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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAACCCCGAGCGACTCAAGAATCAAGTCAGAGAGCTTACCTCCCGTGTGAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacatgagattcaatctctacccctgttgctcatatacaagccataaaatctcaccctctgtttctag

Basic information

species Oryza sativa
transcript LOC_Os06g08730.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g08730.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G154892_T01 (Zea mays), 5'ss of exon 18
--------------AGCAACCCCGAGCGACTCAAGAATCAAGTCAGAGAGCTTACCTCCCGTGTGAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacatgagattcaatctctacccctgttgctcatat-acaagccataaaa-tctcaccctc---tgtttctag----------------------------
               ||||||| || || ||||||||||||||||||||||| |||||||||||||||||||||||||| |||   | |         |     || |||    |    ||  |||    || || || |     ||||| || |  |    || |    ||| |  ||    || ||| |                             
TCGTTGATTTCTTCTGCAACCCTGAACGCCTCAAGAATCAAGTCAGAGAGCTGACCTCCCGTGTGAAAGCTCTCCAGGACTAACCTGTTTCTGTAGGCTGgtaagtatagggcag--gacatgtgattcccagtcccttctaaccttgcttattttgcctatcacattgctctaaaacttgcatgattccaaccattgaaaaatgtctctatgtgcccag
















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|89174999|gb|CI041077.1|CI041077
EST:     GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88520416|gb|CI448070.1|CI448070
EST:     GAAAGCTCTCCAGGAATGAATAGATAGATAGATATCCCTCGTTTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88901697|gb|CI001805.1|CI001805
EST:     GAAAGCTCTCCAGGAATACATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|33795400|gb|CF323570.1|CF323570
EST:     GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88476716|gb|CI413987.1|CI413987
EST:     AAATAGATAGATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: AAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88411473|gb|CI518997.1|CI518997
EST:     ATAGATATCCCTCGTCTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: ATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|88515858|gb|CI443512.1|CI443512
EST:     GGAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTGTAGTTTG                         CATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
genomic: GAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC
EST: gi|89178386|gb|CI391565.1|CI391565
EST:     TAGATAGATATCCCTCGTGTAGTTTG                         CATTTGTGTGCCAGGTCCTCCCGCGAAATGGGAAGCCACAGCCAAGCTCGC
genomic: TAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGC

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: 75 (upstream exon), 69 (downstream exon)
Score: 8

AGCAACCCCGAGCGACTCAAGAATCAAGTCAGAGAGCTTACCTCCCGTGTGAAAGCTCTCCAGGAATAAATAGATAGATAGATATCCCTCGTCTAGTTTGgtaagcacat ... ctgtttctagCATTTGTGTGCCAGGTCGTCCCGCGAAATGGGAAGCAACAGCCAAGCTCGCAATGATGCTGTTGCTTGCAAAGTTTCCCTTCCTCCAATGCGAAGTTTGG




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