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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02410.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 7
GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgat-atctgttggttaaact-tgcag
|||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||   |||||||||  |||| || ||||  | |  ||            |  |   ||  |  |||||   | ||||||||| |     | ||       || |||| |||||
GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTGGGCAAGTTCGACCTCAATGGCATTCCGTCAGCTCCGAGgtgcgttgctgct--------gctcatctttttgttgaatggccgattgaatccagtgttgtctgatgaacgaattgaactgtgcag

upper sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 7
GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgt------ttgctcatgtccagaaaaaaatgttagcttactcaaatggataaatgaatccagcgcctgatatctgttggttaaacttgcag
|||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||    |||||| |  |||| |||||||       | |    |||| || | ||||  |  ||   |   ||| ||  | ||||   |   |   | |    || | ||   |||||
GTCTTTGAGGGTGAGCGCAGTATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTCAACGGCATTGCGCCAGCTCCAAGgtgagcagctaccggagtccggagataaattattactctttttgatgaatggacgaat---gaatccagtgttgtctgatgaactgtgcag
















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|58605366|gb|CK033399.1|CK033399
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTCTCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGGATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|29655799|gb|CB652074.1|CB652074
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|428460|gb|D24610.1|D24610
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|58661511|gb|CK050191.1|CK050191
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|55411112|gb|CV723488.1|CV723488
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|5004223|gb|AU069372.1|AU069372
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
EST: gi|29660696|gb|CB656971.1|CB656971
EST:     TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAG                         GGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT
genomic: TGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCT

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: 74 (upstream exon), 74 (downstream exon)
Score: 222

GTCTTTGAGGGTGAGCGCAGCATGACCAAGGACTGCCGTCTTCTCGGCAAGTTCGACCTATCTGGCATTCCAGCAGCACCAAGgtttgctcat ... aaacttgcagGGGCACCCCCCAGATTGAGGTGACCTTCGAGGTGGACGCCAACGGCATCCTGAACGTGAAGGCTGAGGACAAGGGCACCGGCAAGTCGGAGAAGATCACG




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