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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaatattgcattgaacttatttgcccctactcagttggtgcttatactgagatttgttgccattttaggcattttagtgaaacctcacctaatacattcaatcagagaagctaatgtttcattctctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCCCCTCTTTCTATGACGCTTACTTCAAG

Basic information

species Physcomitrella patens
transcript PP1S83_158V6.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_158V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os03g02640.1 (Oryza sativa), 3'ss of exon 7
gtgagtaaatattgcattgaacttatttgcccctactcagttggtgcttatactgagatttgttgccattttaggcattttagtgaaacctcacctaatacattcaatcagagaagctaatgtttcattctctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCCCCTCTTTCTATGACGCTTACTTCAAG
                                 |  |||  || || | || |   ||||  | |   | |||   ||   |    |    ||    | | ||||  | | |||| || ||   |  ||  || |    |||||| ||||| |||||||||||||| |||||||||||||| || |||||       ||||||  | | || ||  ||
---------------------------------tgttca--tgttgat-atgcctggattactggttgtcttatctatggcacatcatgaccagtagaca-attcgttaacagaaacttattgctgtttaactgc----agATGGCCACAACGAAGCGGAGTTTGGTATGTCATGGTGCGCTGGATTTGGGGGGGAATTCTATAGCTCCTATTTTGAG

upper sequence: PP1S83_158V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G61080.1 (Arabidopsis thaliana), 3'ss of exon 7
gtgagtaaatattgcattgaacttatttgcccctactcagttggtgcttatactgagatttgttgccattttaggcattttagtgaaacctcacctaatacattcaatcagagaagctaatgtttcattctctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCCCCTCTTTCTATGACGCTTACTTCAAG
                                                         ||  | |  |||| |     | ||  | | |  | |||    |  ||||| ||  |    |    | ||||||        |||||||||| || || ||||| ||||||||||| ||||||||||| |||||    ||||||||  | || || ||||||
-------------------------------------------------------gtataagctttcattctcaaattcttgat-atattttacc----attttcaagcaccg---ttttgatctcattcctcctccacagATGGGCATAACGAGGCGGATTTTGGAATGTCGTGGTGCGCAGGATTTGGAGAATCTTTCTACAATGCCTATTTCAAG
















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|208396828|gb|DC920424.1|DC920424
EST:     TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCNTGCATGTTATT                         ATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
genomic: TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATTgtgagtaaat ... ctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
EST: gi|18333323|gb|BJ165337.1|BJ165337
EST:     TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATT                         ATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
genomic: TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATTgtgagtaaat ... ctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
EST: gi|162187661|gb|FC364105.1|FC364105
EST:     TGCCACGGATGCAAAAGGATCCCCCGTAATACTTGATCCTGCATGTTATT                         ATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
genomic: TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATTgtgagtaaat ... ctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
EST: gi|37838919|gb|BJ596927.1|BJ596927
EST:     TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATT                         ATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC
genomic: TGCCACGGATGCAAAAGGATCCCCCGTAGTACTTGATCCTGCATGTTATTgtgagtaaat ... ctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctcacctaatacattcaatcagagaagctaatgtttcattctctacgaccagATGGGCACAATGAAGCGGAGTTTGGAATGTCATGGTGCGCAGGGTTTGGCCCCTCTTTCTATGACGCTTACTTCAAG
                            agctaat  putative branch site (score: 3)
                                    tttcattctct  CT-rich tract
         taatacatt  TA-rich tract