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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcggtgtagtttgaggtcttgattttggttgttacgaatctgtattgtacgtgtgtgtacaatttatgttggagaatgtgcatttctcttggacattagGAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTATAGAAAGAAGAGGGTAGATAAGCAGGACATGCCTAATGGTGCTGACCCTT

Basic information

species Physcomitrella patens
transcript PP1S83_84V6.1
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|67571167|gb|BJ943991.1|BJ943991
EST:     GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAG                         GAATTTGCTAAGAAGCAATCA
genomic: GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAGgtgatatttt ... tggacattagGAATTTGCTAAGAAGCAATCA
EST: gi|100411006|gb|BY956282.1|BY956282
EST:     GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAG                         GGAATTTGCTAAGAAAGCA-TCAGGAGGNTATACCAAGCCTAGCACGAGTT
genomic: GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAGgtgatatttt ... tggacattagG-AATTTGCTAAGAA-GCAATCAGGAGGTTATACCAAGCCTAGCACGAGTT
EST: gi|100398116|gb|BY954096.1|BY954096
EST:     GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAG                         GA-TTTGCNTA-GAAGCA-TCAGGAGGTTATACCAAGCCTAGCACGAGTTA
genomic: GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAGgtgatatttt ... tggacattagGAATTTGC-TAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTA
EST: gi|100440874|gb|BY962362.1|BY962362
EST:     GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAG                         GAATCTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTAT
genomic: GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAGgtgatatttt ... tggacattagGAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTAT
EST: gi|18348787|gb|BJ180836.1|BJ180836
EST:     GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAG                         GAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTAT
genomic: GGATCACCTCTAATGTGAAACGCAACCTTCATCTACTGAAGATCTTTAAGgtgatatttt ... tggacattagGAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacgtgtgtgtacaatttatgttggagaatgtgcatttctcttggacattagGAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTATAGAAAGAAGAGGGTAGATAAGCAGGACATGCCTAATGGTGCTGACCCTT
                                    catttctctt  CT-rich tract
             tacaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcggtgtagtttgaggtcttgattttggttgttacgaatctgtattgtacgtgtgtgtacaatttatgttggagaatgtgcatttctcttggacattagGAATTTGCTAAGAAGCAATCAGGAGGTTATACCAAGCCTAGCACGAGTTATAGAAAGAAGAGGGTAGATAAGCAGGACATGCCTAATGGTGCTGACCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG