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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgaatacttgagtgacttctatgatgcttggagacagttcagcattttgatgtatctagtatagctctaaagccttcccttttgtttttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACATAAGGTTGAAATTGAAAAAACAGATTAACTTGTTTAACCACTTATTGGA

Basic information

species Oryza sativa
transcript LOC_Os05g12170.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g12170.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0046g00990.t01 (Vitis vinifera), 3'ss of exon 4
ctattgaatacttgagtgacttctatg-atgcttggagacagttcagcattttgatgtatctagtatagctctaaagccttcccttttgtttttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACATAAGGTTGAAATTGAAAAAACAGATTAACTTGTTTAACCACTTATTGGA
 | |   |  |||   || ||  ||   ||| |    |   ||  |    ||  | | |   | | |      |   |||   ||||  || ||   ||||||||||||||  | |||||||||||| |||| || ||  |||| || |||||||| || |||||||| ||||| || |  |||||||| || ||  | ||
-tttgagaagcttagctgcctaataaatatgatatttgtttgtctaatgcttccaagcaagcattgttttctgatgtcctcttctttctttgttaactcagTATGGCAGAAGTTGGAAGAAGAAAATGCTGATTTTTTCAGGGCCTATTACATAAGATTAAAATTGAAGAAACAAATCATTTTGTTTAATCATTTGCTTGA
















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|163929224|gb|EG711009.1|EG711009
EST:     TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAG                         TATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
genomic: TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAGgtaaggttct ... tttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
EST: gi|29671008|gb|CB667283.1|CB667283
EST:     TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAG                         TATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
genomic: TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAGgtaaggttct ... tttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
EST: gi|29664499|gb|CB660774.1|CB660774
EST:     TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAG                         TATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
genomic: TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAGgtaaggttct ... tttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
EST: gi|29671009|gb|CB667284.1|CB667284
EST:     TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAG                         TATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA
genomic: TAGGACTCTTTCTACTCGTGCAAGAATTGAACCTGGTTTCACTACTTTAGgtaaggttct ... tttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttgatgtatctagtatagctctaaagccttcccttttgtttttttttcagTATGGCAGAAACTCGAAGAAGAAAATTCTGAGTTCTTTCGGGCTTACTACATAAGGTTGAAATTGAAAAAACAGATTAACTTGTTTAACCACTTATTGGA
                       ctctaaa  putative branch site (score: 3)
                               ccttcccttttgtttt  CT-rich tract
                                      ttttgtttttttttca  TA-rich tract