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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgagcgcttagatgactctgggtcgcctagcctggtcccgatcaggcccggggtcgcgctaaacctgactcgctctacctccatgcttcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCT

Basic information

species Chlamydomonas reinhardtii
transcript EDO98586
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|49459322|gb|BP087235.1|BP087235
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10778656|gb|AV635336.1|AV635336
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161823510|gb|FC108510.1|FC108510
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10126032|gb|BE724736.1|BE724736
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161795111|gb|FC078255.1|FC078255
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|9459905|gb|BE452968.1|BE452968
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|49469821|gb|BP097682.1|BP097682
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|6551890|gb|AV397674.1|AV397674
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|49469501|gb|BP097362.1|BP097362
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161812620|gb|FC099437.1|FC099437
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161799718|gb|FC085252.1|FC085252
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|239842030|gb|GR283887.1|GR283887
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10786678|gb|AV643350.1|AV643350
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10785226|gb|AV641898.1|AV641898
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161799786|gb|FC083253.1|FC083253
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|9210917|gb|BE337832.1|BE337832
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|49470095|gb|BP097956.1|BP097956
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161813926|gb|FC104552.1|FC104552
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161802603|gb|FC089099.1|FC089099
EST:     GTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|161820324|gb|FC105889.1|FC105889
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCGGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCTGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10127475|gb|BE726179.1|BE726179
EST:     GTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|22049242|gb|BQ808677.1|BQ808677
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
EST: gi|10127829|gb|BE726533.1|BE726533
EST:     GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGG                         GCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA
genomic: GTGAAGAAGTCGGTTGGCGACCTGCACAAGGCTGACCTGGAGGgtgagctcac ... tcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggcccggggtcgcgctaaacctgactcgctctacctccatgcttcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCT
                    acctgac  putative branch site (score: 3)
                                           cttcgctc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgagcgcttagatgactctgggtcgcctagcctggtcccgatcaggcccggggtcgcgctaaacctgactcgctctacctccatgcttcgctcgcagGCAAGCGCGTGTTCGTCCGCGCGGACCTGAACGTGCCTCTTGACAAGGCCACCCTGGCCATCACCGACGACACCCGCATTCGCGCGGCCGTCCCCACCCT

ttttgag