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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcatggacctgtagctaagtgggttagctttgctgagtttcgcaattccttattatcaagtcagtttgcatggtcttcgtgtttttagagctttgtgtcatgttaagcagactacacgtcttctgtaacttgtagtctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA

Basic information

species Physcomitrella patens
transcript PP1S83_25V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
gtaagtttcatggacctgtagctaagtgggttagctttgctgagtttcgcaattccttattatcaagtcagtttgcatggtcttcgtgtttttagagctttgtgtcatgttaagcagactacacgtctt-ctgtaacttgtagtctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA
                                                                                                                    | ||  | | ||  |   |  ||| | |   ||   || | | ||| | | |  |  ||| ||| |   | |  |  || ||||| || |||||  | |||||||| ||||| ||||| || ||||||||  || ||||||||||||| ||||| || || || || ||||| || |||||||
--------------------------------------------------------------------------------------------------------------------gtctg-atgcctaaccacatgttgaaatgctatacgttttctgccagttttagctaatttcttttt--ctgcgttaatg-cagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 11
gtaagtttcatggacctgtagctaagtgggttagctttgctgagtttcgcaattccttattatcaagtcagtttgcatggtcttcgtgtttttagagctttgtgtcatgttaagcagactacacgtcttctgtaacttgtagtctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA
                                                                          | | |     | || |||   |  |||  |     |||    |  || |  |  | | |||     |  |  ||| |           | | | ||   | |||| |   |  | | ||  ||||| || |||||  | || ||||||||||| ||| | |||||||| || ||| |||| || ||||| ||||| || || || ||||| |||||||||||||
--------------------------------------------------------------------------gtaagactaacatgattt--aaattttaag----attataaggtttaaaatttctttttaa-----aaacgaattgt---------gcttttaattgaatgtttttttaataaattattcccagGTCCATTTTTTCCGTCCCGTTCCAAAGGAATATATGCACTCTGCTGAATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA

upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtttcatggacctgtagctaagtgggttagctttgctgagtttcgcaattccttattatcaagtcagtttgcatggtcttcgtgtttttagagctttgtgtcatgttaagcagactacacgtcttctgtaacttgtagtctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA
                                                                             | ||||   | |   |         | | |  ||||  | |||       |  |||   ||| | |   | | | | |  |    | | | |||||| ||| || | ||        | |||| ||||||||| |||||||||| || || ||||| |||||||| ||  | || || |||||||| |||||||| |||||||||||||| ||||| ||||
---------------------------------------------------------------------------gttagtctcaatataaatgttatacattatgactttaaaaaaactgt-----tattgttgtttggaattcaaatctatgttgttggatttgaatttgttgtttgctttctt--------gtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattttttctattccattctcactttgtttttttctattttcactcttggcagGTGCACTTTTTTAGACCGGTTCCAAAGGAGTATCTACACTCTGCAGAGTTGCGAGATATCATGCAGTTTGGCAGTAGTAACACTGCTGTATTTTTTAAAA
                  ttctcac  putative branch site (score: 2)
             ttccattctcactttg  CT-rich tract
                         tttgtttttttctatt  TA-rich tract