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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgcacacctgaacatgcgcgtgcttgtgctgtggcgcggaccccaccgtgcccccatttttaataattatgaatgtgcccctaccaccgcacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCGAAGGAGCCCGCGGCTGCAGCGGCGGCTCCGGTGGCAGATGGTAATCTCT

Basic information

species Chlamydomonas reinhardtii
transcript EDO97274
intron # 9
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|14233440|gb|BG852256.1|BG852256
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|16429696|gb|BI994922.1|BI994922
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|14233441|gb|BG852257.1|BG852257
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|16432417|gb|BI997643.1|BI997643
EST:     TGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: TGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|16431541|gb|BI996767.1|BI996767
EST:     CGGCGGCGGGCACCGAATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: CGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|22074645|gb|BQ823556.1|BQ823556
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|23363567|gb|BU651387.1|BU651387
EST:     GGCGCCAGGCCATTACGGCGGCGGGAGCCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|15696321|gb|BI720626.1|BI720626
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACAAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|15703538|gb|BI727843.1|BI727843
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|12251850|gb|BF861713.1|BF861713
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|16436063|gb|BM001283.1|BM001283
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|22057037|gb|BQ812478.1|BQ812478
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|15703448|gb|BI727753.1|BI727753
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACAAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|14236265|gb|BG855081.1|BG855081
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
EST: gi|15369966|gb|BI529392.1|BI529392
EST:     GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAG                         GCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG
genomic: GGCGCCAGGCCATTACGGCGGCGGGCACCGGATGCATGGCGGCGCTGGAGgtgcgagggt ... cacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgtgcccccatttttaataattatgaatgtgcccctaccaccgcacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCGAAGGAGCCCGCGGCTGCAGCGGCGGCTCCGGTGGCAGATGGTAATCTCT
             ttttaat  putative branch site (score: 3)
           atttttaataattatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgcacacctgaacatgcgcgtgcttgtgctgtggcgcggaccccaccgtgcccccatttttaataattatgaatgtgcccctaccaccgcacactgcagGCGGAGCACTTCATCTCGGCGCACGAGGCGGAGCCGGAGGCGGACGGGGCGAAGGAGCCCGCGGCTGCAGCGGCGGCTCCGGTGGCAGATGGTAATCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
-cgcacac
- - - - - - acatgcg
- - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - accccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgaat