Sequence
atgc intronic sequence ATGC exonic sequencegtttggaatgtctagttttgcattatactttatattattcatttgcagttataatgacacagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60040.2 |
intron # | 27 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 9
gtttggaatgtctagttttgcattatactttatattat--tcatttgcagttataatgaca--cagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
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gtttggaactcactcgcatgctatctatttttctgcatgcttatttttggtcactacaataattaacaactgtttgtttgtcatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCGTGGGTTGCTGCAGCCCAAC
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 26
gtttggaa-----tgtctagttttgcattatactttatattattcatttgcagttataatgacacagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
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gtttggaactaactcccatgttatctttactcctgcatgcttttatttggtcgctaccataactgaca-actgtttgtttgttatgaagGGTATTTTGGCAGATGTGCTGAAGTGTCTTGGTGACAATAAGAAGCACATGCGAGAATGCACATTGACTGCTCTAGATTCATGGATTGCTGCAGCCCAAC
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 29
-------------gtttggaatgtctagttttgcattatactttatattattcatttgcagttataatgacacagatattttctatttgtta--tgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
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gtaagtggattctgttctgtttttgtattttttttccccatttggtactatt---ttgctgttttctgtttgaacatttcttgaaatggtttgttgcagGGTATTCTGTCTGATATATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTACTGAATACCTTAGATGCTTGGCTGGCTGCTGTCCATC
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 27
--gtttggaatgt---ctagttttgcattatactt---tatattattcatttgcagttataatgacacagatattttctatttgtta--tgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
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gtaagaggattctgttctgtttttgtatttttttcccatttggtactgttttgccgttttctatttgaatatttcttgaaatggtttgttgcagGGTATTCTGTCTGATGTATTGAAATGTCTTGGTGACAACAAGAAGCACATGAGAGAATGTGTGCTGAATACATTAGACGCTTGGCTGGCTGCTGTTCATC
upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 27
lower sequence: Vv10s0116g00460.t01 (Vitis vinifera), 3'ss of exon 18
---gtttggaatgtctagttttgcattatactttatattattcatttgcagttataatgacaca-gatattttctat-------ttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
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gtttgttggcttctcatgatatttatttaatcctttgttgtgttttcattatcctttagaaacttgaagtttatcatggcattgtttttttgcagGGCATTCTTTCTGATATTCTGAAATGCCTTGGTGACAATAAAAAGCATATGAGAGAATGCACATTGACTACTCTAGATGCTTGGCTTGCTGCTGTTCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatattattcatttgcagttataatgacacagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
ttttctattt CT-rich tract
atattttctatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggaatgtctagttttgcattatactttatattattcatttgcagttataatgacacagatattttctatttgttatgaagGGTATTTTGGCAGATGTCCTAAAATGTCTTGGCGACAATAAGAAGCACATGAGGGAATGCACATTGACTGCTCTAGACTTATGGGTTGCTGCAGCTCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA