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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggcttatccaagtgggagctgtccgcaacccagtgcaaggaatttcgcgaatatggtagattttgtaactagggtttgcttgtttttcttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCGTGTTGCGCATCATGCGCATGCTCGGCATGTCAGGGGGTAGCAAGTGGTA

Basic information

species Physcomitrella patens
transcript PP1S78_51V6.1
intron # 1
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|208384937|gb|DC903444.1|DC903444
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100423001|gb|BY958106.1|BY958106
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18365524|gb|BJ197601.1|BJ197601
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCCGGATGTTTGGCGTC
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAG-CCGGATGTTTGGCGTC
EST: gi|18342437|gb|BJ174472.1|BJ174472
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208364652|gb|DC939419.1|DC939419
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100442251|gb|BY981275.1|BY981275
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100402810|gb|BY973367.1|BY973367
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGTATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|18358497|gb|BJ190556.1|BJ190556
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100387846|gb|BY970591.1|BY970591
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100420684|gb|BY993463.1|BY993463
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|100434128|gb|BY978972.1|BY978972
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
EST: gi|208391063|gb|DC929375.1|DC929375
EST:     CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTA                         GGGTGTTGAAGTANAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG
genomic: CGTTTTCGATTCTGCGGTTGCGTGATATTCGCGAAGTTTACACTTTCCTAgtaagattcg ... cttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgcgaatatggtagattttgtaactagggtttgcttgtttttcttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCGTGTTGCGCATCATGCGCATGCTCGGCATGTCAGGGGGTAGCAAGTGGTA
                    ttgtaac  putative branch site (score: 2)
                                tttgcttgtttttctt  putative PPT
                                        tttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggcttatccaagtgggagctgtccgcaacccagtgcaaggaatttcgcgaatatggtagattttgtaactagggtttgcttgtttttcttttcacagGGGTGTTGAAGTAGAAGAATCAGGATGTGGGCAGCCGGATGTTTGGCGTCGTGTTGCGCATCATGCGCATGCTCGGCATGTCAGGGGGTAGCAAGTGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG