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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacctgactgggctctacaccgtcgtccaatgacggccacgcctccgccgctacccgcactctccaatggcccttcgcctctccaatggcccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGACAAGGTGACCATTGACGTCAAGGCGCCGGCGGCCGGCTTCCTGCACAAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP04488
intron # 1
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|8932566|gb|BE227327.1|BE227327
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|8514107|gb|BE122002.1|BE122002
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|16437877|gb|BM003097.1|BM003097
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|10768177|gb|AV619002.1|AV619002
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|239840701|gb|GR282391.1|GR282391
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|239840709|gb|GR282399.1|GR282399
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|16428816|gb|BI994042.1|BI994042
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
EST: gi|239840718|gb|GR282408.1|GR282408
EST:     CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAG                         GTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC
genomic: CAATGGGCGAGTCCATCAAGGAGGGCACAATTGCGGCAGTGCTCAAGCAGgtgcgtgttg ... cccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgccgctacccgcactctccaatggcccttcgcctctccaatggcccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGACAAGGTGACCATTGACGTCAAGGCGCCGGCGGCCGGCTTCCTGCACAAAG
                                             cccctctc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacctgactgggctctacaccgtcgtccaatgacggccacgcctccgccgctacccgcactctccaatggcccttcgcctctccaatggcccctctcagGTTGGCGCGGCTGTGCGCGAGGACGAGGTGATTGCACAGATCGAGACGGACAAGGTGACCATTGACGTCAAGGCGCCGGCGGCCGGCTTCCTGCACAAAG

- - - - - - - - -acaccgt
- - - - - - - - - - - - - - caatgac
- - - - - - - - - - - - - - - - - - - - - - - - - - -acccgca