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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgattgctttcaccagactaaattttagggaattccgataattagaatatgttttgcgtaaagcccatttctgacaatctatttttgaagttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAGAATCAGCGGCGCCTCTAATCAGCTTCTTACAGAACCCAGCTCTTGTTCA

Basic information

species Physcomitrella patens
transcript PP1S73_26V6.1
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|18375480|gb|BJ207058.1|BJ207058
EST:     CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAG                         ATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG
genomic: CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAGgtctgaaatg ... agttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG
EST: gi|18346243|gb|BJ178286.1|BJ178286
EST:     CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAG                         ATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG
genomic: CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAGgtctgaaatg ... agttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG
EST: gi|100388025|gb|BY988498.1|BY988498
EST:     CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAG                         ATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG
genomic: CGCTATGGATATCCACAAGAGCCTCTACCACACCGAAGACGTCCCACAAGgtctgaaatg ... agttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatatgttttgcgtaaagcccatttctgacaatctatttttgaagttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAGAATCAGCGGCGCCTCTAATCAGCTTCTTACAGAACCCAGCTCTTGTTCA
                         ttctgac  putative branch site (score: 2)
                                               ttttcc  putative PPT
                                    tatttttgaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgattgctttcaccagactaaattttagggaattccgataattagaatatgttttgcgtaaagcccatttctgacaatctatttttgaagttttccagATATGGTGGACAGGAGAGCAGAGGTTGTTGGTCGGCTGAAGGTGCTGGAAGAATCAGCGGCGCCTCTAATCAGCTTCTTACAGAACCCAGCTCTTGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC