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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgctgggatcctaaaccctccttggaattctatgtagcatactgcttttgaggacgggcttttggagttgcaaggattgtaaacgtgggccgaatggggatggcatgtttgtgggcggggttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATCAGGTCTCTGAAGCCATTCGATATGTACACAATCGGGGAGTCCGTGAAGA

Basic information

species Physcomitrella patens
transcript PP1S101_170V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_170V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT2G34590.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgatgctgggatcctaaaccctccttggaattctatgtagcatactgcttttgaggacgggcttttggagttgcaaggattgtaaacgtgggccgaatggggatggcatgtttgtgggcggggttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATCAGGTCTCTGAAGCCATTCGATATGTACACAATCGGGGAGTCCGTGAAGA
                                     |||  | |   |     |   |     ||    |        |     |||   |  | ||| | |      | |  |    |  |  |  |||||||||||||||| |||||| ||| |||||| || |||||| | |||||||| |||||  ||||||| || ||| | ||||||||                 
-------------------------------------gtactaaatcacaaccaaaagctcttcttcattgaaattgaaac----aacacagaactaatagagtacttgtatcagGTACCATG--TAATGCAGGCTGCAAAGACGCTGGTGAACAAAGGGTATGATCCAGAGGTTATCGACATAAGGTCGTTGAAGCCGTTTGATCTCTACACAATT----------------
















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|162249333|gb|FC424835.1|FC424835
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162166415|gb|FC342397.1|FC342397
EST:     TGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: TGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162171201|gb|FC347178.1|FC347178
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208393784|gb|DC946078.1|DC946078
EST:     CCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162233986|gb|FC410499.1|FC410499
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|37835367|gb|BJ593379.1|BJ593379
EST:     GGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCNTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: GGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162188985|gb|FC364375.1|FC364375
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208359737|gb|DC946613.1|DC946613
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208397914|gb|DC916669.1|DC916669
EST:     GACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: GACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162166416|gb|FC342398.1|FC342398
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162154877|gb|FC331919.1|FC331919
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|37829882|gb|BJ587894.1|BJ587894
EST:     GGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCNTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: GGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|67720088|gb|BJ970347.1|BJ970347
EST:     TCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: TCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162233959|gb|FC410498.1|FC410498
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208374788|gb|DC948704.1|DC948704
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162191607|gb|FC367652.1|FC367652
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCTAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208367666|gb|DC955011.1|DC955011
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162249334|gb|FC424836.1|FC424836
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|37845062|gb|BJ603070.1|BJ603070
EST:     ATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: ATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162191606|gb|FC367651.1|FC367651
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCTAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|67726686|gb|BJ976945.1|BJ976945
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|208371208|gb|DC956000.1|DC956000
EST:     CGGACATCACNATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162168640|gb|FC343902.1|FC343902
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
EST: gi|162171200|gb|FC347177.1|FC347177
EST:     CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAG                         GCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC
genomic: CGGACATCACAATCTTGACCTACTCCCGGATGAGATATCACGTGACGCAGgtgatgctgg ... gttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgctgggatcctaaaccctccttggaattctatgtagcatactgcttttgaggacgggcttttggagttgcaaggattgtaaacgtgggccgaatggggatggcatgtttgtgggcggggttggtgcagGCTGCAAAGACCCTGGTGGACAGAGGGTACGACCCAGAGATCATCGACATCAGGTCTCTGAAGCCATTCGATATGTACACAATCGGGGAGTCCGTGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA