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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCCTCAAGGCGGCAGTGATGAAGTATGGGCTCAACCAGTGGGCCCGTATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacaggcgcggcgggctacggggcggggttgctgagcggcaggctacggcgttgccaacgggttatcccaccgatggctgctgctttggtagaac...

Basic information

species Chlamydomonas reinhardtii
transcript EDP03322
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03322 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: AC203535.4_FGT001 (Zea mays), 5'ss of exon 1
AAATCCTCAAGGCGGCAGTGATGAAGTATGGGCTCAACCAGTGGGCCCGTATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacaggcgcggcgggctacggggcggggttgctgagcggcaggct-----acggcgttgcc----------aacgggttatcc-caccgat-ggctgctgctttggtagaac---------------
                                   ||||||||||| || || ||||||||||| || || ||||| |||||||||||||| || |||||||  |    |      | | | |    |   |||  | ||  |   | ||     ||||   || |            | |  || || ||| |   ||  || | | |   |                   
-------------------------------CAAGAACCAGTGGGCGCGCATCTCGTCGCTGCTCGTCCGCAAGTCCGCCAAGCAGTGCAAGGCCCGCTGGTATGAGTGGCTCGATCCGTCCATCAAG-AAGgtaaccgactgctcgcctctcttacggttctgtcttcctctctcggcagactagcctcactgcccggtcgccgttctatcactgattttcgctttgcttg
















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|10784250|gb|AV640922.1|AV640922
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
EST: gi|10787044|gb|AV643716.1|AV643716
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
EST: gi|10785473|gb|AV642145.1|AV642145
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
EST: gi|10784017|gb|AV640689.1|AV640689
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGC
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGC
EST: gi|10789114|gb|AV626834.1|AV626834
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
EST: gi|10785001|gb|AV641673.1|AV641673
EST:     ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTG                         GTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA
genomic: ATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacag ... tgcgccgtagGTACGAGTGGCTGGACCCGGCCATCAAGAAGACGGAGTGGACGCGCGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATCCTCAAGGCGGCAGTGATGAAGTATGGGCTCAACCAGTGGGCCCGTATTTCGTCGCTGCTGGTGCGGAAGTCTGCCAAGCAGTGCAAAGCACGCTGgtgagcacaggcgcggcgggctacggggcggggttgctgagcggcaggctacggcgttgccaacgggttatcccaccgatggctgctgctttggtagaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctgc