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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttctactttctcaattgatacttcagcacttcttgtctagagttgcattttttcctttttagtagcacatgctcttgcatttatttcttgcatcatttcag

Basic information

species Oryza sativa
transcript LOC_Os01g08200.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08200.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G107696_T02 (Zea mays), 5'ss of exon 11
TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttgg-ttctactttctcaattgatacttcagcacttcttgtctagagttgcattttttcctttttagtagcacatgctcttgcatttatttcttgcatcatttcag
|||||||||||| ||| |||||||||| ||||||||||  |||||||| |||||| |||||  || ||||||    |||  |  ||   ||     |   || | ||| |||||| |||||||  |  |   |  ||     || |||||              
TTGCTATATGGCTTCAATAATGCAAGTCATGTTTTCAATCCATCCTTTCATATCAAGgttgccttttacttttcacattagtttttgtaca-----tagttacatttgtatttttccctttttctttac---tattccctttttcatttcag------------
















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|58606193|gb|CK034226.1|CK034226
EST:     ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG                         CTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
genomic: ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
EST: gi|29622184|gb|CB627195.1|CB627195
EST:     ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG                         CTACTTTGAGAAGCATAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
genomic: ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
EST: gi|58693785|gb|CK082472.1|CK082472
EST:     ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG                         CTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
genomic: ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
EST: gi|33674839|gb|CF303078.1|CF303078
EST:     ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG                         CTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
genomic: ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
EST: gi|58661919|gb|CK050599.1|CK050599
EST:     ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG                         CTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA
genomic: ATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGA

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: 57 (upstream exon), 75 (downstream exon)
Score: 36

TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACGgttggttcta ... atcatttcagCTACTTTGAGAAGCAGAGCTTGAAAGCTGCATTTGCAATTGCCCCAGCTGATCCAACATTGGACTTGAACATGCAAAT




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