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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggtctatctttttatacatactgtgttcacgagggtggattttcctcagaccgcatgctatgtagtggtgttcattttgcactattgactccagttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGTTCACCACGTAGTCGCAG

Basic information

species Physcomitrella patens
transcript PP1S173_12V6.2
intron # 9
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|67698067|gb|BJ958300.1|BJ958300
EST:     TCTTTCATTCGG                         GTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT
genomic: TCTTTCATTCGGgtgagtggtc ... ttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT
EST: gi|208353229|gb|DC926154.1|DC926154
EST:     GACTCAGAATTCCGCAACCCATTTTCTCGTTCTTTCATTCGG                         GTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT
genomic: GACTCAGAATTCCGCAACCCATTTTCTCGTTCTTTCATTCGGgtgagtggtc ... ttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT
EST: gi|37846921|gb|BJ604929.1|BJ604929
EST:     AGTTGGACGACTCAGAATTCCGCAACCCATTTTCTCGTTCCTTCATTCGG                         GTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT
genomic: AGTTGGACGACTCAGAATTCCGCAACCCATTTTCTCGTTCTTTCATTCGGgtgagtggtc ... ttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgcatgctatgtagtggtgttcattttgcactattgactccagttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGTTCACCACGTAGTCGCAG
                                 tattgac  putative branch site (score: 2)
                                             ttctccac  putative PPT
                     ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggtctatctttttatacatactgtgttcacgagggtggattttcctcagaccgcatgctatgtagtggtgttcattttgcactattgactccagttctccacagGTGAAAGAAGATAAAGGTTACGGATCTCGAAGGAGCGTCACTCGAAGCCGTTCACCACGTAGTCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG