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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgagttgattcgagaatcggagtttgcgagaacatttttaggtggagttgggagcttagacagttttgaaggcttatccaacctgctgtcctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCCGCCCCGATCAAGACAGTATCGAGTTTGAGGTCTACCGTTTCGAAGCTGA

Basic information

species Physcomitrella patens
transcript PP1S48_46V6.1
intron # 1
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|100440620|gb|BY962307.1|BY962307
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|18375321|gb|BJ206899.1|BJ206899
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|18327556|gb|BJ159559.1|BJ159559
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGGTGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|18371471|gb|BJ203073.1|BJ203073
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|100408025|gb|BY955876.1|BY955876
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|18357107|gb|BJ189166.1|BJ189166
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|100397422|gb|BY972491.1|BY972491
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGCGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
EST: gi|18371775|gb|BJ203377.1|BJ203377
EST:     AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGG                         AAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC
genomic: AATTGGTGGAAGACGAGTTCTAGGGTTTTTCATGTGTCCGCAAACTCTGGgtaggcagac ... ctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgggagcttagacagttttgaaggcttatccaacctgctgtcctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCCGCCCCGATCAAGACAGTATCGAGTTTGAGGTCTACCGTTTCGAAGCTGA
                                           tcctgttt  CT-rich tract
                  ttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgagttgattcgagaatcggagtttgcgagaacatttttaggtggagttgggagcttagacagttttgaaggcttatccaacctgctgtcctgtttgcagAAATTTGAAGAGATGAATTGGCGTTAGTGGTGATTGTTCGTCATCACCGCCGCCCCGATCAAGACAGTATCGAGTTTGAGGTCTACCGTTTCGAAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA