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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaag

Basic information

species Oryza sativa
transcript LOC_Os02g01280.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 11
TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaag
 || ||||||||||| ||||| || ||||||||||| |||||| |||||||||||||||||||||| |||||||| || |||||||| |||||||||||||||||     || |    || | | |    |       ||   |   |  | | || |   |||| || |||   |   || |    || ||||           
AGTCGAGGAAGGTATCGTTGTAGGTGGTGGCTGTACCCTTTTGAGGCTTGCATCAAAAGTTGATGCAATTATAGAGACCCTTGAGAACGATGAACAGAAGgtaggtttgaaagt---ttagtttctaaaaaaga----atgctactttttgattaatg---ttgtattttatatgcccgaactgtttttcctttacaag------

upper sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G18760.3 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtagg----------aaaacaaatgaaataa----tctttggttattgtttcatttc--atcctaggttc-----aaggcatttgttttctattgtcaat----aattaaaatttctttttggcttcaag---------------------------
    |||||||||||||||||||| ||||| || || ||| || | ||||||||||| || ||||| || |  || |  ||||| ||||||||| | || ||  |           | |   |   ||||     |   ||| | ||||   ||||    |  | ||| |     || ||   ||  |  | || ||||     | |  |||  |  |  || ||||||                            
----GAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAGTGAgtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcaggttggag

upper sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G18760.1 (Glycine max), 5'ss of exon 10
TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtagg----------aaaacaaatgaaataa----tctttggttattgtttcatttc--atcctaggttc-----aaggcatttgttttctattgtcaat----aattaaaatttctttttggcttcaag--------------------
||| |||||||||||||||||||| ||||| || || ||| || | ||||||||||| || ||||| || |  || |  ||||| ||||||||| | || ||  |           | |   |   ||||     |   ||| | ||||   ||||    |  | ||| |     || ||   ||  |  | || ||||     | |  |||  |  |  || ||||||                     
TGTAGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTTCTGAGACTTGCATCAAAGGTGGATGCAATCAAGGATAGCCTTGATAATGATGAAGAAAAAgtgagtcatttatttgatatggagagaatataagtttcctggatgttgtgatattttttgttttgggtgctgggaaatgctcctgactgttgttttcaaattcaactccaaacatggtcatgacttcaaaattgtgtttaatttttgcag

upper sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaag
|||||||||||||||||| ||||| ||||| || || ||  | |||||||||||||| || |||||||| |  || || ||||| ||||||||| | |||||        |||| ||  | | |    || ||     ||| | | ||    | |  |||||| |   |||||  | ||   ||                     
TGTTGAGGAAGGTATTGTCGTTGGTGGTGGTTGCACTCTGCTCCGGCTTGCATCAAAGGTCGATGCCATCAAGGATACCCTTGAAAATGATGAAGAAAAGgtgattggcaaaatcaagaattttgaaattttttgcaaattgcttgct---cttactgcattt-tcaactatttcccatctctag--------------------

upper sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaacaaatgaaataatctttggttattgtttcatttcatcctaggttcaaggcatttgttttctattgtcaataattaaaatttctttttggcttcaag
||| |||||||||||||||||||| ||||| || || ||  | || ||||| || || ||||||||||||| ||  || ||||| ||||||||| | ||||||    ||  ||| ||    ||||  | | ||   ||||         | |||      |||| |    |||  |  ||                         
TGTCGAGGAAGGTATTGTTGTTGGTGGTGGTTGCACTCTGCTTCGTCTTGCTTCCAAGGTTGATGCCATTAAAGCCACGCTTGATAATGATGAAGAAAAGgta----aatcaatcaa---gtcttcagattttaactcatgaaccttcggtttctctaactttgctgatgattccctttag------------------------

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: 75 (upstream exon), 70 (downstream exon)
Score: 42

TGTTGAGGAAGGTATTGTTGTTGGAGGTGGCTGTACGCTTTTGCGGCTTGCATCAAAAGTTGATGCCATTATAGAAACACTTGAGAATGATGAACAGAAGgtaggaaaac ... tggcttcaagGTTGGGGCTGAAATCGTAAGGAAGTCCTTGAGTTACCCACTTAAATTAATAGCAAAAAATGCTGGTGTTAACGGCAGTGTTGTTACTGAGAAG




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