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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtccctggtcttagctctcggggaggcggcggtctgagttttcgaagcggcattgagacgctgttcaattgctgaagagtatctatatgtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGATCAAGTTTTGAAAGAATTTGGCAAGCAATCAAAG

Basic information

species Physcomitrella patens
transcript PP1S61_255V6.2
intron # 2
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|100413465|gb|BY956684.1|BY956684
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|100448443|gb|CJ972742.1|CJ972742
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|67578053|gb|BJ950220.1|BJ950220
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGNTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTAC
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTAC
EST: gi|67716881|gb|BJ967140.1|BJ967140
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|67717261|gb|BJ967520.1|BJ967520
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|100423951|gb|BY976602.1|BY976602
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|100406296|gb|BY955561.1|BY955561
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
EST: gi|162199930|gb|FC376197.1|FC376197
EST:     CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGG                         GTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT
genomic: CACCATCGCTGGGTCTTGAAGTTGTTGAGACTAACCTTGCCAACTCCAGGgtatagaact ... gtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagcggcattgagacgctgttcaattgctgaagagtatctatatgtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGATCAAGTTTTGAAAGAATTTGGCAAGCAATCAAAG
                                    tatctatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtccctggtcttagctctcggggaggcggcggtctgagttttcgaagcggcattgagacgctgttcaattgctgaagagtatctatatgtgcttgcagGTTCAGTTGAAAGTACACGTTCCAGTTAGCGTTTGTAAAGACTGCTACGATCAAGTTTTGAAAGAATTTGGCAAGCAATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA