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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTTCCGTCCAAGGATGCAAACTTTGTTGGCTATACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactctctctctctctctaatgaaattgtaaatgatgatgcctttctttagattatgcatttttagtgtcttttgtttgaaaaaaaatgttgtgcttatggaacag

Basic information

species Oryza sativa
transcript LOC_Os05g43570.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43570.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G375904_T01 (Zea mays), 5'ss of exon 11
ATGCTTCCGTCCAAGGATGCAAACTTTGTTGGCTATACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactctctctctctctctaatgaaattgtaaatgatgatgcctttctttagattatgcatttttagtgtcttttgtttgaaaaaaaatgttgtgctt-atggaacag
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ATGCTTCCATCCAAAGATGCAAACTTTGTTGGGTATACGTACAAGAACTTTGAAATTGTGAATGATGATGAAGTGGCAGGAATTGgttagttctcccatta---ctatgttcatcctttctactat--ttcacttatttagttgctatatgtttagtctgacaacaacaaaaaatgatttggtgctttgtgcaacag

upper sequence: LOC_Os05g43570.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv10s0003g05720.t01 (Vitis vinifera), 5'ss of exon 12
ATGCTTCCGTCCAAGGATGCAAACTTTGTTGGCTATACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactctctctctctctctaatgaaattgtaaatgatgatgcctttctttagattatgcatttttagtgtcttttgtttgaaaaaaaatgttgtgcttatggaacag-
|||||||| |||||||||| ||| || ||||| |||||||| ||||||||||||||||| || ||  || | ||  | || ||||||||| | |  |       || |||  || ||||||    |     |||  | |   | |   |     | | |  | || | ||   | |||  | |  || |   ||   
ATGCTTCCATCCAAGGATGTAAATTTCGTTGGTTATACATACAAGAATTTTGAAATTGTCAACGAGCATCATGTGCCTGGCATTGgttagtattgac-------ctataa-aaatttgtaatcagtag---cttgttatgattcaaaaacccaaacttttctatgatagacccataattctatattt-tattacgaa
















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|325494464|gb|JG458988.1|JG458988
EST:     TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG                         CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
EST: gi|86827108|gb|CI270824.1|CI270824
EST:     TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG                         CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
EST: gi|86477542|gb|CI120175.1|CI120175
EST:     TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG                         GTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
EST: gi|55408515|gb|CV720891.1|CV720891
EST:     TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG                         CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
EST: gi|88850051|gb|CI091346.1|CI091346
EST:     ATTGTAAATGATGATGAGGTTGCAGGAATTG                         CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: ATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
EST: gi|29623780|gb|CB628791.1|CB628791
EST:     TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTG                         CTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT
genomic: TACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACAT

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: 44 (upstream exon), 68 (downstream exon)
Score: 15

ATGCTTCCGTCCAAGGATGCAAACTTTGTTGGCTATACATATAAGAATTTTGAAATTGTAAATGATGATGAGGTTGCAGGAATTGgttagcactc ... tatggaacagCTGAGTTGAAGAAGAAGAGTTCCAAGTCAAAGCGGCCAACTATCAAGACATTATTTG




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