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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcgcctgatgggcaataaggctacgtgcattgacgtgcttaactgctgacctgtaaaaacgtgtcagctgcttgctggtgctcacattcatatatggtgtttgcatcggacccatgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTGGTGCGGGTGGCGGACATGCTGGCGGACCCCCGCTGCACGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP00871
intron # 12
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|22054028|gb|BQ811113.1|BQ811113
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACCCGGCGCGGCAGGAACGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22054029|gb|BQ811114.1|BQ811114
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACCCGGCGCGGCAGGAACGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22076143|gb|BQ824919.1|BQ824919
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCACGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|15369143|gb|BI528569.1|BI528569
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|14227440|gb|BG846256.1|BG846256
EST:     GCCAAGGAG-ACAACTTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCAACCCGGCGCGGCAGGAGCGGTTTGT
genomic: GCCAAGGAGAACAAC-TTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGT
EST: gi|22076142|gb|BQ824918.1|BQ824918
EST:     GTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTTAACCCGGCGCGGCAGGAACGGTTTGTG
genomic: GTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22076228|gb|BQ825004.1|BQ825004
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|15691957|gb|BI716262.1|BI716262
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGGGCGTTCGACCCGGCGCGGCAGGAACGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|34983593|gb|CF557510.1|CF557510
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAATTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|10127159|gb|BE725863.1|BE725863
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22064854|gb|BQ816063.1|BQ816063
EST:     AAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACCCGGCGCGGCAGGAACGGTTTGTG
genomic: AAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22072693|gb|BQ822031.1|BQ822031
EST:     CTGGGCGCCGCGAGAAAATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTTGACCCGGCGCGGCAGGAACGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|14230365|gb|BG849181.1|BG849181
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|8286609|gb|BE024168.1|BE024168
EST:     CAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCAACNCGGCGCGGCAGGAACGGTTTGTG
genomic: CAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22075187|gb|BQ823947.1|BQ823947
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTTGACGCGGCGCGGCAGGAACGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22055484|gb|BQ811846.1|BQ811846
EST:     CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGACCGGTTTGTG
genomic: CTGGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG
EST: gi|22076227|gb|BQ825003.1|BQ825003
EST:     GGGCCCCGCGAGAAAATGGTGATCGCCAAGGAGAACAACTTCATGCAG                         GCCGGCGCTCGCTGGCGCGCGTTCAACCCGGCGCGGCAGGAACGGTTTGTG
genomic: GGGCGCCGCGAGAAGATGGTGATCGCCAAGGAGAACAACTTCATGCAGgtgggcgcct ... tgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgctggtgctcacattcatatatggtgtttgcatcggacccatgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTGGTGCGGGTGGCGGACATGCTGGCGGACCCCCGCTGCACGCAG
         tgctcac  putative branch site (score: 2)
                attcatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggcgcctgatgggcaataaggctacgtgcattgacgtgcttaactgctgacctgtaaaaacgtgtcagctgcttgctggtgctcacattcatatatggtgtttgcatcggacccatgtggcgcagGCCGGCGCTCGCTGGCGCGCGTTCGACGCGGCGCGGCAGGAGCGGTTTGTGGTGCGGGTGGCGGACATGCTGGCGGACCCCCGCTGCACGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG