Sequence
atgc intronic sequence ATGC exonic sequencegtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctctttccccttcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 3
gtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctctttcccct-tcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
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----------------------gttagtttttatcaactgctcac---acaaactccccttgattgctgtt-catatctctttctcggattgctgcctaaaacaacatgactcattcctctatt---tcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
upper sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 2
gtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctc---tttccccttcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
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-------------------------gttagtgtttatcaactcctcacacaaactcgtcttgattgctgtt-catatctctttctgggattgctacctcaagcaa--catgactcgtacctctatt---tcttgtttcagGTATGGAGACGAACACAAGCTTGCTGGTTTTTCAGCAACTTTGCAAGCAATCATTTCCTTTGTGGAGAATGG
upper sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G28390.1 (Arabidopsis thaliana), 3'ss of exon 2
------gtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctctttccccttcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
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gtttagacatttcttcatattgaatcgtcagctagagaatggtt---gtattgtggggtttatcgttt-taacttttaactgatttactctcgttgcatttcg--tttttaatcg-ttgtat--------------cgtttagATATGGAGATGAACATAAGCTTGCTGGATTTTCAGCTACTCTTCAAGCTATTATTTCTTTTGTGGAGAATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctttccccttcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
ttctt CT-rich tract
ttcaattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttcttttcttttataaaaagaagaacaaccacttatgcacaaaacaaacgaccctttgccaccctcacttaatgcattctctttccccttcaatttttccaccacttgtgcaaaaaacaaaccaattcttagGTATGGAGATGAGCATAAGCTTGCTGGGTTTTCCGCCACGTTGCAAGCAATCATTTCTTTCGTTGAGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA