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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaagttctatgtgcatctctcttttctcattgttggcagaagcgcttattgccttctatgttatatcacag

Basic information

species Oryza sativa
transcript LOC_Os05g50280.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50280.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G097768_T01 (Zea mays), 5'ss of exon 15
GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaagttctatgtgcatctctcttttctcattgttggcagaagc--gcttattgccttctatgtta-tatcacag
||||||||| ||  |||||| || |||||||||||||||||||||||||| ||||  || |||||||||||||  | | ||||       | | |     | ||||||  | ||||  | ||| |||||| | | ||  |||  |||
GACAACATAGCTGCTGGTTCGCACTTATACTCTGTAATGAGTATGCTTTCACTGGCTGGACTTGTGgttagttccactactattacagattgtttgccgcccttgttgagataagcttgtttaatgccttgtcttttgctattccag
















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|29632218|gb|CB637227.1|CB637227
EST:     CTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: CTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|89182912|gb|CI045670.1|CI045670
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|29678789|gb|CB675064.1|CB675064
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|29678790|gb|CB675065.1|CB675065
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|7274036|gb|AU083580.1|AU083580
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|29674764|gb|CB671039.1|CB671039
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
EST: gi|58679421|gb|CK068108.1|CK068108
EST:     GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTG                         GCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA
genomic: GTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 60 (downstream exon)
Score: 44

GACAACATAACTAATGGTTCTCATTTATACTCTGTAATGAGTATGCTTTCGCTGGTCGGGCTTGTGgttagttgaa ... tatatcacagGCATTTGTGATTTCATTTTCTCTTGGTTTGGGAGCCATACCATGGATCATAATGTCTGAG




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