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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgctgcgcgcaccatggccatcaagaggcgccgcctagtctcgctccttacaatccttacctgccgctccttacagctcgcatctgttgctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGACATCCTGTCCCGCTGCAGCGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDO97898
intron # 3
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|14237546|gb|BG856362.1|BG856362
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|10781917|gb|AV638597.1|AV638597
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|161795576|gb|FC085038.1|FC085038
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|161793333|gb|FC078167.1|FC078167
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|10191456|gb|BE761532.1|BE761532
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|49470481|gb|BP098342.1|BP098342
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
EST: gi|22065898|gb|BQ816624.1|BQ816624
EST:     GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAG                         GTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC
genomic: GACTTGTGTTTGAGCAAGCCCGAGACGGCGGCCCCATCTTCGTAGCCGAGgtgagcgact ... ctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccttacaatccttacctgccgctccttacagctcgcatctgttgctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGACATCCTGTCCCGCTGCAGCGCAG
                       tccttac  putative branch site (score: 2)
                                          ttgctcctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgctgcgcgcaccatggccatcaagaggcgccgcctagtctcgctccttacaatccttacctgccgctccttacagctcgcatctgttgctcctcacagGTCACGGCGGGCGGTAACGCGGACAAGAGCGGCGCAGTGGCGGTGGGCGACATCCTGTCCCGCTGCAGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - cgcgcac
- - - - - - - - - - - - - - - - - - - - - - - - - acaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atctgtt