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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccatttccgcggctgcctatggggtagcatctggcacgcgcgctccgtctccccaccgcttgacatgcccttgtcgcgctcctatttcccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTCCCGCACCATCTCGACCAAGGGCATGCTGTCCGTCTACAACTCGTTCAAC

Basic information

species Chlamydomonas reinhardtii
transcript EDP06428
intron # 4
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|8287449|gb|BE025008.1|BE025008
EST:     CTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|10772882|gb|AV623705.1|AV623705
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|15372787|gb|BI532213.1|BI532213
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|22071957|gb|BQ821295.1|BQ821295
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|10788599|gb|AV626319.1|AV626319
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|10789052|gb|AV626772.1|AV626772
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATC
EST: gi|49469826|gb|BP097687.1|BP097687
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGC
EST: gi|15695715|gb|BI720020.1|BI720020
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|15702302|gb|BI726607.1|BI726607
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|10777725|gb|AV634405.1|AV634405
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|161813009|gb|FC094834.1|FC094834
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|15370924|gb|BI530350.1|BI530350
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
EST: gi|16073375|gb|BI875371.1|BI875371
EST:     CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAG                         CGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC
genomic: CACGGCATTGTGGAGGCGCTGTTCCGCCGCTACACCCGCCAGGGCATGAGgtgagcgccg ... ccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgtctccccaccgcttgacatgcccttgtcgcgctcctatttcccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTCCCGCACCATCTCGACCAAGGGCATGCTGTCCGTCTACAACTCGTTCAAC
              gcttgac  putative branch site (score: 4)
                                 cgctcctatttccc  putative PPT
                                       tattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccatttccgcggctgcctatggggtagcatctggcacgcgcgctccgtctccccaccgcttgacatgcccttgtcgcgctcctatttcccaaccgcagCGACGAGGAGGCCTTCAAGCAGTCCGTGGAGTCGATCACCGGCCCCATCTCCCGCACCATCTCGACCAAGGGCATGCTGTCCGTCTACAACTCGTTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - cacgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgcc