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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacaatgttgtggttatccagtgtgatcaaacctgtgtctcgattggaaagtgttctgtctatgttatttctcacatagtttggaacaaattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGGTAGGTTGGTGTGGGTTAAGATGTCGATCGGGGAAGCCGAGCACGCGGAG

Basic information

species Physcomitrella patens
transcript PP1S9_318V6.2
intron # 2
splice site 3'
intron type U2

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|208349770|gb|DC905894.1|DC905894
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|67576346|gb|BJ949170.1|BJ949170
EST:     CTGCCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: CTG-CTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|100443994|gb|BY982222.1|BY982222
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|162172920|gb|FC348925.1|FC348925
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|162160287|gb|FC336573.1|FC336573
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|18332321|gb|BJ164334.1|BJ164334
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|18327338|gb|BJ159340.1|BJ159340
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
EST: gi|67568989|gb|BJ941813.1|BJ941813
EST:     TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAG                         GGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG
genomic: TCTGCTCCAGAACGTGCATTGTTCCTGCACGCCTACGTATGCATCAAAAGgtttgtgtct ... aattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaagtgttctgtctatgttatttctcacatagtttggaacaaattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGGTAGGTTGGTGTGGGTTAAGATGTCGATCGGGGAAGCCGAGCACGCGGAG
                         ttctcac  putative branch site (score: 2)
                 tatgttattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacaatgttgtggttatccagtgtgatcaaacctgtgtctcgattggaaagtgttctgtctatgttatttctcacatagtttggaacaaattttgcagGGACTTGCTATCATTGTGATTTAAATCATCACGTGGTAGAAAGCCTACGGGTAGGTTGGTGTGGGTTAAGATGTCGATCGGGGAAGCCGAGCACGCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG