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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgagagcacccaggccgcggggtatgcggcacgtatactggctgttgcccccgtgcacttgccggccatcctagccacggcaaggttgtaacggaagccccctgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAAAGTGCAGCAGATTCAGATTTTGGCGCATGAGTATAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP06459
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|49466029|gb|BP093942.1|BP093942
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|6548195|gb|AV393979.1|AV393979
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|10790751|gb|AV628117.1|AV628117
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTGCTGCGCTTGGAGCAGACGTGCGA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|6548498|gb|AV394282.1|AV394282
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|10791902|gb|AV629268.1|AV629268
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|10790650|gb|AV628016.1|AV628016
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|10789097|gb|AV626817.1|AV626817
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
EST: gi|49466688|gb|BP094601.1|BP094601
EST:     CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAG                         GTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA
genomic: CGCGAACTCCTCTACCACAGCCCGCAGACGCGTGGATGGCAGTCGCCCAGgtgcgagagc ... tgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgccggccatcctagccacggcaaggttgtaacggaagccccctgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAAAGTGCAGCAGATTCAGATTTTGGCGCATGAGTATAAG
                            ttgtaac  putative branch site (score: 2)
                                        ccccctgcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgagagcacccaggccgcggggtatgcggcacgtatactggctgttgcccccgtgcacttgccggccatcctagccacggcaaggttgtaacggaagccccctgccattcagGTTCTGCAAATACCCTCAGGAGATCGTCCTGCGCTTGGAGCAGACGTGCAAAGTGCAGCAGATTCAGATTTTGGCGCATGAGTATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT