Sequence
atgc intronic sequence ATGC exonic sequenceTCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
Basic information
species | Oryza sativa |
transcript | LOC_Os04g11880.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G040247_T01 (Zea mays), 5'ss of exon 5
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
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TCATGGAAAAATGATGAGCTTACTACAGATGCTCTGCCTATTCATGGTTATGAGCATTACAAGGCAAAGGACTATGCTCTTGCACATGCACCTTTCTCAGgtttaattgattgtgctctaaca-tcagtgg-catttcttttcttattgatgagaacttttctaatgaaggaaccctgattctcttgtcctgtcattcag
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA12G08840.1 (Glycine max), 5'ss of exon 5
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgttta---atgaaatgtgct-ttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
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ACATGGAATAATGATGAGCTTTCTACAGATGCTCTTCCAGTACATGGGTTTGAGCATTACAGGGCGAAGGACTATTCTCTTGCTCATGCTCCCTTCTCAGgttaacatatggtttgtgttgtttatgatgttttgaagcatatt--cagctatgttgaatatgctgtatttgatcagtgtgatataaatacctgcatggtgg--
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G19660.2 (Glycine max), 5'ss of exon 5
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaa---tgaaatgtgct-ttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
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ACATGGAATAATGATGAGCTTTCTACAGATGCTCTGCCAGTACATGGGTTCGAGCATTACAGGGCAAAGGACTATTCTCTTGCTCATGCTCCCTTCTCAGgttaacatttggtttgtgttgtttatgctgttttgaagcatatttgg--ctatgttgaatatgctgtatttgatcagtgtgatataaatacctgcatggtgg--
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G08190.1 (Arabidopsis thaliana), 5'ss of exon 5
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacc-cag
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TCATGGAACAATGATGAACTCACAATGGATGCTCTTCCTGTACACGGCTTTGAGCATTACAAGGCGAAAGACTATTCCCTTGCTCATGCTCCTTTCCCAGgtc---agagatttg-ttggaaagtag-------tttgttttctaggggaaggaaagcatatgtttgaa--tacttactcggaaaattgatgtgagtgtag
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0024g01120.t01 (Vitis vinifera), 5'ss of exon 3
-------------------------------------------------------------TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
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ATTTAGCAGCACCATTCCATCACGCCAGGGAAATGCGCAAAGACCTGAAGTACGCATAGTCACATGGAATAATGATCAGCTTGCGACAGATGCCTTGCCTgtacatggctttgagcattacaaggcaaaggattattcccttggtcatgctcttttctcag----------------------------------------------------------------------------------------------------
upper sequence: LOC_Os04g11880.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0061g00940.t01 (Vitis vinifera), 5'ss of exon 5
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
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ACATGGAATAATGATGAGCTTGCGACAGATGCCTTGCCTGTACATGGCTTTGAGCATTACAAGGCAAAGGACTATTCCCTTGCTCATGCTCCTTTCTCAGgta-aacatattttgctttca---------aacttcagtcttgtgcatgaacagataattaactctgaaatcattgtatcacttttacatttgaatatagMapped 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|58675059|gb|CK063746.1|CK063746EST: GGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAG GAAGCAGCAATGCAGGTGGACA
genomic: GGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaa ... taccacccagGAAGCAGCAATGCAGGTGGACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCATGGAAAAATGATGAACTTACCACAGATGCTCTTCCTATTCATGGTTATGAGCATTATAAGGCAAAGGATTATGCTCTTGCTCATGCTCCTTTCTCAGgtttaatgaaatgtgctttaacagtgaatgaacttctcttttcttcttcactgaaacttttctaatgaaggaattttattgttatatttttaccacccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG