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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagggttgtgcggcctggtgtgtcgtgtcgccctcctctccctaccaccatggctaactggcatgccctgtttccctctgccgcacctcggtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGGGCAAACGAGCAGTCGGAGTCGGGCACGGACTACGCCTCCAAGCTGCTGC

Basic information

species Chlamydomonas reinhardtii
transcript EDO98296
intron # 8
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|161806974|gb|FC091756.1|FC091756
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAANNNNNNNCGG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGG
EST: gi|161799655|gb|FC086138.1|FC086138
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAANNNNNNNCGG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGG
EST: gi|16430150|gb|BI995376.1|BI995376
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAA
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAA
EST: gi|34982149|gb|CF556066.1|CF556066
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGTCANNNNNNN-CG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAG-CAAGGGGGGGCG
EST: gi|49468556|gb|BP096417.1|BP096417
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAANNNNNNNCGG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGG
EST: gi|34982150|gb|CF556067.1|CF556067
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAANNNNNNNCGG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGG
EST: gi|161799625|gb|FC087265.1|FC087265
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAANNNNNNNCGG
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGG
EST: gi|10786541|gb|AV643213.1|AV643213
EST:     TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAG                         ACAAACCGGTTCGCCATC
genomic: TTGAAGCGTCGCGCGACCCGATGCGGAAGCGCCTGCAGCAGCCGGCCAAGgtgggtggtc ... gtacctgcagACAAACCGGTTCGCCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccatggctaactggcatgccctgtttccctctgccgcacctcggtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGGGCAAACGAGCAGTCGGAGTCGGGCACGGACTACGCCTCCAAGCTGCTGC
      ggctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagggttgtgcggcctggtgtgtcgtgtcgccctcctctccctaccaccatggctaactggcatgccctgtttccctctgccgcacctcggtacctgcagACAAACCGGTTCGCCATCCGCAACAAGAACGGGCCCAGCAAGGGGGGGCGGGCAAACGAGCAGTCGGAGTCGGGCACGGACTACGCCTCCAAGCTGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - -ttgtgcg
- - - - - - - - ggtgtgt
- - - - - - - - - - - - - - - - - - - - - -accacca