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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcacatgcgtacagaacggagtgtgctgtgacttgtgagtgttttaccttagtccgaagcgccgctaccgcgaaacggcctcaagcatgcatttaccgtcacgccttgatgcgagcaccttctctgactatcgtgacctccttcctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAAACCGAGATCACAGACAAGCTGCGGCAAGAAATCAACAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP00834
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|22058843|gb|BQ813132.1|BQ813132
EST:     TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAG                         GGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
genomic: TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAGgtaggcacat ... ctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
EST: gi|6547112|gb|AV392896.1|AV392896
EST:     TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAG                         GGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
genomic: TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAGgtaggcacat ... ctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
EST: gi|10191266|gb|BE761342.1|BE761342
EST:     TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAG                         GGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
genomic: TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAGgtaggcacat ... ctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
EST: gi|161804509|gb|FC088837.1|FC088837
EST:     TGCAGGACGTGACACTGCACGACCTGGACTCCGCCAACGCGCGGCCACAG                         GGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGANA
genomic: TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAGgtaggcacat ... ctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
EST: gi|22058844|gb|BQ813133.1|BQ813133
EST:     TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAG                         GGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA
genomic: TGCAGGACGTCACGCTGCACGACCTGGACTCCGCCAACGCGCGGCCACAGgtaggcacat ... ctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacgccttgatgcgagcaccttctctgactatcgtgacctccttcctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAAACCGAGATCACAGACAAGCTGCGGCAAGAAATCAACAAG
                      ctctgac  putative branch site (score: 3)
                                     cctccttcctccgtcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcacatgcgtacagaacggagtgtgctgtgacttgtgagtgttttaccttagtccgaagcgccgctaccgcgaaacggcctcaagcatgcatttaccgtcacgccttgatgcgagcaccttctctgactatcgtgacctccttcctccgtccagGGCGGCGGCGACATTATGAGCGTCATGGGCAGCATGCTCAAACCCAAGAAAACCGAGATCACAGACAAGCTGCGGCAAGAAATCAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA