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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataatactttcaccaattcaccattctaattatgtttttccgagccaaagatcaattagtactttgtgaatgccctcgtacactcgaagagcacaagaaaatgattcaacataaatcgactcatcttttacctttcatttcttaattcattttgtgtctcaatctttttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCGCTATCATTCTACGAAAAGTCTGGCTATGATCAGATCCTTGTACAAGCAA

Basic information

species Physcomitrella patens
transcript PP1S9_318V6.5
intron # 8
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|18335610|gb|BJ167630.1|BJ167630
EST:     TGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: TGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|162160286|gb|FC336572.1|FC336572
EST:     TCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTTG-GGAGGTGGCTGCCGAGAATGC
genomic: TCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGG-TGTGGAGGTGGCTGCCGAGAATGC
EST: gi|162237714|gb|FC413329.1|FC413329
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|37840414|gb|BJ598422.1|BJ598422
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|37846633|gb|BJ604641.1|BJ604641
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|208382589|gb|DC919785.1|DC919785
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|18341674|gb|BJ173709.1|BJ173709
EST:     CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGTAAAGTTCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|67692207|gb|BJ952440.1|BJ952440
EST:     TGTAAAGTTNCCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: TGTAAAGTT-CCCTGGTGCTTTGGCTGATCCTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
EST: gi|67699862|gb|BJ960095.1|BJ960095
EST:     CTGAAGGTCTCGTATCGCAG                         GTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG
genomic: CTGAAGGTCTCGTATCGCAGgttataatac ... ttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttacctttcatttcttaattcattttgtgtctcaatctttttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCGCTATCATTCTACGAAAAGTCTGGCTATGATCAGATCCTTGTACAAGCAA
                 tcttaat  putative branch site (score: 3)
                                  tctcaatctttttcct  putative PPT
          tttcatttcttaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttataatactttcaccaattcaccattctaattatgtttttccgagccaaagatcaattagtactttgtgaatgccctcgtacactcgaagagcacaagaaaatgattcaacataaatcgactcatcttttacctttcatttcttaattcattttgtgtctcaatctttttcctattagGTTTTGCGAGCTGCATGGGAGCAGGGTGTGGAGGTGGCTGCCGAGAATGCGCTATCATTCTACGAAAAGTCTGGCTATGATCAGATCCTTGTACAAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA