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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacgcctcactttattcacaaagtcctccaagtgatctagggtttagtaatgcgaaactgcacgatcgtttctgtcatgccgccatttcatcgttgccttcttgatgtactcatggttgtcaattttgcgacaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGCAACGCTGAAAGCCCCTTTGGAGTGGCGGACCTGAAGCAGTCTGAGCGAA

Basic information

species Physcomitrella patens
transcript PP1S286_16V6.1
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|67571874|gb|BJ944698.1|BJ944698
EST:     GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAG                         GCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
genomic: GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAGgtaattacgc ... acaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
EST: gi|208375555|gb|DC940525.1|DC940525
EST:     GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAG                         GCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
genomic: GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAGgtaattacgc ... acaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
EST: gi|100438348|gb|BY979912.1|BY979912
EST:     GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAG                         GCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
genomic: GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAGgtaattacgc ... acaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
EST: gi|100422558|gb|BY976433.1|BY976433
EST:     GCCACAACCTCCGACAAAGCTCATCGTGTCTTAGAAGAA-TATACTCCAG                         GCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCCTTGGT
genomic: GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAGgtaattacgc ... acaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGT
EST: gi|100355587|gb|BY946009.1|BY946009
EST:     GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAG                         GCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC
genomic: GCCACAACCTCCGACAAAGCTCATCGTGTCTAAGAAGAAATATACTCCAGgtaattacgc ... acaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatcgttgccttcttgatgtactcatggttgtcaattttgcgacaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGCAACGCTGAAAGCCCCTTTGGAGTGGCGGACCTGAAGCAGTCTGAGCGAA
              tcttgat  putative branch site (score: 4)
                                  tcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattacgcctcactttattcacaaagtcctccaagtgatctagggtttagtaatgcgaaactgcacgatcgtttctgtcatgccgccatttcatcgttgccttcttgatgtactcatggttgtcaattttgcgacaaatccagGCATTCGAGCCAAATTTTTCTAAAGGCGCAACGTCGGCATTGGTGGTTTGCAACGCTGAAAGCCCCTTTGGAGTGGCGGACCTGAAGCAGTCTGAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC