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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccggcgaggaaccgggactgctggggagctgccgcgccgtggcactgtcccataacaggcggccgcaggtcactgccgtggaggacactcgggacaaaaaatcgctctgggcactttcctgaagctgacgagcctaccctgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGCTGACGCCAGAGTACACGGAGGCGGCG

Basic information

species Chlamydomonas reinhardtii
transcript EDP00834
intron # 2
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|161798903|gb|FC084645.1|FC084645
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAGAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
EST: gi|6547112|gb|AV392896.1|AV392896
EST:     GAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: GAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
EST: gi|161804509|gb|FC088837.1|FC088837
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAGAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
EST: gi|161795055|gb|FC078199.1|FC078199
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAGAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
EST: gi|161810747|gb|FC098512.1|FC098512
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAGAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
EST: gi|9441582|gb|BE442071.1|BE442071
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGA
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGA
EST: gi|9458853|gb|BE452558.1|BE452558
EST:     CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCG                         GCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC
genomic: CGAGGTCAAGAAGACGGAGGTGCTGATGGAGAACTTTCGGAGAGCCATCGgtgaggccgg ... tgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaaatcgctctgggcactttcctgaagctgacgagcctaccctgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGCTGACGCCAGAGTACACGGAGGCGGCG
                            agctgac  putative branch site (score: 3)
                                      cctaccct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggccggcgaggaaccgggactgctggggagctgccgcgccgtggcactgtcccataacaggcggccgcaggtcactgccgtggaggacactcgggacaaaaaatcgctctgggcactttcctgaagctgacgagcctaccctgctgcccagGCCTGCGCATCAAGGAAAACAAGGAGGTTTATGAGGGCGAGGTGACGGAGCTGACGCCAGAGTACACGGAGGCGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA