Sequence
atgc intronic sequence ATGC exonic sequenceATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaattaattaaacaaacatgtgtttgcatgcatgatcttgtgaaattttatatgctcctacttaatatctccccttctctggctctctctc...
Basic information
species | Oryza sativa |
transcript | LOC_Os09g32260.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g32260.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G386163_T02 (Zea mays), 5'ss of exon 1
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaattaattaaacaa-acatgtgtttgcatgcatgatcttgtgaaattttatatgctcctacttaatatctccccttctctggctctctctc---
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ATCACGTACTACCTGCGGCAGAAGATCGCCGACGCCAGCTTCACGGCGAGGGCCATCGCCGAGGTCGACCTCAACAAGTGCGAGCCATGGGATCTCCCGGgtaaggatcggaggaaaccaactgtatatatatgtacacgcacatgcatgc---atacagcatactca-gttcgtcagttattcacgatcaaatctcaattaat
upper sequence: LOC_Os09g32260.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G008374_T02 (Zea mays), 5'ss of exon 1
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaatta-------attaattaattaaacaaacatgtgtttgcatgcatgatcttgtgaaattttatatgctcctacttaata-tctccccttctctggctctctctc--------------------------------------------------------------------------------------------
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ATCACGTACTACCTGCGGCGGAAGATCGCCGACGGCAGATTCACGGCGAGGGCCATCGCCGAGGTCGACCTCAACAAGTCCGAGCCGTGGGATCTCCCGGgtaatcatcatcggagaaaccaactgttaattaacctgttcatgtgtatatacacgcacatgtacatgcatgcatatgtagtaatcttttctcctctc-ttctctccttatttggaacatgcatgcgggagtgtcagaacgtaacaatttcttatattttccagtatatatataagtgatcgattatatatgcatgccag
upper sequence: LOC_Os09g32260.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 5'ss of exon 1
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaatta---attaaac----aaacatgtgtttgcatgcatgatc-ttgtgaaattt-tatatgctcctacttaatatctccccttctctggctctctctc---------------------------------------------------------
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GTGAGCTTCTACCTGGTCCGGAAGATTAGCAACCCTCAAGTCGTTGTGAAGACGATTCCAAACGTGGACCTCAACAAGTGCGAGCCTTGGGATCTTCCAGgtatttttttcttttcgcattatccttcagaacatttggt-gtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcag
upper sequence: LOC_Os09g32260.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ11746 (Selaginella moellendorffii), 5'ss of exon 1
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaattaattaaacaaacatgtgtttgcatgcatgatcttgtgaaattttat--atgctccta---cttaatatctccccttctctggctctctctc------------------------------------------------------------------------------------------
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ATCACCTTCTACCTCGTCAAGAAGGTCGTCAACACAAAATTCGTGGCGCACGCCATCGCCGAGGTCGATCTCAACAAGTTCGAGCCATGGGATCTACCCGgtaaggaggaactctctcatcttctctcgcattcgcttctatcatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcag
upper sequence: LOC_Os09g32260.2 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ22540 (Selaginella moellendorffii), 5'ss of exon 1
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaattaattaaacaaacatgtgtttgcatgcatgatcttgtgaaattttat--atgctccta---cttaatatctccccttctctggctctctctc------------------------------------------------------------------------------------------
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ATCACCTTCTACCTCGTCAAGAAGGTCGTCAACACAAAATTCGCGGCGCACGCCATCGCCGAGGTCGATCTCAACAAGTTCGAGCCATGGGATCTACCCGgtaaggaggaactctcccatcttctctcgcattcgtttctatgatttcctctcactctctcgacgttcttgggcttgaatttgctgcattgcattcatggcattccaaggaacttggaatcgatcacttgggtcgagttgcctggacgaaattcctctaaaaatctctcctttgttcttttttctttcccggcagMapped 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|88356937|gb|CI620825.1|CI620825EST: GGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAG AGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTACCCTAAGGGATC
genomic: GGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaatt ... tgtgctccagAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATC
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 |
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATCACCTACTACCTGCGGCAGAAGATCGCCGACGGCGGCTTCACGGCGAGGGCCATCGCCGAGGTCGATCTCAACAAGTGCGAGCCATGGGATCTCCCAGgtaattaattaattaattaaacaaacatgtgtttgcatgcatgatcttgtgaaattttatatgctcctacttaatatctccccttctctggctctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct