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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacgcggagtatgttttttccgcatcgtcccctttctgactcacatgtcactctctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGCGACGAGCAGGACATGGAGGGAGGGGACGAACCCGCTGTCCAGGGTCAGC

Basic information

species Chlamydomonas reinhardtii
transcript EDP09786
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|14239380|gb|BG858196.1|BG858196
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|16073072|gb|BI875068.1|BI875068
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|14237582|gb|BG856398.1|BG856398
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGNG
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTG-G
EST: gi|14232081|gb|BG850897.1|BG850897
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCTAATGGCGAAGGGGAGGGTGG
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTC-AATGGCGAAGGGGAGGGTGG
EST: gi|8513690|gb|BE121585.1|BE121585
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAATGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|15701797|gb|BI726102.1|BI726102
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|8286628|gb|BE024187.1|BE024187
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|6552006|gb|AV397790.1|AV397790
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|23365396|gb|BU653216.1|BU653216
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|49470919|gb|BP098780.1|BP098780
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|15695046|gb|BI719223.1|BI719223
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
EST: gi|8514321|gb|BE122216.1|BE122216
EST:     GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGAT                         CCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC
genomic: GCAAATCTGGCAACACGAGAGCCAGGCGTCTGTCCTACGTGACAAACGATgtaagaacgc ... ctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttttttccgcatcgtcccctttctgactcacatgtcactctctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGCGACGAGCAGGACATGGAGGGAGGGGACGAACCCGCTGTCCAGGGTCAGC
                            gactcac  putative branch site (score: 2)
                                         ctctctgctt  putative PPT
     ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacgcggagtatgttttttccgcatcgtcccctttctgactcacatgtcactctctgcttgcagCCCAACGCCTCGCCGGGCAACCTGAAGCTCAATGGCGAAGGGGAGGGTGGCGACGAGCAGGACATGGAGGGAGGGGACGAACCCGCTGTCCAGGGTCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG