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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag

Basic information

species Chlamydomonas reinhardtii
transcript EDO96600
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO96600 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: PP1S91_243V6.1 (Physcomitrella patens), 5'ss of exon 6
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag
||| ||||| || ||||||||||||||||| |||||||| || |||||||||||    || ||  | |||||||||||||| || ||      ||| |||||| |||    | |   || |  | | ||    ||  |  | ||| |  ||  |  |||||   ||   ||    |||| |  |   | |  |||| |   ||  |                   
CGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCGTGGGCAACAAATCAGATCTTGCTTCGAAGAAGGTGGTGGATTATGAAACCGCTAAGgtgtgtgaagcgaaa--accgaggcgatgttttccatgcatgggaagatagtga--tgttg--taggttggatttagctgtgtgttttccatcgttggtggtgatt-------------------

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: PP1S95_20V6.1 (Physcomitrella patens), 5'ss of exon 6
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag
 || || || || || || || ||||||||||| |||||||| ||||||||||||  ||| ||  | || ||||||||||| || ||| |    || ||||| |  |       |   |   |  | | | |  |  ||   | ||| |    || ||||  |   |       ||  |  ||  |      |     |  | | |                   
TGAAATCGATCGTTATGCAAGTGAGAACGTGAATAAGCTGCTTGTGGGCAACAAGTCCGATCTTGCATCCAAGAAGGTGGTGGACTACGCAACTGCGAAGgtacacgaatgatgctatccactttgataa-gatcaagg---gaaggtcg---aaatgttatctttcttaagttcatatcgtgtagtaagaacagaataattccttt------------------

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: EFJ23285 (Selaginella moellendorffii), 5'ss of exon 6
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag
|||||| || || ||||| ||||||||||| |||||||| || || ||||||||| ||||  | ||  | ||||| || || || ||       |||||||||         |     |        |   |  |   ||    |      |   |||   |                                                               
CGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCGTCGGCAACAAGTGCGATTTAACTGCAAAGAAAGTCGTGGATTATCAGACTGCCAAGgtgacaacttctgttattctttctttctactgtacaaagtaaaaatcttttcttcgtgacag---------------------------------------------------------------

upper sequence: EDO96600 (Chlamydomonas reinhardtii), 5'ss of exon 7
lower sequence: EFJ20286 (Selaginella moellendorffii), 5'ss of exon 6
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag
|||||| || || ||||| ||||||||||| |||||||| || || ||||||||| |||| || ||  ||||||| || || || |||      |||||||||               |   |  |   || |  |    |   |  |   |   |||   |                                                               
CGAGATCGATCGCTACGCGAGCGAGAACGTAAACAAGCTTCTCGTCGGCAACAAGTGCGATCTAACTGCGAAGAAAGTCGTGGATTACCAAACTGCCAAGgtgacaaaatctcttattctt-tccgtctactgtacaaagtaaaaatctttcttcgtgacag---------------------------------------------------------------

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|10779798|gb|AV636478.1|AV636478
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCTTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|161796597|gb|FC082914.1|FC082914
EST:     ACAAGAGCGACCTGACGTCTAAGAAGGTGGTTGATTACTCCGTCGCCAAG                         GCGTTTGCCGACGAGATTGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|22074950|gb|BQ823726.1|BQ823726
EST:     GGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: GGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|10771327|gb|AV622150.1|AV622150
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|22068890|gb|BQ818649.1|BQ818649
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|22067408|gb|BQ817540.1|BQ817540
EST:     GGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: GGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|16432961|gb|BI998187.1|BI998187
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|6546326|gb|AV392110.1|AV392110
EST:     CAAGAGCGACCTGACGTCGAAGAAAGTGGTTGAGTACTCCGTCGCCCAAG                         -CGTTCGCCGACGAGATCGGCA
genomic: CAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCC-AAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCA
EST: gi|10777853|gb|AV634533.1|AV634533
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
EST: gi|16430540|gb|BI995766.1|BI995766
EST:     ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAG                         GCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC
genomic: ACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgc ... ctctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGATTGACCGGTACGCCAGCGAGAACGTGAACAAGCTGCTGGTGGGCAACAAGAGCGACCTGACGTCGAAGAAGGTGGTTGAGTACTCCGTCGCCAAGgtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG