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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG

Basic information

species Physcomitrella patens
transcript PP1S200_112V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 9
tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataatt-ttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
| ||||    | | | |   || || |  ||     ||    |  |  |   | ||   |   | |    |  ||      |    || |  |  | |||| ||| | ||||| || || |||||||||||||||||||| ||||| || ||||||||  | || || || ||||| ||||||||||||||  | |||
tttatttct-attgttttgtggaatgtggttggatccacacataattctattataatttatggtctccaattgtaaaacataatcttacttttcatggcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTGAAGGCTGGTGCTAATGTTGTACTGACCACTAAGGGAATTGATGATATGTCACTGAAG

upper sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G039263_T02 (Zea mays), 3'ss of exon 7
----tatat-tggggagtttgtcacgg--gatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
    ||||| ||      |   ||| |   |         |  ||| |  | ||||        |||   ||  ||  | | ||  |      |     |||  ||| ||| | ||||| || || |||||||||||||||||||||||||| || ||||||||  |  | || || ||||| ||||| |||||||| || |||
ttcctatatctgatagaatcagcactgtaaacacacagtctgccatataatctatttgaggtctcaaacgttcatc--catgtttcttgctctt-----tttctcagAGAATCTGACATAACAAAGGAGCGAATTGAGAAAATTCTCAAGGCTGGAGCTAATGTTGTGTTGACCACCAAGGGAATTGACGATATGTCCTTGAAG

upper sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 9
---tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
   | |  |  |    |   ||   |||  || |||  |  || |  |||||  |   |     | |  |    |  | |     || || |||  ||||||| ||||| || || ||||||||||||||||||||| |||| || || || || |||||  |||| ||||| || || |||||||| ||| |  | |||
gattgttctatgattctcagcaaaagatggttgtctaattcttgtaattattttggggatttgctgtgatggagc--actaactgta-cttatatctttgcagAGAAGCTGATATGACTAAAGAGCGAATTGAGAAACTTCTGAAAGCTGGAGCCAATGTTGTTCTAACTACAAAAGGGATTGATGACATGGCACTTAAG

upper sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ34091 (Selaginella moellendorffii), 3'ss of exon 9
tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattt-tgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
               || |  |   |||| | ||||  || ||||| ||            | ||||| ||  | | ||       |  ||  || | ||||||| | |||||||| |||||  | ||| | || ||| | ||||| || ||||||||  |||| |||||||| || || ||||||||||||||||||
---------------gtaatagctattttcttttctttttcttttttttt-----------tcttttttgttatctggtctgacttttctatcttctacagGGAATCGGACATTACAAAAGAAAGGATTCAAAAGATTTTGAAGGCCGGTGCTAATGTCGTTCTCACTACGAAAGGAATAGATGATATGTCTTTAAAG

upper sequence: PP1S200_112V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ12438 (Selaginella moellendorffii), 3'ss of exon 9
tatattggggagtttgtcacgggatttttttcttctcattttttttattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
               || |  |   || ||| || |  ||| |||| |               | | | |||| | | ||| || ||      | | ||||||| | |||||||| |||||  | ||| | || ||| | ||||| || ||||||||  |||| |||||||| || || ||||||||||||||||||
---------------gtaatagctcttctttttttttttttcttttttgt-------------tatctggtctgacttttc-tatct------tctacagGGAATCGGACATTACAAAAGAAAGGATTCAAAAGATTTTGAAGGCCGGTGCTAATGTCGTTCTCACTACGAAAGGAATAGATGATATGTCTTTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcagaaaaccaagtatttttcgtcttattgttcataactaataattttgcagGGAAGCAGACATTACTAAAGAGCGAATTGAGAAAATTCTCAAGGCAGGGGCTAATGTGATTCTTACTACGAAGGGCATTGATGATATGTCTTTAAAG
                                      aactaat  putative branch site (score: 2)
                           ttattgttcataacta  TA-rich tract