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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcggctttgcaacatgaaccgtggaaggcattacatttacaaatgtcagaaccatttgaatttacgaagccttgattttttcgttaatttcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAAATTTTATTCTGCAGCGTGATGGATATCCTAG

Basic information

species Physcomitrella patens
transcript PP1S341_73V6.2
intron # 3
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|100386514|gb|BY951310.1|BY951310
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|100406162|gb|BY991570.1|BY991570
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162185274|gb|FC361784.1|FC361784
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162173953|gb|FC349753.1|FC349753
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162187116|gb|FC362898.1|FC362898
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162158810|gb|FC335333.1|FC335333
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|100435045|gb|BY979058.1|BY979058
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|100446505|gb|CJ970804.1|CJ970804
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162165683|gb|FC342250.1|FC342250
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162193527|gb|FC370430.1|FC370430
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|100389902|gb|BY971254.1|BY971254
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162171492|gb|FC346767.1|FC346767
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|18329867|gb|BJ161873.1|BJ161873
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCC
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCC
EST: gi|18326623|gb|BJ158622.1|BJ158622
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTC
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTC
EST: gi|162151892|gb|FC328138.1|FC328138
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|18363059|gb|BJ195131.1|BJ195131
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGA
EST: gi|67568954|gb|BJ941778.1|BJ941778
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
EST: gi|162157215|gb|FC332849.1|FC332849
EST:     CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGG                         GAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA
genomic: CGCCATTGCCAAAGCCAAGCATTATTTATCTATGACCTCAGGGGGCGTGGgtacgtcatc ... tcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagaaccatttgaatttacgaagccttgattttttcgttaatttcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAAATTTTATTCTGCAGCGTGATGGATATCCTAG
                                     cgttaat  putative branch site (score: 4)
                                           tttctt  CT-rich tract
                              attttttcgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcggctttgcaacatgaaccgtggaaggcattacatttacaaatgtcagaaccatttgaatttacgaagccttgattttttcgttaatttcttgaacagGAGCTTACAGTGATTCCAGAGGACTTCCGGGGGTGCGGCAGGAGGTTGCAAATTTTATTCTGCAGCGTGATGGATATCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA