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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC

Basic information

species Physcomitrella patens
transcript PP1S142_132V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os10g26600.1 (Oryza sativa), 3'ss of exon 3
atctagcaatg-gttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
    ||||  | ||| | | |||   |  |||| |         |  | |    ||| |   |        |||    |||  ||    |||  |    ||||| | |||||    ||||| |||||||||||||||||||| |||||||||| |||  ||||||||                                  
-gtaagcatcgtgttcataatatatttgtcatcaaattgaagcaaacactgcgatttatttcaggatgcatctggacctgacatgt---ttttttttgtagGTTGTTGAGATCACAAAGGGGAGCAAAGTGAAGTATGAGCTTGACAAGAAGACTGGAATGATCAAG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 3
--------atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
         | || | ||  | ||   | |    ||||  | |    |   |   | |      ||      || |   ||   |  ||||      |  |   ||||||| | |||||   |||||||||||||||||| |||||||| |||||||| | |||  |||| |||                                  
attgttctgtttaacgattctagaagctttat-ctacagtcggttcctgaca-gtgcatgcaacctaca---tggttaatggcttccatttata---tcacaccacagGTTGTTGAGATCACCAAGGGAAGCAAAGTGAAATATGAGCTTGACAAGAAAACTGGACTGATTAAG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 2
atctagcaatggttgacattatgggttacatc-cagccattaggacaagtagattttctgggaattgatccctgag--attgatttgggaatttgc-tgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
     | ||  |    |   |   |  ||  | ||     |    |   | ||||| |    | ||||     ||    ||  ||   |  ||||| || | ||||| | |||||   |||||||||||| |||||||| |||||||||||||| |  || || |||| |                                  
-----gtaagcgccctcgccacatgccacgccacaagggattcttcccttggatttacactcacttgactaacgatgcgtttcttcttggttttgcgtggatagGTTGTGGAGATCTCCAAGGGAAGCAAGGTGAAGTACGAGCTCGACAAGAAAACGGGGTTCATCATG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 2
atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaat-ttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
          |  |    |  |   ||| | ||  | | || | |   |  | | |||     |   |   |  | || |   | ||   |  |||  |||||  | |||||    ||||||||||||||||| ||||| |||||||| ||||  ||| | ||||||                                  
----------gtattgtctcttaacttataacc--caagtaagccttctttaatctctctctctctcttggtctg-ttaacgagagagcctctctggtcagGTGGTTGAGATCACAAAGGGAAGCAAAGTGAAATATGAACTCGACAAAAAGACCGGTCTTATCAAG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 2
atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
                                               || ||  |||      ||| |   |   |||| ||   ||||  | |   |||||  | || || | ||| || |||||||| |||||||||||||||||| | ||||| |||||||||                                  
-----------------------------------------------gt-gagcttcatcctcttgtttggtagcattgctt---gaatcggttttccagGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAAAGTGGATTGATCAAG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 1
atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
                  || |||    |    ||   |||  ||     ||  |||      ||| |   |   |||| ||   ||||  | |   |||||  | || || | ||| || |||||||| |||||||||||||||||| ||||||| |||||||||                                  
-----------------gttctggagctcccttagttttta--actgcgtgagcttcatcctcttgtttggtagCATTGCTT---GAATCGGTTTTCCAGGTCGTGGAAATCGCCAAAGGCAGCAAAGTCAAGTATGAGCTCGACAAGCAGAGTGGATTGATCAAG----------------------------------

upper sequence: PP1S142_132V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 2
atctagcaatggttgacattatgggttacatccagccattaggacaagtagattttctgggaattgatccctgagattgatt-tggg---aatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
                                      | ||     |   |||||| | || ||||||  |||| |||||  || |       |  ||  |||||| | |||||  |||| ||| |||||||||| || ||||| ||||||||||||||| | ||||||                                  
-------------------------------------gtaagtcgctgcccattttccgcga-ttgatct-tgagcttgatggtgagtgaggcctcgtgtgcagGTTGTGGAGATCAGCAAAGGAGGCAAAGTGAAATACGAGCTGGACAAGAAGAGTGGTCTCATCAAG----------------------------------

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|162244893|gb|FC424669.1|FC424669
EST:     GTCCTGAGGCACCACCCATTTTCAAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAA
genomic: GTCCTGAGGCACCAGCCATTTTC-AACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAA
EST: gi|162236289|gb|FC412032.1|FC412032
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|208396434|gb|DC920086.1|DC920086
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTNGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|208381293|gb|DC919183.1|DC919183
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|162259318|gb|FC436209.1|FC436209
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|162264798|gb|FC440365.1|FC440365
EST:     AGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: AGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|208380290|gb|DC922712.1|DC922712
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|208400875|gb|DC925155.1|DC925155
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
EST: gi|67698989|gb|BJ959222.1|BJ959222
EST:     GTCCTGAGGCACCAGCCATTTTCAACTGT                         GTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG
genomic: GTCCTGAGGCACCAGCCATTTTCAACTGTgtaagttaca ... tgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtagattttctgggaattgatccctgagattgatttgggaatttgctgaacagGTTATCGAGATTGGCAAGGGAAGCAAAGTGAAGTATGAGCTCGACAAGAAGAGTGGTTTGATCAAGGTTGATCGTATTCTGTATTCATCTGTTGTGTACC
                             gattgat  putative branch site (score: 4)
                              attgattt  TA-rich tract