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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcagcgaatggcgtaaaactgagttttggagaatttcattttgaaagaggtgttttgccttccccgacttgttctggatttgaattgatcacgagttcggctttcaattgtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGGTAAGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAG

Basic information

species Physcomitrella patens
transcript PP1S2_667V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 4
gtaggcagcgaatggcgtaaaactgagttttggagaatttcattttgaaagaggtgttttgccttccccgacttgttctggat-ttgaattgatcacgagttcggctttcaattgtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGGTAAGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAG
                     | |    |||| |   | |    |   ||   || |   |||      |||| |   ||  | ||||  |  | || || |  |   |   || || ||  |||||||| |||||||||||||| |||||||||||||| ||| | ||  | || ||| |   ||||  | |  || | |||||  |||| |   | ||||||
---------------------attttaatttgaattgtctagggtctgaaatagt-tcaagcccctaatgactagagttgattattgatcttcttactagattagtgattc-ttatgttt-tagGTACCCAAATTTGAAGAGTGTCCGTGAATTGATCTACAAGAGGGGCTATGGAAAGCTCAACAAGCAAAGAATCCCTCTTACAAACAACAAAGTCATCGAG

upper sequence: PP1S2_667V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 5
gtaggcagcgaatggcgtaaaactgagttttggagaatttcattttgaaagaggtgttttgccttccccgacttgttctggatttgaattg-atcacgagttcg---gctttcaattgtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGGTAAGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAG
                                              | ||| |    ||   || |   || |      |    | |  || | || |  |        || ||| |   ||| ||||||||||||||||||||||||| | ||||||||||| ||| | ||  | || || |||  ||||    |  | ||  | || |||||  | ||||| || 
----------------------------------------------gtaagtgaaagttcaactacattgattctcatggttcattacctgcaccatggttcttaatatttgcaaatccactt-cagGTACCCTAATTTGAAGAGTGTTAGAGAATTGATCTACAAGAGGGGCTATGGAAAAGTTAACAAGCAGAGAATTGCTTTGACAGACAACTCTATTATTGAA
















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|208376427|gb|DC902738.1|DC902738
EST:     AAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGG                         GTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGG
genomic: AAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGGgtaggcagcg ... gtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGG
EST: gi|162220043|gb|FC396520.1|FC396520
EST:     AAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTCCGG                         GTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCG
genomic: AAAGCCACGATGAACATGTTGAGTCGAGTCGAGCCATATGTGACCTACGGgtaggcagcg ... gtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgacttgttctggatttgaattgatcacgagttcggctttcaattgtgcttgcagGTACCCTAATTTGAAGAGTGTTCGTGAATTGATCTATAAGCGTGGGCACGGTAAGGTTGTCAAGTCACGTGTCGCCCTTACTGACAATACCATTATCGAG
                  aattgat  putative branch site (score: 4)
             atttgaatt  TA-rich tract