATACACGAATTTGGAACTTCTTGAACACTATGGGTTTCTTTTAGATGAAAACCCAAATGATAAGGCTTTCATTCCCTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggtgtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
aaaatatactgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaagtcctcaactagcttttgttacagctgcgaaactaatgaagcggaagcacaacgtagaaaatatactgaatggtgaggattgtatttgtgggtgtagGTTCTTCTATGTTATGGGACTTACACGAATCTAGAGCTTCTTGAGCACTATGGGTTTATGTTAGAAGAGAACTCAAATGACAAGGTCTTCATTCCTCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA