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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttctacaagtgcttgtctcacatctttctaacatttctacgtaacacatttccatatcttgcatgttcttagtttgtgttacggattctgttgaagtccttcatgcgttctcaatttcatgggaccaaggggttgcttatttgcaactgataatgttttgggtccgaacattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCCAAGAAACTTGCACCATGCAAAGAGATTCCTTCTCTTCAGCTAATCAATC

Basic information

species Physcomitrella patens
transcript PP1S68_29V6.1
intron # 6
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|18337739|gb|BJ169763.1|BJ169763
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
EST: gi|37840297|gb|BJ598305.1|BJ598305
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
EST: gi|162209020|gb|FC385572.1|FC385572
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATT
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATT
EST: gi|162209019|gb|FC385571.1|FC385571
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
EST: gi|162264778|gb|FC440345.1|FC440345
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
EST: gi|208387224|gb|DC945523.1|DC945523
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGGGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
EST: gi|208358537|gb|DC946498.1|DC946498
EST:     AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGAT                         GATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC
genomic: AGATACTGATGTTTGCGTCCGATCAAGAGTTGCTGGCATACGTTCTGGATgtaagtattt ... cattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accaaggggttgcttatttgcaactgataatgttttgggtccgaacattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCCAAGAAACTTGCACCATGCAAAGAGATTCCTTCTCTTCAGCTAATCAATC
                     aactgat  putative branch site (score: 3)
                          ataatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttctacaagtgcttgtctcacatctttctaacatttctacgtaacacatttccatatcttgcatgttcttagtttgtgttacggattctgttgaagtccttcatgcgttctcaatttcatgggaccaaggggttgcttatttgcaactgataatgttttgggtccgaacattattcagGATCATCCGGATTGGGAGATTCGCGGCACCAGGGTGTATTTTCAAAGAGCCAAGAAACTTGCACCATGCAAAGAGATTCCTTCTCTTCAGCTAATCAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT