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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcataaggacaatcggacagccctggcccgctcaaacacgcaacactgttgacgcgtcaccggtccgggtttctatccccgtccacacacaacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGCAACGGCTCCATGAATGGCGCGCAGAGCCTGGCGTGCGACACAGCCAAGG

Basic information

species Chlamydomonas reinhardtii
transcript EDP06523
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|14226869|gb|BG845685.1|BG845685
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
EST: gi|14237950|gb|BG856766.1|BG856766
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
EST: gi|14236776|gb|BG855608.1|BG855608
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
EST: gi|14230515|gb|BG849331.1|BG849331
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
EST: gi|15372755|gb|BI532181.1|BI532181
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTGT-AGCCTGTAGAAGGTGGAGTTCAAACTGAACCAGGCCGG
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTT-TCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGG
EST: gi|22054655|gb|BQ811455.1|BQ811455
EST:     GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAAT                         GTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC
genomic: GCAAGGCGACCATGAAAGCGAACATGAAGACGTACCACTATTATGAAAATgtaagtccgg ... aacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgacgcgtcaccggtccgggtttctatccccgtccacacacaacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGCAACGGCTCCATGAATGGCGCGCAGAGCCTGGCGTGCGACACAGCCAAGG
 tgttgac  putative branch site (score: 3)
                        tttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcataaggacaatcggacagccctggcccgctcaaacacgcaacactgttgacgcgtcaccggtccgggtttctatccccgtccacacacaacataacagGTGTGGACTTTCAGCCTGGAGAAGGTGGAGTTCAAACTGAACCAGGCCGGCAACGGCTCCATGAATGGCGCGCAGAGCCTGGCGTGCGACACAGCCAAGG

- - aaggaca
- - - - - - tcggaca
- - - - - - - - - - - - - - - - - -acacgca
- - - - - - - - - - - - - - - - - - - - - acactgt