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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcatacctcattgatcacctgtagtttacatttttttaccaactttttattacatttatttcactgaggtgtggataattcagattattattattatttaaaaaaaaactgttaatgcaattaacaccatttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGACCAAGTCTCTTTGGGAGTACGCTGGAGGAGCAAGCAATTGTCGATCAGTG

Basic information

species Physcomitrella patens
transcript PP1S46_325V6.2
intron # 4
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|208384029|gb|DC919599.1|DC919599
EST:     TGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: TGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208349859|gb|DC905983.1|DC905983
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|37828943|gb|BJ586955.1|BJ586955
EST:     AACAAGTTNCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: AACAAGTT-CCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|37833115|gb|BJ591127.1|BJ591127
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCT-TATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208365936|gb|DC955483.1|DC955483
EST:     TGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: TGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208344704|gb|DC905153.1|DC905153
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|162269338|gb|FC444816.1|FC444816
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208387810|gb|DC941379.1|DC941379
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|37836448|gb|BJ594456.1|BJ594456
EST:     TTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCNGGAAATACAAAGGCCAGGGAC
genomic: TTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208379946|gb|DC927672.1|DC927672
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|18357078|gb|BJ189137.1|BJ189137
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208363225|gb|DC954383.1|DC954383
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208378933|gb|DC922779.1|DC922779
EST:     GACTTTCATCTGTATG                         -ATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: GACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|162269339|gb|FC444817.1|FC444817
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208393393|gb|DC942491.1|DC942491
EST:     CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: CCTTTTAAACAAGTTCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
EST: gi|208380990|gb|DC919872.1|DC919872
EST:     TCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATG                         AATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC
genomic: TCCAGTGTTCGAGTGTGGTGACTTTCATCTGTATGgtgcgtcata ... ttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattattattatttaaaaaaaaactgttaatgcaattaacaccatttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGACCAAGTCTCTTTGGGAGTACGCTGGAGGAGCAAGCAATTGTCGATCAGTG
                                 aattaac  putative branch site (score: 2)
     ttattatttaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcatacctcattgatcacctgtagtttacatttttttaccaactttttattacatttatttcactgaggtgtggataattcagattattattattatttaaaaaaaaactgttaatgcaattaacaccatttgtgcgcagAATCCCGAGCTATAGTGCGTTACATAGCCCGGAAATACAAAGGCCAGGGACCAAGTCTCTTTGGGAGTACGCTGGAGGAGCAAGCAATTGTCGATCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA