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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaatttctaaccacctatagattcatattttctggatattgagttcagtttaagaatgtgcttctcattgttgtaaactgggactgatttaagttttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAATGCCTTGGCCATG

Basic information

species Physcomitrella patens
transcript PP1S68_234V6.1
intron # 10
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|37829592|gb|BJ587604.1|BJ587604
EST:     TTAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAA                         TTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
genomic: TTAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAAgtatgaattt ... tttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
EST: gi|208395924|gb|DC920346.1|DC920346
EST:     GTCATC-TTTTAATGATGGCNGTGGCTGTTACCCCCACTGTGGG-TACAA                         -TTTGTGAACGTACACAAAGTGGTGA-GGGAAGAGGTTCCAGCTTTAGGAA
genomic: GTCATCTTTTTAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAAgtatgaattt ... tttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
EST: gi|208389101|gb|DC945677.1|DC945677
EST:     TCATCTTTTTAATGATGGCGGTGGCTGTTACCCCCCACTGTAGGTTACAA                         TTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
genomic: TCATCTTTTTAATGATGGCGGTGGCTGTTA-CCCCCACTGTGGGTTACAAgtatgaattt ... tttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
EST: gi|67700196|gb|BJ960429.1|BJ960429
EST:     TAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAA                         TTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
genomic: TAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAAgtatgaattt ... tttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
EST: gi|208378180|gb|DC918801.1|DC918801
EST:     GTCATC-TTTTAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAA                         TTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA
genomic: GTCATCTTTTTAATGATGGCGGTGGCTGTTACCCCCACTGTGGGTTACAAgtatgaattt ... tttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagaatgtgcttctcattgttgtaaactgggactgatttaagttttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAATGCCTTGGCCATG
                                gactgat  putative branch site (score: 3)
                                            ttttgtt  putative PPT
                                     atttaagttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaatttctaaccacctatagattcatattttctggatattgagttcagtttaagaatgtgcttctcattgttgtaaactgggactgatttaagttttgttgtagTTTTGTGAACGTACACAAAGTGGTGAGGGGAAGAGGTTCCAGCTTTAGGAATGCCTTGGCCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG