Sequence
atgc intronic sequence ATGC exonic sequence...gctataatttgagaatggtggtactgtctatttttgtacttgtcaaaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g18310.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 5
gctataatttgaga----atggtggtactgtctatttttgtacttgtcaaaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
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ttgatttcttgccatcctatgatcgttgtaacagcatctgaatccgtcaaaact-tgttacttcattttttgtcac---aatttctgacagctgcctccagcagGGTATGCCAGCAGCAGAAGGGGCTGTTGCAGCAGCTGCTGTAGCTGATCAGATGTATGGACCAAAAGAGGACCGCAAGTTGGCCATCGTATTG
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
gctataatttgagaatggtggtactgtctatttttgtacttgtcaaaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaact--agcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
| | |||| | || | || ||| | | | | || |||| || || || | | | || | | | ||| | || | |||||||| |||| |||||||||||| |||||||| ||||||||||||||| ||| || || || ||| | | | |||||||| |||
-gtttggcctgagc-tagt--ttctatctttcagtagagtcatctgaaatttgagaattttttatatttttctcacccttgtattcgttttaattttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG
upper sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
---gctataatttgagaa----tggtggtactgtctatttttgtactt--gtcaaaaatatgt----tgtttcc------ttttctgtcatcttaagttctgacagctg-taactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
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gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
atcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctataatttgagaatggtggtactgtctatttttgtacttgtcaaaaatatgttgtttccttttctgtcatcttaagttctgacagctgtaactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT