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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatgccacgcgcaatcgtggtgcactggtgttcgtcctgacactgccctcctccttaaccttgcatggaccacccgccccactatggctttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATAACCTGATTAAGGGCACGAAGAGCGAGCAGCTGGCCGTGGTGCGTCAGCA

Basic information

species Chlamydomonas reinhardtii
transcript EDP05930
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|161812303|gb|FC098352.1|FC098352
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
EST: gi|22068057|gb|BQ818025.1|BQ818025
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
EST: gi|161792254|gb|FC080338.1|FC080338
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
EST: gi|22063346|gb|BQ815167.1|BQ815167
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGA
EST: gi|161821921|gb|FC110281.1|FC110281
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
EST: gi|161790429|gb|FC079964.1|FC079964
EST:     CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGG                         GCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA
genomic: CCTGCAGGAGCAGATGGTGCCCTACATGCGCGAGATGGTGCCCCTGCCGGgtgggtactg ... ttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctcctccttaaccttgcatggaccacccgccccactatggctttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATAACCTGATTAAGGGCACGAAGAGCGAGCAGCTGGCCGTGGTGCGTCAGCA
        ccttaac  putative branch site (score: 3)
                                           ctttttac  putative PPT
                                            ttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatgccacgcgcaatcgtggtgcactggtgttcgtcctgacactgccctcctccttaaccttgcatggaccacccgccccactatggctttttacgcagGCATCTACGACCCCGACTTCGTGGCCGCCAACCAGGAGGAGCGCGCTGATAACCTGATTAAGGGCACGAAGAGCGAGCAGCTGGCCGTGGTGCGTCAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - cacgcgc
- - - - - - - - - - - - - - -tgttcgt
- - - - - - - - - - - - - - - - - - - tgacact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacccgc