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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaagttgcctttgtaaattacgaaccttggtgtcattctattgtaacaccacctttgtaattttacgggtcagaagttaaaattgcaagcatgtatgtgtctgatgctgtatttagtgctctcggagtttgaagatgcatccacaggtacatgtctctgacgcttgatggatttttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAAGCGATTGAAAGGGGCCACGCTCAAACGTATGGTAGTTTATTGTGCGCCA

Basic information

species Physcomitrella patens
transcript PP1S65_2V6.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S65_2V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G035928_T01 (Zea mays), 3'ss of exon 3
gtatgtaagttgcctttgtaaattacgaaccttggtgtcattctattgtaacaccacctttgtaattttacgggtcagaagttaaaattgcaagcatg-tatgtgtctgatgctgtatttagtgctctcggagtttgaagatgcatccacaggtacatgtctctgacgcttgatggatttttttcgt-agGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAAGCGATTGAAAGGGGCCACGCTCAAACGTATGGTAGTTTATTGTGCGCCA
                                                                                     | || |  |  |  ||| |||  |||   || | |  || |||    | || ||    |   |     ||   |  | |||  |     | ||| || |  | ||||  | ||||||||||| || |||||||||||||| |||||||| || ||||| |||||| | || || |     || || |||||| |  ||  | | |
-----------------------------------------------------------------------------------gcagtttcttgtttactatttgttcgatcaagtttgttttggtct----gcttcaacccactgtcgttcata---gcatttgattcaactggaattgttctgatcagGCTTTATCAAAGATCACTTCGACTGGTGCAATGACATTCTGCTTCATCCAAGCTATTGAACGTGGACAGGGCACCACCTACGGTAGTATCCTGAACTCTA

upper sequence: PP1S65_2V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G02170.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatgtaagttgcctttgtaaattacgaaccttggtgtcattctattgtaacaccacctttgtaattttacgggtcagaagttaaaattgcaagcatgtatgtgtctgatgctgtatttagtgctctcggagtttgaagatgcatccacaggtacatgtctctgacgcttgatggatttttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAAGCGATTGAAAGGGGC---CACGCTCAAACGTATGGTAGTTTATTGTGCGCCA
                                                                                         | ||| | | | |  ||| ||  |   | |  |||| | | ||||    | | | ||| |     ||||  |   || | |             |  |||| ||||| ||||||||||| || ||||| ||||| ||||| ||||||||||| |||||| |  ||   || |    ||| ||||| ||  |  ||       
-----------------------------------------------------------------------------------------gtaagta-gaacgactctaatcatacgtct--tgctgttgtagtt----ggttcctcctct----catgattaaaacacata------------cacagGCGCTGTCGAAGATCACGTCTACGGGTGCTATGACTTTCTGTTTTATTCAAGCAATTGAACGCAGCGCACAAGGCACAACCTATGGAAGCCTTCTGAATT---
















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|67579208|gb|BJ951353.1|BJ951353
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|67508564|gb|BJ941427.1|BJ941427
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|208359473|gb|DC954026.1|DC954026
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|37843824|gb|BJ601832.1|BJ601832
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|67691781|gb|BJ952014.1|BJ952014
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|67692649|gb|BJ952882.1|BJ952882
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|162232654|gb|FC409205.1|FC409205
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
EST: gi|37835112|gb|BJ593124.1|BJ593124
EST:     CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCG                         GCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA
genomic: CTTACTCTTTCAGTGGTTGTGACGACAGCCAAACATCGGCTGATACTTCGgtatgtaagt ... tttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagatgcatccacaggtacatgtctctgacgcttgatggatttttttcgtagGCACTGTCAAAGATCACGTCAACTGGTGCAATGACCTTCTGCTTTATTCAAGCGATTGAAAGGGGCCACGCTCAAACGTATGGTAGTTTATTGTGCGCCA
                                           tttttttcgt  CT-rich tract
                                          attttttt  TA-rich tract