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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCATTCAGATGGATCACCTTGCTATTGACGCAGGAATTCAAGTTTCGCGACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaactgccattcctagttccatgccatctgagaattttttgaaatgcactataaaactcttattatcttattgcag

Basic information

species Oryza sativa
transcript LOC_Os04g30880.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g30880.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G022308_T02 (Zea mays), 5'ss of exon 9
CGCATTCAGATGGATCACCTTGCTATTGACGCAGGAATTCAAGTTTCGCGACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact---gccattcctagttccatgccatctgagaattttttgaaa-tgcactata--------aaactcttattatcttattgcag
||||||||||||||||||||||||  | |||||||| ||| |||| || |||||| ||    | |||||  ||||||| || || || ||||| |||||||||||  |     || ||   | ||   | |||||  ||   |  ||  |||   | ||  |        |||| ||| |  ||    |||||
CGCATTCAGATGGATCACCTTGCTGCTAACGCAGGAGTTCCAGTTCCGTGACTGCCTCAGCCTGTGGGACACACTGTTGGGCGACCCAGAGGGGCCTCAGgttagggaaccacgcgatctttggtcttacgccatgagattgtgcttcaaaagcacgctggacctggactaaacccttctgttcggggtgcag
















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|218479200|gb|FG960290.1|FG960290
EST:     ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAG                         GCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
EST: gi|27546849|gb|CA767268.2|CA767268
EST:     GCTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAN                         GCCACCTTACTTCGAATCTGNTGTGCTATGCTAATTCTTGNTCGAANGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
EST: gi|29626498|gb|CB631509.1|CB631509
EST:     ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAG                         GCCACCTTACTTGGAATCTGTTGTGTTATGCTAATTCTTGTTCGAAGGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
EST: gi|88510509|gb|CI438015.1|CI438015
EST:     ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAG                         GCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
EST: gi|86494334|gb|CI136967.1|CI136967
EST:     ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAG                         GCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
EST: gi|88505436|gb|CI432942.1|CI432942
EST:     ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAG                         GCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG
genomic: ACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGG

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: 69 (upstream exon), 59 (downstream exon)
Score: 6

CGCATTCAGATGGATCACCTTGCTATTGACGCAGGAATTCAAGTTTCGCGACTGCATCCATATATGGGATGCACTGTTAGGTGATCCTGAGGGACCTCAGgttagaaact ... cttattgcagGCCACCTTACTTCGAATCTGTTGTGCTATGCTAATTCTTGTTCGAAGGCGGCTCTTGGCCGGGGATTTCACAGCAAACCTAAAGCTTCTCCAGAGCTATC




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