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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgtttaccgtatgttttagcgtgcgtggtatgtatgcgtgtggatgtgcccgttggccataaccggcatggccctgcccacgcgttcacgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCAGCTGGTGCGCAACATCGTCACCGCTGCGGCAAATGCGCCCTGGAAGAGC

Basic information

species Chlamydomonas reinhardtii
transcript EDP04474
intron # 4
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|15367980|gb|BI527406.1|BI527406
EST:     GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|49464106|gb|BP092019.1|BP092019
EST:     GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|161815169|gb|FC105314.1|FC105314
EST:     GGCAGCCCCGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|161811907|gb|FC096097.1|FC096097
EST:     GGCAGCCCCGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|14229438|gb|BG848254.1|BG848254
EST:     GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|15701172|gb|BI725477.1|BI725477
EST:     GCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGNTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAG-TTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
EST: gi|161821457|gb|FC109752.1|FC109752
EST:     GGCAGCCCCGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCAC                         CAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA
genomic: GGCAGCCCGGAGCTGCGCAAGTGCCGGGACGGGCACGAGTTCGTGTTCACgtgagcgcgc ... acgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgtgcccgttggccataaccggcatggccctgcccacgcgttcacgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCAGCTGGTGCGCAACATCGTCACCGCTGCGGCAAATGCGCCCTGGAAGAGC
              ccataac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtttaccgtatgttttagcgtgcgtggtatgtatgcgtgtggatgtgcccgttggccataaccggcatggccctgcccacgcgttcacgcacgtagCAAGTTCTGGAGTGACACGGGCGACCTGAAGGGCACCAGCACTGAGGAGCAGCTGGTGCGCAACATCGTCACCGCTGCGGCAAATGCGCCCTGGAAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
-tgtgttt
- - - - - - tatgttt
- - - - - - - - - - - -gtgcgtg
- - - - - - - - - - - - - - - gtatgta
- - - - - - - - - - - - - - - - - - -tgcgtgt
- - - - - - - - - - - - - - - - - - - - - - ggatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cataacc