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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA

Basic information

species Physcomitrella patens
transcript PP1S18_8V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA
                                     |  | |    ||  |   |  |   | || ||  |    || |||||   |  | | | || |   ||  ||    | ||||  |   |   ||     |||  | ||||   | ||  |        || ||| | |   ||  ||||||||||||| ||  | |||||||| |||||||| || ||||||||||| |||||||| ||||||||||| ||||| || ||  | || || |||||| |
------------------------------------gtgagtagaaaatcttgttgccccttttagattttact--tcctgttttgcttctctgtctatt---gtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatctt--ttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA

upper sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G64650.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtct-ccattg--tgtctttggattga--cagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA
                                                                                               | | |    |||  | | || |||    ||  | |  ||   ||||      |   |  | |  ||| ||| |      ||||  ||| |  ||||||||||||| || ||  | ||||| || ||||| ||||||||||| |||||||| || ||||| || || ||||| || || |||||||| |||||  |
----------------------------------------------------------------------------------------------gtgaatctcttaccttaccttggtttttgacatact--gtaatatgtctttgcttccagctttattcttccactaaccacctttttattaaatcagATGAGAAGATCGCATTACTCGGTGCTATTCAGTCTCTGTTTGAAGGGTCCATGTACACCTTTGTGTTTCTCTGGACTCCTGCTTTGAGCCCAAACGAAGA

upper sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA
                                                                       | |  | || ||||| || | | || | |||  |  | |||||      ||    |||||  |    | ||     | || ||| |  | |   || ||| |   |     |||||||||| || || ||| ||||||| || ||||| || |||||||| || ||||| || ||||| ||||||||||| || || ||||| || || ||  |
-----------------------------------------------------------------------atatattttctttctttcttct-ttgatttattttatatgctt------gg----aagtttct--tttttattttctttttattttaatatt-gttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162268232|gb|FC444521.1|FC444521
EST:     CAAGAGCTTCACCCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTG                         ATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCA
genomic: CAAGAGCTTCACCCATCAATTTACGCAGGCAGCTTCAGCTATTGCTTCTGgtgagaactt ... ggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA
                 tcttaat  putative branch site (score: 3)
              aattcttaatt  TA-rich tract