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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctcgaatataatctgtgggtcttggacgagtgaagatcgaggaacttagcggatgatttgattctgtttataatgctgcacgtgtattttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGGGGATCTTTCCT

Basic information

species Physcomitrella patens
transcript PP1S46_64V6.1
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|18364226|gb|BJ196299.1|BJ196299
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|100388749|gb|BY970897.1|BY970897
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|208353889|gb|DC942787.1|DC942787
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|208356778|gb|DC906440.1|DC906440
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|18354047|gb|BJ186102.1|BJ186102
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|18325412|gb|BJ157408.1|BJ157408
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
EST: gi|162189180|gb|FC365987.1|FC365987
EST:     CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAG                         GCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG
genomic: CCCCTCGTGATCATCAATTCTTCTGCGCTGTAGCAATGTTTCTGCGGCAGgtttgcgttt ... ttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttagcggatgatttgattctgtttataatgctgcacgtgtattttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGGGGATCTTTCCT
            atttgat  putative branch site (score: 5)
                                         tattttcttt  putative PPT
                 attctgtttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctcgaatataatctgtgggtcttggacgagtgaagatcgaggaacttagcggatgatttgattctgtttataatgctgcacgtgtattttctttgcagGCATACAAGACTGCTACCTTCGTCTCCTATGGATACATGAACTGGACTCGGGGATCTTTCCT

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