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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatgatttctcatgttttgacgtgtaagtatgtgtatagtcttgcctcagttagacacgttagaagattacactgagtttaccttagcatttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCACAGCGTGTGAATCCTTTTCTGGTTGCATTCAATTGCATAAGGAATGTTGT

Basic information

species Physcomitrella patens
transcript PP1S9_37V6.3
intron # 5
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|208350152|gb|DC926107.1|DC926107
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|208393082|gb|DC929577.1|DC929577
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATANAG                         GTTATGAAGGATACGAGGAAATTTCGAGTTCGAGCATCC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCC
EST: gi|18333102|gb|BJ165116.1|BJ165116
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|208365628|gb|DC944112.1|DC944112
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|208383754|gb|DC928057.1|DC928057
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|208378446|gb|DC923082.1|DC923082
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACGATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|208382557|gb|DC923199.1|DC923199
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
EST: gi|162196408|gb|FC373554.1|FC373554
EST:     GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAG                         GTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC
genomic: GGTTCAGGAACTCATGCGAGCACGCCCAATGACTGTATCTCACAATAGAGgtttgtgtta ... tttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcagttagacacgttagaagattacactgagtttaccttagcatttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCACAGCGTGTGAATCCTTTTCTGGTTGCATTCAATTGCATAAGGAATGTTGT
                                            atttgat  putative branch site (score: 5)
                                            atttgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatgatttctcatgttttgacgtgtaagtatgtgtatagtcttgcctcagttagacacgttagaagattacactgagtttaccttagcatttgatatagGTTATGAAGGATACGAGGAGATTTCGAGTTCGAGCATCCCAACACAATCACAGCGTGTGAATCCTTTTCTGGTTGCATTCAATTGCATAAGGAATGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA