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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaccaaccaaacacgcccgttcccggccccactctcccacgctgccgccgccgccctcaccctgtaccactgttccaaccatccttgcaaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACCTGCCCATTGGCCTGCTGCGCGACGTGTACGACTGGGCGCGCCAGTTCGC

Basic information

species Chlamydomonas reinhardtii
transcript EDP00001
intron # 6
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|23360070|gb|BU647890.1|BU647890
EST:     GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCACGACC
genomic: GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
EST: gi|10780943|gb|AV637623.1|AV637623
EST:     GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
genomic: GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
EST: gi|49461242|gb|BP089155.1|BP089155
EST:     GCGAGAAGCTG-TCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
genomic: GCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
EST: gi|15692454|gb|BI716759.1|BI716759
EST:     GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
genomic: GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
EST: gi|10769258|gb|AV620083.1|AV620083
EST:     GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
genomic: GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
EST: gi|239841472|gb|GR283329.1|GR283329
EST:     CCCTT-GAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGGGCGTGTCCGG                         GCGCGCGCA-GCAACGGGGCCCTATTTCCGCGTGGGGGGCGTGAGCCAGG
genomic: -CCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCC-Ggtgagtgggg ... aaccccccagGCGCGCGCATGC-ACGCGG-CCTACTTCCGCGTGGGCGGCGTGAGCCAGG
EST: gi|22072439|gb|BQ821777.1|BQ821777
EST:     GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCG                         GCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC
genomic: GGCCTTCGAGGAGCGCGAGAAGCTGTTCGAGTTCTACGAGCGCGTGTCCGgtgagtgggg ... aaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgccgccgccctcaccctgtaccactgttccaaccatccttgcaaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACCTGCCCATTGGCCTGCTGCGCGACGTGTACGACTGGGCGCGCCAGTTCGC
          ccctcac  putative branch site (score: 3)
                                               cccccc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaccaaccaaacacgcccgttcccggccccactctcccacgctgccgccgccgccctcaccctgtaccactgttccaaccatccttgcaaccccccagGCGCGCGCATGCACGCGGCCTACTTCCGCGTGGGCGGCGTGAGCCAGGACCTGCCCATTGGCCTGCTGCGCGACGTGTACGACTGGGCGCGCCAGTTCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - ccaacca
- - - aaccaaa
- - - - - - -cacgccc
- - - - - - - - - - - - - - - - - -ctcccac