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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacctagcatgcaagctcattccttccttgcctccttccttctcatctccttcctgccccccccccctgcgcccttccctcctgcctgccggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGACGTGGTGGTCACCGAGATCCCCGAGAAGGAGAAGGCGCCCGCGCCCGCC

Basic information

species Chlamydomonas reinhardtii
transcript EDP03982
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03982 (Chlamydomonas reinhardtii), 3'ss of exon 15
lower sequence: GRMZM2G083716_T03 (Zea mays), 3'ss of exon 12
--------ctacctagcatgcaagctcattccttccttgcctccttccttctcatctccttcctgccccccccccctgcgcccttccctcctgcctgccggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGACGTGGTGGTCACCGAGATCCCCGAGAAGGAGAAGGCGCCCGCGCCCGCC
         || || |  | | |    |  |   |||  |     |        |||  | |  |  |    || |   ||         ||| |||  || |   || ||||   ||||| |||||| ||||||||||||||||||||||    | || || ||||||  ||| |||   |||  ||||   || || |        
agtccttggtaacttgtcttcgataggagccagacctgactgatgtttgatatttcttttcctggagcaaaacctcaaagctgcgatgaactgtctgtagGTGGTGAGATGCTGCTTGGAGCACGCCGCGTCGGTGGCCAAGACCTTCCTGACATCAGATGTTGTGGTCGTCGATATCAAGGAGCCGGAGGCTGCACCTG--------
















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|10778875|gb|AV635555.1|AV635555
EST:     TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCG                         CTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCC
genomic: TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCGgtgagtacgg ... cggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCC
EST: gi|16435375|gb|BM000595.1|BM000595
EST:     TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCG                         CTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA
genomic: TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCGgtgagtacgg ... cggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA
EST: gi|8828679|gb|BE212409.1|BE212409
EST:     TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCG                         CTGCTCGCTGG
genomic: TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCGgtgagtacgg ... cggcgcgcagCTGCTCGCTGG
EST: gi|9460610|gb|BE453322.1|BE453322
EST:     TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCG                         CTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA
genomic: TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCGgtgagtacgg ... cggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA
EST: gi|9458439|gb|BE452240.1|BE452240
EST:     TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCG                         CTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA
genomic: TTCGAGGACCTGATGGAGGCCGGCATCATCGACCCCACCAAGGTGGTCCGgtgagtacgg ... cggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctccttcctgccccccccccctgcgcccttccctcctgcctgccggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGACGTGGTGGTCACCGAGATCCCCGAGAAGGAGAAGGCGCCCGCGCCCGCC
       tcctgccccccccccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacctagcatgcaagctcattccttccttgcctccttccttctcatctccttcctgccccccccccctgcgcccttccctcctgcctgccggcgcgcagCTGCTCGCTGGAGAACGCCGTGTCGGTGGCCAAGACCTTCCTGCTGGCTGACGTGGTGGTCACCGAGATCCCCGAGAAGGAGAAGGCGCCCGCGCCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - -aagctca