Sequence
atgc intronic sequence ATGC exonic sequencegtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttcccttttttagtgttttagtttgactgactaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os04g18030.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g18030.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 5
gtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttcccttttttagtgttttagtttgactgactaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
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-----------------------------gtttcttagctc-catttgttggtcattgacatgtaatattct--tttgacagatggtcatgttgtttacagtgagg--ttattattctgatt---------ttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
upper sequence: LOC_Os04g18030.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 9
gtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttcccttttttagtgttttagtttgactgactaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
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-----------------------------gtttcttagctc-catttgttggtcattgacttgtaatattct--cttgacaaatggtcatgttta------cagtgaggt-------tattattctgat-tttgtagATTGCTCCTGTGATACATGAATGGACTTATGATGCCATGTGTCATGATTTGCTGAATATGGAGGGAAATAAATATGTTCATGAA
upper sequence: LOC_Os04g18030.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 9
gtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttccctttttta-gtgttttagtt-tgact-gactaccacattgaatgaagca-atgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
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--------------------------------------------------gttttccctctctcacattcactgattatgatttggttcacggattgtctattttatatgggctgaca--atgaccaacttacatttttagATTGCACCTATCATACATGAATGGACCTATGATGCCATGTGCCATGATTTACTAAATATGGAAGGAAATAAATATGTCCATGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
tgttttc CT-rich tract
ttaatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaggtggaatgtcaaacttcaagtcatttctggggtgatttttgcaattttcccttttttagtgttttagtttgactgactaccacattgaatgaagcaatgatttgttctcatgtttccttaatgttttcagATCGCACCAATTATTCACGAATGGACCTATGATGCCATGTGTCATGATCTACTCTGCATGGATGGCAACAAGTATGTACAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA