Sequence
atgc intronic sequence ATGC exonic sequenceGCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactccttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt...
Basic information
species | Oryza sativa |
transcript | LOC_Os08g08820.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G130442_T02 (Zea mays), 5'ss of exon 3
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactccttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt
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GCACCCGGACGACAAGCAGCGGAAGGAGCTGAGCCGGGAGCTCGGCCTCGAGCCGCTGCAGGTCAAGTTTTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagc---aagctctactgcacacacaccgttcctgattccgtgacgtacgttgctgctgataatgcaaaccaac--gtgattactgcag---------
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G118063_T03 (Zea mays), 5'ss of exon 4
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactcc------ttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt------------------------------
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ACACCCGGATGACAAGCAGCGAAAGGAGCTGAGCCGGGAGCTCGGTCTCGAGCCGCTGCAGGTCAAGTTCTGGTTCCAGAACAAGCGCACACAGATGAAGgcaagctctaatacaccactgtgctgtgcatccatacatagtaccatgccacgcatagaaagagggatcatatatatacgcatagtc-tcgctgacaatgcaaacgtgattatattatatatatgggcgtatgcag
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ34024 (Selaginella moellendorffii), 5'ss of exon 2
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactccttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt
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TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtagg-atagaagctccaaaagcttttctttggcgtttctgatgtaaagatcttccttgtct--gtccag------------------------------
upper sequence: LOC_Os08g08820.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ37532 (Selaginella moellendorffii), 5'ss of exon 2
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactccttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt
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TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtagg-atagaagctccaaaagcttttctttggcgtttctgacgtaaagatcttccttgcct--gtccag------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58670718|gb|CK059404.1|CK059404EST: AACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAG AACCAGCACGAGAGGCACGAGAACGCGCAGCTGCGGGCGGAGAACGACAAG
genomic: AACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataa ... attaattcagAACCAGCACGAGAGGCACGAGAACGCGCAGCTGCGGGCGGAGAACGACAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCACCCAGACGACAAGCAGCGCAAGGAGCTGAGCAGGGAGCTGGGTCTTGAACCTCTGCAGGTTAAATTCTGGTTTCAGAACAAGCGCACACAGATGAAGgcaagtataaaaactccttatagatatatagagtgttctttggttatttaatttgatggcttcagactaaaatgattgggaattactgaaaaataaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata