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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG

Basic information

species Physcomitrella patens
transcript PP1S540_7V6.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 9
gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
       ||  ||| |  |      |||||||      |  |    || ||| |   ||     | | ||  |  |   | |||  || | | ||   | |     |  ||       ||||||| ||||||||||||||  |  | ||| | || |||||||| ||||| ||| |||||||||||   || ||||||||||||||||| || ||||| |||
-------tttccaatagttgc----ttcatatacagaatcggc---aggcaatagtcttccttttggtgcaatagact-tgtctccttacggcattccacgtcacttcctt-------tcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 9
gtatgccttatcaacatctctagagttcatatgtgagctttgtcaaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
               | ||  | || | | || | || ||   |    |     ||||   | ||  | | ||  |   ||| |  |     |     |||  | |  |   || || ||||||| |||||||| ||||| ||||||||  ||||||||||||| || ||||| || ||||| ||  | || |||||| | ||||||||  | |||  | | 
--------------taactagaaagatgacatcttagattcaacttgattgtggcaat---gtatgcctcagtagaagttctgtgttgatcaa---caatgtggtaacg--atgcgtttcagGGTAAAGAGCCAACTGAAAAGGATTGCCCGACCAATGTACTCTAATCCACCGGTACACGGGGCTAGGATAGTTGCCGATGTTGTTGGAAACCCAGTTCTC

upper sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
gtatgccttatcaacatctctagagttcat-atgtgagctttgtc-aaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgct----ggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
                       |  |||| |||   | ||| || |||||  |  ||  ||     || |  |        || |   || |  | ||| |  |      ||| || |   | ||||||| ||||| ||| |||| ||||||||  |||||||||||||||| || ||| |||| || ||  | ||||||||||| |||||||| || ||| || | 
-----------------------atatcatgatgaatggtttatctaaagttgatccaggtgattcctgagtggc-----aactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC

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|18339711|gb|BJ171738.1|BJ171738
EST:     TGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: TGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208386964|gb|DC956933.1|DC956933
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGNTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|37838764|gb|BJ596772.1|BJ596772
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATG-TGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCCAAANNNNN
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACT-CAAA-CCCA
EST: gi|162158558|gb|FC334561.1|FC334561
EST:     TCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: TCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208382292|gb|DC919280.1|DC919280
EST:     ATCAATGCGATTGTATCCTNTGCAGATGNTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: ATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|67698272|gb|BJ958505.1|BJ958505
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162196656|gb|FC373802.1|FC373802
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208386221|gb|DC952934.1|DC952934
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162217709|gb|FC393801.1|FC393801
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162217708|gb|FC393800.1|FC393800
EST:     CTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|208366815|gb|DC940129.1|DC940129
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162158559|gb|FC334562.1|FC334562
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162196657|gb|FC373803.1|FC373803
EST:     CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: CGTGTGGGTGCTATCAATGCGATTGTATCCTCTGCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
EST: gi|162167594|gb|FC343739.1|FC343739
EST:     GCAGATGTTGCTGCTAG                         GGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC
genomic: GCAGATGTTGCTGCTAGgtatgcctta ... tgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgttcatagtctctaattgcagaatctgatgctggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG
              tctaatt  TA-rich tract