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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaaaagaaactggaaacgtttcgcgtcctgatgcagcagtgtgcacaagattgttactgaagtattaactttataaatgtcgtcggctggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAAAACAAAATTTATACATCGCCTGGTGTATATCAGGTGAAGGTACCATGTG

Basic information

species Physcomitrella patens
transcript PP1S334_25V6.1
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|15327205|gb|BI487739.1|BI487739
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|162184192|gb|FC359653.1|FC359653
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|37832173|gb|BJ590185.1|BJ590185
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|162216337|gb|FC392130.1|FC392130
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|208365360|gb|DC954801.1|DC954801
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATGATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|162216336|gb|FC392129.1|FC392129
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
EST: gi|208373977|gb|DC944710.1|DC944710
EST:     TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACG                         GTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA
genomic: TTGATCAGCATCGACCTATGGCTGGCTCTCCCGGAATTTATAATGTAACGgtatgtgcct ... ggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaagattgttactgaagtattaactttataaatgtcgtcggctggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAAAACAAAATTTATACATCGCCTGGTGTATATCAGGTGAAGGTACCATGTG
                   tattaac  putative branch site (score: 1)
                                               ctttcc  putative PPT
              tgaagtattaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaaaagaaactggaaacgtttcgcgtcctgatgcagcagtgtgcacaagattgttactgaagtattaactttataaatgtcgtcggctggctttccagGTTACTCTTCTAGTTCCAGGCAACTACCAAGGACTCAAGCGATTGGTGCAAAACAAAATTTATACATCGCCTGGTGTATATCAGGTGAAGGTACCATGTG

- - - - - - - - - - - - - - - tgatgca
- - - - - - - - - - - - - - - - - - - - - gtgcaca