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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggttgtgcaccatttatccaaattaggttaattgggatttgagggttagcaacgacgatctggcagacttcttttaataccgaaattgttgaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGATGTTGGGAAGACCATCCTGAAG

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.2
intron # 10
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|18338652|gb|BJ170676.1|BJ170676
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208365272|gb|DC946817.1|DC946817
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208352527|gb|DC918236.1|DC918236
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67724647|gb|BJ974906.1|BJ974906
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|18334936|gb|BJ166954.1|BJ166954
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67691893|gb|BJ952126.1|BJ952126
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67727713|gb|BJ977972.1|BJ977972
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|208397427|gb|DC916353.1|DC916353
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|37829801|gb|BJ587813.1|BJ587813
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
EST: gi|67695119|gb|BJ955352.1|BJ955352
EST:     TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAG                         GTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT
genomic: TCATGAAGTGTGATGTTATTGCTGCTGGAATTGTGGCTGCTGCTAAACAGgtatacttgt ... gaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagcaacgacgatctggcagacttcttttaataccgaaattgttgaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGATGTTGGGAAGACCATCCTGAAG
                          ttttaat  putative branch site (score: 3)
                       ttcttttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggttgtgcaccatttatccaaattaggttaattgggatttgagggttagcaacgacgatctggcagacttcttttaataccgaaattgttgaatctgcagGTGAATTTGAAAGTTCCACTAGTAGTACGTTTGGAGGGTACGAATGTGGATGTTGGGAAGACCATCCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG