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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggacttctaatctcctacaaacttaaagcatctcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g55974.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124091_T04 (Zea mays), 3'ss of exon 6
gtttggacttctaatctcctacaaacttaaagcatctcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
||||||   | | |  ||||||| | ||| | ||  |||||||  |    | | ||| |   | |  | || |||  |  |   ||| |||||||| ||||| ||||||||||| |||||||| ||||| ||||||||||| |||
gtttggttgtttgag-tcctacacaattata-cacttcattaaacttttatcaaaagattt-actggttttatgtgtttattcttttacagAAATTGTATGTCACCATGTTCCCATGCAATGAATGTGCCAAGATTATTATTCAG

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G03380.1 (Glycine max), 3'ss of exon 6
-----gtttggacttctaatctcctacaaactta--aagcatctcat--taatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
        | || || ||| |    |  |  ||   || || || ||  |||  |       | | | |    |  | |  | || |||  ||  |||||    ||||||| |||||||| || |||||||| ||||||||||| || ||||||
aagattccttgagttataaacaaacagtatttttttaaccacctgatactaagatattccacttaacaactttttttttaatcttgtctgatcaatgcagCGGCTATATGTGACCATGTTTCCGTGCAATGAATGTGCTAAGATCATAATCCAG

upper sequence: LOC_Os01g55974.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G13950.1 (Glycine max), 3'ss of exon 6
---gtttggacttctaatc---tcctacaaacttaaagcatctcat--taatttgcctttataagctaagaataatctt-gtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
    |||  | || ||| |      ||  |  || || || || ||  |||          | | ||     |  | ||  | || ||   ||  |||||    ||||||| |||||||| ||||||||||| ||||||||||| || ||||||
ttccttttaagttataaacaaacagtattatttttaaccacctgatactaagagattccacttatctcttttttttttttatattgtccaatcaatgcagCGGCTATATGTGACCATGTTTCCCTGCAATGAATGTGCTAAGATCATAATCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattaatttgcctttataagctaagaataatcttgtgttatcttctctttgcagAAATTATATGTTACCATGTTCCCCTGCAATGAGTGTGCTAAGATTATTATCCAG
 cattaat  putative branch site (score: 3)
                                    tgttatcttctcttt  putative PPT
                      taagaataat  TA-rich tract