Sequence
atgc intronic sequence ATGC exonic sequenceCACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g08070.2 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g08070.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G855347_T02 (Zea mays), 5'ss of exon 3
CACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
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CCCAAGCACGTGAAGCTCCTGTTCAAAGGCTCGCAGATTCCATCGCAGGACCATTTGTGTATACTGTTATGACGTTGGCTGCAACAACCTTTTCCTTCTGgtgtgctc------------ttgtttttttatttcttctatgaaaatcttatgactaaaa------------atattgcctttttatccctcaccccct---tcccaag
upper sequence: LOC_Os03g08070.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA06G05890.1 (Glycine max), 5'ss of exon 9
CACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
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CTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACATTTGCATTTTGgtaagtacttata----tttccacagaagttctttagtt--gataattttatg-atttgctccactgatcccaattcccaaatggt--agtggggtttgtcatggctat
upper sequence: LOC_Os03g08070.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA04G05900.1 (Glycine max), 5'ss of exon 7
CACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
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CTCAATCACGTGAAGCACCTGTACAAAGGCTTGCAGATTCAATAGCAGGGCCATTTGTATACAGTGTAATGACTTTGTCAGCAGCAACATTTGCATTTTGgtaagt----acttgtatttccatacaaattttttagtt--gataattctatg-atttgctccactgatcccaaatggaagtggggtttgccatgactattattaat--
upper sequence: LOC_Os03g08070.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv04s0008g01960.t01 (Vitis vinifera), 5'ss of exon 9
CACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
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CTCAAGGCCGTGCAGCACCCATACAAAGGCTTGCAGATTCAATTGCTGGACCATTTGTCTATATTGTGATGACTTTATCAGCAGCAACTTTTACCTTTTGgtataaacttgctc-cttcatccttttttcttttcctatttaatggaagtatgaaaccatgctagttgaacatgatgtaagaggagatggaaggcaaccac--------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|29622946|gb|CB627957.1|CB627957EST: CCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTG GTATTACATTGGCACCCACATCTTTCCAGAGGTCCTTCTAAATGATATTTC
genomic: CCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctccc ... ctattccaagGTATTACATTGGCACCCACATCTTTCCAGAGGTCCTTCTAAATGATATTTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACAAGCACGTGAAGCTCCCGTTCAAAGGCTTGCAGATTCAATTGCAGGGCCATTTGTTTATACTGTTATGACATTGTCTGCAGCAACATTTTCTTTCTGgtatgctcccattctcctttttgttgttgtttttcccttccaaaaagaatacacatgaaatttactggggctacattaacgttgcttcggcaaccttctctattccaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG