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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggctgacgcacctgttgttttcactttcttgattctgattatggccaccggcgacggcggcggcggcggcggcgaggtgaccgtggttagtgtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCCGCCCGGCCACCATCG

Basic information

species Oryza sativa
transcript LOC_Os06g44140.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 1
---------------gtttggctgacgcacctgttgttttcactt-tcttgattctgattatggccaccggc-gacggcggcggcggcggcggcgaggtgaccgtg-gttagtgtgggt-gcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCCGCCCGGCCACCATCG
               ||||  ||    |  ||||  |||||  || | ||  | ||   |  | |     |  ||   |||      |  |    |     |   | |   |||||| | ||||||||||| ||| || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| | |||| ||| ||||
gtccgtccctcctttgtttttcttcttcctctgtgtttttcttttgtgtttttgctacgtgcgtcggtttgttgatctcggtaagtcctccactcaccccgctccgagcctgtgtggattgcagAAGGACCCGCTCGCCGTGAAGGTGAATCAGCTGAGCTCCATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGGCACAATCG

upper sequence: LOC_Os06g44140.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G170281_T01 (Zea mays), 3'ss of exon 1
-----------gtttggctgacgcacctgttgttttcactttc-ttgatt--ctgattatggccaccggcgacggcggcggcggcggcggcgaggtgaccgtggttagtgtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCCGCCCGGCCACCATCG
            |||  ||  |||  || ||     || |  |  | |||  |||    | |   |   || |   ||    | |  | | | |  |  ||||||  |  ||| ||||||| |||  ||| || ||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||| | |||| ||||||||
gtcttggatttctttctcttccgccactctttcacacagtcccactcatttcctggcccttggtcctcacg-cactgggtctgtcatctgtgtgtgggtcgtggt--ggctggttgcagAACGACTTGCTCGCCGTGAAGGTGAACCAGCTGAGCTCCATCAAGACGCAGCTGCCATACTCCTACTACTCCCTCCCCTTCTGCAGGCCGGACACCATCG
















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|29634380|gb|CB639389.1|CB639389
EST:     CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAG                         AAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
genomic: CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAGgtttggctga ... gtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
EST: gi|88422957|gb|CI615257.1|CI615257
EST:     CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGGGACTTCCGCAAG                         AAGGACCAGCTGGGGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
genomic: CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAGgtttggctga ... gtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
EST: gi|88372301|gb|CI619631.1|CI619631
EST:     CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAG                         AAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
genomic: CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAGgtttggctga ... gtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
EST: gi|88825298|gb|CI775863.1|CI775863
EST:     CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAG                         AAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG
genomic: CCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAGgtttggctga ... gtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAG

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: 64 (upstream exon), 62 (downstream exon)
Score: 2

GCCCCTCCTCCTCCTCCTCGTCGTCGTCATGGTCCTCGCCGGCGCCGGCGCCGCCCGAGGGTTCTACCTCCCCGGCGTCGCCCCCCGCGACTTCCGCAAGgtttggctga ... gtgggtgcagAAGGACCAGCTGGCGGTGAAGGTGAACCAGCTGAGCTCGATCAAGACGCAGCTGCCCTACTCCTACTACTCCCTCCCCTTCTGCCGCCCGGCCACCATCG




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