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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgagcacaatgaattttatttttacactagaaaactagtatctcttctaactatctccacatgatatatctgattgaacatgtatcactatcag

Basic information

species Oryza sativa
transcript LOC_Os07g37750.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G335287_T01 (Zea mays), 5'ss of exon 14
GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgagcacaatgaattttatttttacactagaaaactagt--atctcttctaa---------ctatctcca---catgatatatctgattgaacatgtatcac-tatcag
|||| |||||||||| ||||| ||| | ||||||||||||||  ||||||| || ||||| ||||| |||||||| ||||| ||||||||||||| ||| | || | |   ||  || |  | |  | | | ||  |  || |||  |||          | |||          | | |||||| |||  || |||| | || |||
GATGTTGGAGAAAGTTTGCAAAGATCCCCAAATGCTTGCAGATGTGTTTGTGAACTATGACTGTGATCTTGAGGGACCAAATCTTTTTGAACGCACGgtaatcatatttt-ttaaatgtccagaaaacatagcttctgaatttctcataaaatgtgtttttttctttggcttgcaacacatctgactgataatctatctcctaccag

upper sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G17610.1 (Glycine max), 5'ss of exon 16
GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgag----cacaatgaattttatttttacactagaaaactagtatctcttctaactatctccacat-gatatatctgattg-aacatgtatcactatcag-------------
|||| | |||||||| || |||||| |||| |||||||  ||||| ||||| |||||||||||||| |||||||  |||||| | |||||||| |||||        |||  | | | | || |  || || | |   || || |    ||  |||  || | | | || || | ||   ||  | | | | | ||               
GATGTTAGAGAAAGTATGTAAGGATCCACAGATGCTTGTTGACATCTTTGTGAATTATGATTGTGATCTTGAGGCACCAAACTTGTTTGAACGAATGgtattatcttacagagcaatcttttatggcattataga--cagcatgtaaattagttatgacctctttggtaaatataataataatctctgttattttcctattcaatttgtag

upper sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA17G04890.1 (Glycine max), 5'ss of exon 16
GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgag----cacaatgaattttatttttacactagaaaactagtatctcttctaactatctccacat-gatatatctgattg-aacatgtatcactatcag-------------
|||| | |||||||| || |||||  |||| |||||||  ||||| ||||| |||||||||||||| |||||||  |||||| | |||||||| |||||        |||  | | | | || |  || || | |   || ||      ||  ||| ||| | | | || || | ||   ||  | | | | | ||               
GATGTTAGAGAAAGTATGTAAGGACCCACAGATGCTTGTTGACATCTTTGTGAATTATGATTGTGATCTTGAGGCACCAAACTTGTTTGAACGAATGgtattatcttacagagcaatcttttatggcattataga--cagcatgaaaattagttatgtcctctttggtaaatataataataatctctgttattttccaattcaatttgtag

upper sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 13
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 5'ss of exon 15
GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgagcacaatgaattttatttttacactagaaaactagtatctcttctaactatctccacatgatatatctgattgaacatgtatcactatcag-----
|||||| |||||||||||||| ||| | || |||||||  ||  ||| |||||| ||||||||||| || ||||  |||||| | ||||| ||||||||| || | ||   ||  ||| ||    || | ||||| | |   |    | | |  |     | |||  || |    |||||| |   | | |      
GATGCTTGAGAAAGTCTGCAAAGATCCTCAGATGCTTGTTGATGTGTATGTAAACTATGATTGTGATCTAGAGGCCCCAAACTTGTTTGAGCGCATGgtgtgctccatt--ttccattctt---ttatataactactgtacttcagcaatgtgactggtagttatgactcacattacatgtttttattttactttag

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: 70 (upstream exon), 70 (downstream exon)
Score: 31

GATGCTGGAGAAAGTCTGCAAGGATTCACAAATGCTTGCAGACATGTTTGTAAATTATGATTGTGACCTTGAGGGGCCAAACCTTTTTGAACGCATGgtgagcacaa ... tcactatcagGTCAGTGCACTCTCAAGGATTGCACAAGGATCTCAAAATGCGGATACAAACACTGCCGCATCTTCTCAAACAGTTTCTGTGAAAGGCTCATCTCTTCAG




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