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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctattattgcaaattaaaaatgttgccttttacatttcgttagcagtgaatcacaattatttcatgtgatgcttgttgaagtctgacactttgttactatgctcattcttttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGAAAATCACTACCGTCGATGGATAA

Basic information

species Physcomitrella patens
transcript PP1S29_123V6.1
intron # 3
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|67698151|gb|BJ958384.1|BJ958384
EST:     AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGG                         AGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
genomic: AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGGgtgcgctatt ... ttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
EST: gi|208388672|gb|DC953448.1|DC953448
EST:     AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGG                         AGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
genomic: AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGGgtgcgctatt ... ttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
EST: gi|208369198|gb|DC944557.1|DC944557
EST:     AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGG                         AGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
genomic: AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGGgtgcgctatt ... ttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
EST: gi|67574732|gb|BJ947556.1|BJ947556
EST:     AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGG                         AGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
genomic: AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGGgtgcgctatt ... ttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
EST: gi|162207957|gb|FC383663.1|FC383663
EST:     AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGG                         AGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA
genomic: AGGTCAAAGAATGTCGACAACTTGACAGGCAACTATGTGTTCTTCCTCGGgtgcgctatt ... ttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgcttgttgaagtctgacactttgttactatgctcattcttttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGAAAATCACTACCGTCGATGGATAA
               gtctgac  putative branch site (score: 3)
                                  tgctcattcttttctt  putative PPT
                                       attctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctattattgcaaattaaaaatgttgccttttacatttcgttagcagtgaatcacaattatttcatgtgatgcttgttgaagtctgacactttgttactatgctcattcttttcttggcagAGCTTATCGAGGATTTTACCTCATCAATTGGATCTATCGGTATTTTACGGAAAATCACTACCGTCGATGGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA