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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttagacttaatttgtcatgtaaaagaatctattatgttcgattttattatcctcgcttagcatattatgacattggtgcgtcttgttggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTTCCTCCTCCCCTCCCAGTAAACCCGTATCAGGCTGGTCTTATGTCTGGAG

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.2
intron # 12
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|37838954|gb|BJ596962.1|BJ596962
EST:     AGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCNTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: AGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162245866|gb|FC419662.1|FC419662
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162261364|gb|FC437797.1|FC437797
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162254429|gb|FC430655.1|FC430655
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTNTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162152880|gb|FC328974.1|FC328974
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTNTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|208399380|gb|DC924810.1|DC924810
EST:     TAGCGANTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162258160|gb|FC433942.1|FC433942
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|22492368|gb|BU052291.1|BU052291
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|37840384|gb|BJ598392.1|BJ598392
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162277159|gb|FC453381.1|FC453381
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGGCTACCGTGCCAGGATCGTCATC
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATC
EST: gi|162245867|gb|FC419663.1|FC419663
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
EST: gi|162261365|gb|FC437798.1|FC437798
EST:     TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAG                         TGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT
genomic: TAGCGATTCAAGCAGCCAACGGTAGAGTACTTTGCGGCAAGTCTGTTAAGgtaaaatgaa ... ggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattatcctcgcttagcatattatgacattggtgcgtcttgttggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTTCCTCCTCCCCTCCCAGTAAACCCGTATCAGGCTGGTCTTATGTCTGGAG
                   atattatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttagacttaatttgtcatgtaaaagaatctattatgttcgattttattatcctcgcttagcatattatgacattggtgcgtcttgttggtattctagTGTTCCTGGGGCAGCAAGCCTACCGTGCCAGGATCGTCATCAGCACCACTTCCTCCTCCCCTCCCAGTAAACCCGTATCAGGCTGGTCTTATGTCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC