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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgggtcccatcgcaccctgtcacggttgcctgtcactgctgtcatcctgtaccatttgcatggatgcgcgttgtgctgtggcatgatacacaatttcgcagcattagcgtgcagcacccaaaacttaccgggctcatgtgatgaacttgcgctttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCAGTGCCTAGACTGGTATGG

Basic information

species Chlamydomonas reinhardtii
transcript EDO98408
intron # 1
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|49459433|gb|BP087346.1|BP087346
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|23362105|gb|BU649925.1|BU649925
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15370556|gb|BI529982.1|BI529982
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15370685|gb|BI530111.1|BI530111
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15368559|gb|BI527985.1|BI527985
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|6540785|gb|AV386569.1|AV386569
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|14239901|gb|BG858717.1|BG858717
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15370835|gb|BI530261.1|BI530261
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15371459|gb|BI530885.1|BI530885
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCA
EST: gi|15370652|gb|BI530078.1|BI530078
EST:     GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCT                         CTACAAGGAAAT-ATGGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGC
genomic: GAGGACTGCAAGCCAGAGTCGGAAGCGCTTGTGCGCGCGACCAACAAGCTgtaagtcggg ... ttcgctgcagCTACAAGGAAATTATGG-AGAAGTCCCCGGAGGAATTCAAGGAGTATGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcagcacccaaaacttaccgggctcatgtgatgaacttgcgctttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCAGTGCCTAGACTGGTATGG
             aacttac  putative branch site (score: 2)
                                           ctttcgct  putative PPT
           aaaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgggtcccatcgcaccctgtcacggttgcctgtcactgctgtcatcctgtaccatttgcatggatgcgcgttgtgctgtggcatgatacacaatttcgcagcattagcgtgcagcacccaaaacttaccgggctcatgtgatgaacttgcgctttcgctgcagCTACAAGGAAATTATGGAGAAGTCCCCGGAGGAATTCAAGGAGTATGCGCAGTGCCTAGACTGGTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG