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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaattcatcatccttggacttcttcaattattgttctgaaccgcttatttctactactgcaaaaaataatttgagaaaaggatgtgtctcattgacttcgaacttttttgactttaggtgctctgagcagcttgtggtgctgtagatgacgtgtgtgagtggcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGTGCTACGCTGCCCAAAGGAACATTTGTGAAACTTCAGCCCCATACAAAAG

Basic information

species Physcomitrella patens
transcript PP1S245_32V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G38930.2 (Arabidopsis thaliana), 3'ss of exon 6
gtataaaattcatcatccttggacttcttcaattattgttctgaaccgcttatttctactactgcaaaaaataatttgagaaaaggatgtgtctcattgacttcgaacttttttgactttaggtgctctgagcagcttgtggtgctgtagat-gacgtgtgtgagtggcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGTGCTACGCTGCCCAAAGGAACATTTGTGAAACTTCAGCCCCATACAAAAG
                                                                                             | |   ||       | |||| |       | |    ||   || |   |  |||   |  |  |   |   | ||   ||||||||||||||||| |||||||||| ||||| ||||| || ||||| |  | ||  || || || || ||||| |  |||||||| || ||||| |||| ||
--------------------------------------------------------------------------------------------gtaacaaacagtagcttgtttttatcaccaatac---aagatactcgatatcttgtgacttaaaatcgattgtttgcttttgcagATGATGCAGAATTTGCTGTTGCAAGAAGGAGACATGGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACCTACGTGAAACTGCAACCCCACACAACAG

upper sequence: PP1S245_32V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT2G21270.3 (Arabidopsis thaliana), 3'ss of exon 6
gtataaaattcatcatccttggacttcttcaattattgttctgaaccgcttatttctactactgcaaaaaataatttgagaaaaggatgtgtctcattgacttcgaacttttttgactttaggtgctctgag-cagcttgtggtgctgta--gatgacgtgtgtgagtggcaca-tgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGTGCTACGCTGCCCAAAGGAACATTTGTGAAACTTCAGCCCCATACAAAAG
                                                                                  ||| ||  || || |   ||| |    ||| ||| |  | || |||||   ||  | |   | |   |  |||    ||  |   ||  | | | ||||||||||||||| ||||| |||| ||||| |||||||| ||||| |  | ||  || || || || ||||| |  || ||||| |||||||| |||| ||
--------------------------------------------------------------------------------gtaagaatcagtttcct---ctttg----tttgtgaatcgaagtactctggatcatgtggacttaccagactgattgtttgcttctttgatataatccagATGATGCAGAATCTGCTGCTGCAAGAAGGAGACATTGTGAGAGTTAGAAATGTCACTCTTCCAAAGGGAACTTACGTTAAACTACAGCCCCACACAACAG
















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|100385818|gb|BY951012.1|BY951012
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100406597|gb|BY955683.1|BY955683
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100418696|gb|BY975696.1|BY975696
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208387770|gb|DC941339.1|DC941339
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTCACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100415871|gb|BY956965.1|BY956965
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|67508675|gb|BJ941536.1|BJ941536
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100448950|gb|CJ973249.1|CJ973249
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208349271|gb|DC906385.1|DC906385
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208346232|gb|DC905221.1|DC905221
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208352262|gb|DC906337.1|DC906337
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208366055|gb|DC935844.1|DC935844
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208372135|gb|DC940317.1|DC940317
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|18358101|gb|BJ190160.1|BJ190160
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCANAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208390049|gb|DC938104.1|DC938104
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100419714|gb|BY957686.1|BY957686
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208358250|gb|DC930691.1|DC930691
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208357678|gb|DC934130.1|DC934130
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100442532|gb|BY963226.1|BY963226
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100366066|gb|BY967268.1|BY967268
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208366022|gb|DC935839.1|DC935839
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|100386786|gb|BY970327.1|BY970327
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208374981|gb|DC956391.1|DC956391
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208363142|gb|DC954342.1|DC954342
EST:     GCGTGCTGGAG-TTGTGGCAGAGGAAGGCATGATTCACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208356440|gb|DC934430.1|DC934430
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208386327|gb|DC932823.1|DC932823
EST:     GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
EST: gi|208387581|gb|DC953323.1|DC953323
EST:     GCGTGCTNGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGG                         ATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT
genomic: GCGTGCTGGAGTTTGTGGCAGAGGAAGGCATGATTTACATGCCGTACTGGgtataaaatt ... gcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaaattcatcatccttggacttcttcaattattgttctgaaccgcttatttctactactgcaaaaaataatttgagaaaaggatgtgtctcattgacttcgaacttttttgactttaggtgctctgagcagcttgtggtgctgtagatgacgtgtgtgagtggcacatgcagATGATGCAGAATATGCTGTTGCAGGAAGGTGACATTGTTAGAGTGAAGAGTGCTACGCTGCCCAAAGGAACATTTGTGAAACTTCAGCCCCATACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA