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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcagattgtcctaaaaactggggttgtaccccaagtgctacaagctcacgccattcatggccctcctgccctgtattacgcccgcgttctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGACCAGGTGGCGCCCATGCTCAAGGCCGTGACCGTGGGCTTTTAAATCAAC

Basic information

species Chlamydomonas reinhardtii
transcript EDO96524
intron # 5
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|16073609|gb|BI875605.1|BI875605
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|14230111|gb|BG848927.1|BG848927
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAACGCACCCAGGAGCTCATCCG
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCG
EST: gi|34981088|gb|CF555005.1|CF555005
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|15692442|gb|BI716747.1|BI716747
EST:     TGGAGCATTGTCAACACGCCCGCTGGCAAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|161822949|gb|FC110640.1|FC110640
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|161822162|gb|FC107662.1|FC107662
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|15701505|gb|BI725810.1|BI725810
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|22072210|gb|BQ821548.1|BQ821548
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAA                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
EST: gi|16435492|gb|BM000712.1|BM000712
EST:     TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGA-                         CGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA
genomic: TGGAGCATTGTCAACACGCCCGCTGGCGAGGTGGTGGGGCTCCCCAAGAAgtgagtacag ... ctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctcacgccattcatggccctcctgccctgtattacgcccgcgttctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGACCAGGTGGCGCCCATGCTCAAGGCCGTGACCGTGGGCTTTTAAATCAAC
 agctcac  putative branch site (score: 3)
                                           ttctgccc  putative PPT
                            tgtatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcagattgtcctaaaaactggggttgtaccccaagtgctacaagctcacgccattcatggccctcctgccctgtattacgcccgcgttctgcccgcagCGACGACAACCAGTCGGTCGTGAAGCGCACCCAGGAGCTCATCCGCTTCGACCAGGTGGCGCCCATGCTCAAGGCCGTGACCGTGGGCTTTTAAATCAAC

- - - - - - - aaaaact
- - - - - - - - - - - - - - -accccaa
- - - - - - - - - - - - - - - - - - - - - -aagctca
- - - - - - - - - - - - - - - - - - - - - - - - - - ccattca