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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccaccccctcctccccttcgatggccctcgtaatcgccttctcaatgttctcgttcgcgcgcttgtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCG

Basic information

species Oryza sativa
transcript LOC_Os02g09060.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09060.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G041561_T01 (Zea mays), 3'ss of exon 1
gtaagccaccccctcctccc-cttcgatggccctcgtaatcgccttctcaatgttctcgttcgcgcgcttgtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCG
|||||||||  |          |||  ||    | | |        ||  ||    | | |||| ||  ||| ||   || |||||||||||||||||||||||||||  | ||||||||||||| ||||||||||||||||| |||| |||||||   |||  | | | ||||  ||||
gtaagccacgactgatagggatttccgtgtggatgggatctagtgacttgat----tggctcgcccgtgtgtgtttgtagTTGGGGAGGAAGCCGCGGGTGTGCGTGCTCGCCGTGCCCAACCACATGACCTACGCCGACTTCTGCCGTTTCTGCGGCGCCTTCGTCCCTCACACACTCG
















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|29677959|gb|CB674234.1|CB674234
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88580349|gb|CI697269.1|CI697269
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88587192|gb|CI704925.1|CI704925
EST:     CCTCCTCCNA-CCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: CCTCCTCC-ACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88436585|gb|CI691313.1|CI691313
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88405001|gb|CI685440.1|CI685440
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88440811|gb|CI693379.1|CI693379
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
EST: gi|88378864|gb|CI681683.1|CI681683
EST:     TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCG                         GTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC
genomic: TCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACC

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: 73 (upstream exon), 47 (downstream exon)
Score: 18

CCTGCCCTTCTCCTCCGGGAACCCACGCATCGAGGAGACCCGCGGCGTCGTCCTCCTCCACCCCGAACCACCCGCCGCCTCGTCCTCGTCCCTTCTCCCGgtaagccacc ... gtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatggccctcgtaatcgccttctcaatgttctcgttcgcgcgcttgtcttgccagGTGGGGAGGAAGCCGCGGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCG
                                          cttgtctt  CT-rich tract