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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattgtacttatcagttcggcttttgctcagaatttcttcattcttttttttataatttgcctcacaacatgttgctttattacctgtgtttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGGGAAGGACCTTCCATGGGTGGAGAAGTTCCCCTTCGGCTACTTCAGAGAT

Basic information

species Physcomitrella patens
transcript PP1S77_293V6.1
intron # 2
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|208376863|gb|DC918776.1|DC918776
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|208367770|gb|DC944016.1|DC944016
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|162231656|gb|FC407638.1|FC407638
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|67694807|gb|BJ955040.1|BJ955040
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|162230514|gb|FC407130.1|FC407130
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|208396102|gb|DC924568.1|DC924568
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|100362195|gb|BY947237.1|BY947237
EST:     CACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTTACAG                         G-TGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTG
genomic: CACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATT-ACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTG
EST: gi|162204361|gb|FC380549.1|FC380549
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|162230513|gb|FC407129.1|FC407129
EST:     CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
EST: gi|208371393|gb|DC955729.1|DC955729
EST:     CCACTTATTTGTGTAGTACTGTTCGCAC-TNGGCAGATTCTGAATTACAG                         GGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG
genomic: CCACTTATTTGTGTAGTACTGTTCGCACTTGGGCAGATTCTGAATTACAGgtaattgggc ... tttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttataatttgcctcacaacatgttgctttattacctgtgtttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGGGAAGGACCTTCCATGGGTGGAGAAGTTCCCCTTCGGCTACTTCAGAGAT
               gcctcac  putative branch site (score: 3)
     tttataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattgtacttatcagttcggcttttgctcagaatttcttcattcttttttttataatttgcctcacaacatgttgctttattacctgtgtttatggcagGGTGTATGATCTGCTGGGGGAAGAAGGAGTATACTACGGAGGGTGCTTTGGGAAGGACCTTCCATGGGTGGAGAAGTTCCCCTTCGGCTACTTCAGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT