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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataattttcattgctttaagaggaagtcaagcgcagcttgcactttctgttttacctcattctagaatttgtggtttacttttgattgttataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTGTTGGAATGCGAAGGAGTTAAGTACGCGGTTCTCACTGAACAG

Basic information

species Physcomitrella patens
transcript PP1S99_13V6.4
intron # 4
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|100436977|gb|BY979621.1|BY979621
EST:     GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAG                         TTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
genomic: GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAGgtgtgaattg ... ataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
EST: gi|100369453|gb|BY948102.1|BY948102
EST:     GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCANAG                         TTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
genomic: GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAGgtgtgaattg ... ataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
EST: gi|100388471|gb|BY952073.1|BY952073
EST:     GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAG                         TTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
genomic: GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAGgtgtgaattg ... ataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
EST: gi|208364075|gb|DC939612.1|DC939612
EST:     GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAG                         TTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
genomic: GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAGgtgtgaattg ... ataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
EST: gi|162209167|gb|FC385386.1|FC385386
EST:     GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAG                         TTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG
genomic: GATTTGTAAAGTTCAAGGCAGACATCATCGATCTTAAAACCGGCGCAAAGgtgtgaattg ... ataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttttacctcattctagaatttgtggtttacttttgattgttataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTGTTGGAATGCGAAGGAGTTAAGTACGCGGTTCTCACTGAACAG
                                  ttttgat  putative branch site (score: 4)
                             tttacttttgattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataattttcattgctttaagaggaagtcaagcgcagcttgcactttctgttttacctcattctagaatttgtggtttacttttgattgttataaatgcagTTACCTGGCATCGTATTTGCGCGAGGCGGCGCTGTAGGGATCCTCATGTTGTTGGAATGCGAAGGAGTTAAGTACGCGGTTCTCACTGAACAG

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