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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcccctgtgtgcctgtttcgcatctggtcacctcctgacctcgaattcgcctgtcgctgaccctccctggcaattttgcatccctcacccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAAGGCCCAGGCGCAGGCCTTTGCCAACGCCCTGACCACCATCGGCAAGTTC

Basic information

species Chlamydomonas reinhardtii
transcript EDP03110
intron # 4
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|9441085|gb|BE441581.1|BE441581
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|49458900|gb|BP086813.1|BP086813
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161802066|gb|FC093775.1|FC093775
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|16073614|gb|BI875610.1|BI875610
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|16071860|gb|BI873856.1|BI873856
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161796578|gb|FC082388.1|FC082388
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|14225877|gb|BG844693.1|BG844693
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|49459689|gb|BP087602.1|BP087602
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTG
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTG
EST: gi|161816445|gb|FC102177.1|FC102177
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|10778114|gb|AV634794.1|AV634794
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161794670|gb|FC077918.1|FC077918
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|9459700|gb|BE452865.1|BE452865
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161815712|gb|FC102672.1|FC102672
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161805951|gb|FC089512.1|FC089512
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161800461|gb|FC082823.1|FC082823
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|161801948|gb|FC090745.1|FC090745
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|14240276|gb|BG859092.1|BG859092
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|10127484|gb|BE726188.1|BE726188
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|15372577|gb|BI532003.1|BI532003
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|9441349|gb|BE441712.1|BE441712
EST:     TTCCTGCTGCCCAACGGTATGGCCAAGATCGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
EST: gi|23366290|gb|BU654110.1|BU654110
EST:     TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAA                         CCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA
genomic: TTCCTGCTGCCCAACGGCATGGCCAAGATTGCCAGCGAGGGCATCCTCAAgtacgtgccg ... ccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattcgcctgtcgctgaccctccctggcaattttgcatccctcacccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAAGGCCCAGGCGCAGGCCTTTGCCAACGCCCTGACCACCATCGGCAAGTTC
                                      ccctcac  putative branch site (score: 3)
                                   catccctcaccccc  CT-rich tract
                            aatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcccctgtgtgcctgtttcgcatctggtcacctcctgacctcgaattcgcctgtcgctgaccctccctggcaattttgcatccctcacccccacacagCCAAATCCGCGCCAAGAAGGAGGACGAGATCCGCAAGAAGCTGGAGGAGAAGGCCCAGGCGCAGGCCTTTGCCAACGCCCTGACCACCATCGGCAAGTTC

- - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccctca