Sequence
atgc intronic sequence ATGC exonic sequencegtgcttcccctgctgcattcatcctaacacaattaatttctgtgggcttttggttgtgattacacaaacttactttctaaagttctcatccagatttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g74460.1 |
intron # | 5 |
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 5
lower sequence: GLYMA12G29450.3 (Glycine max), 3'ss of exon 5
--------------------------------------------------------------------gtgcttcccctgctgcattcatcctaacacaattaatttctgtgg-gcttttggttgtgatt-acacaaacttacttt-ctaaagttctcatccag-atttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
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gtataactgagttggacttgagttggatgcttgtatgtcccaagaaaaatgatttgctgtttgcttgcttgctattcctgtttcttcagcttttgtttctcaacttgctattgtgtctttttttgtcattcagatgaactagttatgttgcagcagttgtatgatatatccctgt-tgttgatatg-tgtgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCGAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT
upper sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G40080.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------gtgcttcccctgctgcattcatcc---taacacaattaatttctgtgggcttttggttgtgatt-acacaaacttactttctaaagttctcatccagatttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
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gtataattgggttggatgcttgtatgtcccaataaaaaaaatggatttgctgtttgcttgctcgctattcctgtttcttcaacttgtgtttctcaacttgctattgtgt-cttttttttgtcattcagatgaactagttatgttgcagcagtgttatgatacatccctgttgttggtatgtatgcagATGATTGTTATACTAACAAAGTCAGTAAACAGATGTTTTGAGAAGAATCCAAAGTTTGATATGACACCCTTGCTTGGTGGAACAGACATTGTCTTCTCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttactttctaaagttctcatccagatttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
tatctgaaaatttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcttcccctgctgcattcatcctaacacaattaatttctgtgggcttttggttgtgattacacaaacttactttctaaagttctcatccagatttctctatctgaaaatttaatttgtagATGCTGCTGATTTTGACCAAGTCTGTCAACAGATGCTTTGAGAAGAACCCTAAATTTGATATGGCACCATTGCTAGGTGGCACAGATGCAGTTTTCCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG