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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccccgagcgctcgggacttggtaccgctgtttggcgtcggccgcatccttgcttacaatggcgcgctgcatttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP02637
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|6548412|gb|AV394196.1|AV394196
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTAAGACAAG
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
EST: gi|6551248|gb|AV397032.1|AV397032
EST:     TTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
genomic: TTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
EST: gi|10793150|gb|AV630516.1|AV630516
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGA
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGA
EST: gi|10788962|gb|AV626682.1|AV626682
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
EST: gi|10792893|gb|AV630259.1|AV630259
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTAACCTG                         GG-AGCTTTGATACGGAG
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTA-CCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAG
EST: gi|6549628|gb|AV395412.1|AV395412
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGT
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGT
EST: gi|6549856|gb|AV395640.1|AV395640
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTAGACAAG
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
EST: gi|49466072|gb|BP093985.1|BP093985
EST:     GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTG                         GGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
genomic: GTGGCAGAGCGCTATCAACAGTTCTGGCAAGCACGTGTACCTGgtgagccccg ... ttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttggcgtcggccgcatccttgcttacaatggcgcgctgcatttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG
                       tgcttac  putative branch site (score: 2)
                                          catttcttt  putative PPT
                                           atttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccccgagcgctcgggacttggtaccgctgtttggcgtcggccgcatccttgcttacaatggcgcgctgcatttctttgcagGGGAGCTTTGATACGGAGGAGGAGGCTGCGCGCATGTTTGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG