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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaaagaacctttcttcttgcattccattaactcttttgtttcccttctgaattcttttgtcttatttttttctgatcagATTGGGAATCCACTTCTGAAGCTTGACAGAGACAGTCCAGCTACCTACGAGTTCTTCTGGTCGCATGGCATGATCTCTGATGAACTAAAACTCACAATCA

Basic information

species Arabidopsis thaliana
transcript AT5G42240.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G025154_T02 (Zea mays), 3'ss of exon 5
gtaagcaaaagaacctttcttcttgcattccattaactcttttgtttcccttctgaattcttttgtcttattttttt---ctgatcagATTGGGAATCCACTTCTGAAGCTTGACAGAGACAGTCCAGCTACCTACGAGTTCTTCTGGTCGCATGGCATGATCTCTGATGAACTAAAACTCACAATCA
||||| ||  ||   |   |  |   | |  | | |  ||  |   |   || |   || |||| | || |||||||     || ||||| |||||||| || || ||||||||||| |||   || || |||||||||| ||||||||| |||||||||||||| || ||  ||   ||  | ||||
gtaagtaaccgagaataa-tagtaataatgtacttatcctccttactaagttttatcttttttttttttttttttttgcgtcgaacagATCGGGAATCCGCTCCTCAAGCTTGACAGGGACGTCCCTGCGACCTACGAGTACTTCTGGTCTCATGGCATGATCTCCGACGAGATATTCCTGGCGATCA

upper sequence: AT5G42240.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G132154_T01 (Zea mays), 3'ss of exon 5
-------------gtaagcaaaagaacctttcttc-------ttgcattccattaactcttttgtttcccttctgaattcttttgtcttatttttttctgat--------cagATTGGGAATCCACTTCTGAAGCTTGACAGAGACAGTCCAGCTACCTACGAGTTCTTCTGGTCGCATGGCATGATCTCTGATGAACTAAAACTCACAATCA
             ||       ||   ||| ||         ||| | |  |     || ||  |||   |    ||  |||||  || |    |  |||          ||||| |||||||| ||||||||||||||||| |||   || || ||||||||||  |||||||| || ||||||||||| || ||   |   ||  | ||||
gtaagtaaactcagtctcagtcagtgtcttcctgagatgagattgaaattgaaagggtcattcctttttttcactaaagcttttcgctcaacactgcctgccttggtcgacagATCGGGAATCCGCTTCTGAAGCTTGACAGGGACGTCCCGGCAACCTACGAGTATTTCTGGTCCCACGGCATGATCTCCGACGAGACATTCCTAGCGATCA


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaactcttttgtttcccttctgaattcttttgtcttatttttttctgatcagATTGGGAATCCACTTCTGAAGCTTGACAGAGACAGTCCAGCTACCTACGAGTTCTTCTGGTCGCATGGCATGATCTCTGATGAACTAAAACTCACAATCA
 cattaac  putative branch site (score: 2)
              tttcccttctgaattc  putative PPT
                         aattcttttgtcttat  TA-rich tract