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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgagcgagcctgtgcggtgtactgcggggctgtggctgggctgagacggtggcgagcagtgcgcccacgtggcgagtactgggtgctggagagaagcagcgagggatctgggctgggcctttgtatgccgcgctcaacgtcgtatgcatacctgtccctgacgatgtgacgcatgcattgccgctcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGCTGGGAGAAGATCCGCGACGTTAACACGAAGCTGTCCTTCTATGTCAATA

Basic information

species Chlamydomonas reinhardtii
transcript EDP04421
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|161818646|gb|FC102807.1|FC102807
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
EST: gi|15696776|gb|BI721081.1|BI721081
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
EST: gi|6552034|gb|AV397818.1|AV397818
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
EST: gi|23359192|gb|BU647012.1|BU647012
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
EST: gi|49459344|gb|BP087257.1|BP087257
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
EST: gi|161803745|gb|FC090813.1|FC090813
EST:     AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAG                         GCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC
genomic: AGACGCGCTTCAGCCACGTGGTGTTCATCGGGCGGGGGCTGGACAAGGAGgtgagcgagc ... tcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtatgcatacctgtccctgacgatgtgacgcatgcattgccgctcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGCTGGGAGAAGATCCGCGACGTTAACACGAAGCTGTCCTTCTATGTCAATA
                ccctgac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgagcgagcctgtgcggtgtactgcggggctgtggctgggctgagacggtggcgagcagtgcgcccacgtggcgagtactgggtgctggagagaagcagcgagggatctgggctgggcctttgtatgccgcgctcaacgtcgtatgcatacctgtccctgacgatgtgacgcatgcattgccgctcgcgtgcagGCGTTGAAGGAGGGGCTCAGCTCGTGCCTGTGGAAGCCGCCGCCGCCCGGCTGGGAGAAGATCCGCGACGTTAACACGAAGCTGTCCTTCTATGTCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG