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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgctgaccttagagagtagatattctgcaactgcacaactggtttctccaaactagcggaacattatattcttcttgcacctctttgccagtt...

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 19
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 11
GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaat-atgctgaccttagagagtagatattctgcaactgcacaactggtttctccaaactagcggaacattatattcttc----ttgcacctctttgccagtt-
| || ||||| |||||||| || ||||   | || |||||||||||||| ||  |||||||||||||||||||||| || |||||||||||  ||  | ||| |||       |  ||   || ||       |  |  || ||||  || |   |  ||  |  | |     ||  ||   || | | || 
GCGACAGTTTCAACTCTTCCTTAGTTGGTATTGTTGCAGTTGAACCAGAGGTTATGAAGGCTTGGGCTGCATCTGAAGGGATCCAGgtaaaagattttaaccatag-----caacgtttgccatctatttgtttcatc-cttcaaaaaagagagtctgtaagtagtccgacactgatccaacttacaattta

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 19
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 20
GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgctgaccttagagagtagatattctg--caactgcacaactggtttctccaaactagcggaacattatattcttcttgcacctctttgccagtt
|||| ||  | ||||| |||||||||||  ||||  |||| || |||||||| || || || |||||||||||||| || |||||||| | | |  |  | |     | |   | |      |||       ||     ||  || | |         |||| || || ||     |  ||     ||
GTGACAGCATGAACTCATCTTTGGTTGCTATAGTGTCAGTGGACCCAGATGTTTTAAAAGCATGGGCTGCATCTGAAGGCATCCAGgtga-tttcttagcttggtttattcagtgtcacaaacaagaaagtgacaatcctcatcagatttttatt-ttttattttattttttattattattatttttt
















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|29630787|gb|CB635796.1|CB635796
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|89185151|gb|CI050885.1|CI050885
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|25806439|gb|CA762400.1|CA762400
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAGAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|88907984|gb|CI090580.1|CI090580
EST:     CATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
genomic: CATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|29665115|gb|CB661390.1|CB661390
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
EST: gi|86851191|gb|CI312592.1|CI312592
EST:     CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAG                         CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC
genomic: CAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgc ... taacctgtagCACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGgtaaatatgctgaccttagagagtagatattctgcaactgcacaactggtttctccaaactagcggaacattatattcttcttgcacctctttgccagtt

- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG