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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccgcaccgaccacccatccacctaccgtatcactgcccgcggcacttgccagccttgcagctaacgctgctgttgctctccctgctgccccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCCAGGACAAGCTGGACGGCTACCTGTGAGCAACCCGTCGTGTGGATGGCAC

Basic information

species Chlamydomonas reinhardtii
transcript EDP01211
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|10774315|gb|AV625138.1|AV625138
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGC
EST: gi|14237456|gb|BG856272.1|BG856272
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
EST: gi|14237457|gb|BG856273.1|BG856273
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
EST: gi|23367259|gb|BU655078.1|BU655078
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
EST: gi|14238698|gb|BG857514.1|BG857514
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
EST: gi|22059968|gb|BQ813638.1|BQ813638
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGT
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGT
EST: gi|7687654|gb|AW758300.1|AW758300
EST:     GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
EST: gi|14238697|gb|BG857513.1|BG857513
EST:     GTGGGCGCCCATCCTGCTG-TCTTCGGCGTCACCGGCTTCCCCACTGCCG                         GCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC
genomic: GTGGGCGCCCATCCTGCTGTTCTTCGGCGTCACCGGCTTCCCCACTGCCGgtaagcgcgg ... ccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgccagccttgcagctaacgctgctgttgctctccctgctgccccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCCAGGACAAGCTGGACGGCTACCTGTGAGCAACCCGTCGTGTGGATGGCAC
              agctaac  putative branch site (score: 2)
                         ctgttgctctccctgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccgcaccgaccacccatccacctaccgtatcactgcccgcggcacttgccagccttgcagctaacgctgctgttgctctccctgctgccccccctccagGCTACCTGTTCATCAAGGGCGTCAACGGCTTCAACGAGGAAGCCGAGCGCCAGGACAAGCTGGACGGCTACCTGTGAGCAACCCGTCGTGTGGATGGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - ccaccca
- - - - - - - - - -cacctac
- - - - - - - - - - - - - - - - - - - - - -cacttgc