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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatgcaccagccgcccgactaagccaattgtcagggccccgcagccatatcgtgcttatcgtgtgccggaccccacgccgctgtttctaaccaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTGGCCAATGACCCCACCATTGAGCGCATCATCACGCCGCGTATCGCGCTGA

Basic information

species Chlamydomonas reinhardtii
transcript EDP06821
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP06821 (Chlamydomonas reinhardtii), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 8
acatgcaccagccgcccgactaagccaattgtcagggccccgcagccatatcgtgcttatcgtgtgccggaccccacgccgctgtttctaaccaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTGGCCAATGACCCCACCATTGAGCGCATCATCACGCCGCGTATCGCGCTGA---------------------------------------------------
                           ||  | |         ||   |||  |  |||| || ||   |     |   |    |||  |||||      | ||||         ||||      ||     | |    |        | |||||| |||||||||||||| ||||||||||| || || || || || |                                                   
---------------------gtatttat-attaaattaatatagtggtat--ttattattgtttgt--ggtgtaaattctaaattttaaacca------ggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacagGCCAACGACCCCACCATTGAACGCATCATCACTCCTCGAATTGCTCTCACCACTGCTGAATATTTAGCATATGAATGTGGCAAACATGTTCTTGTCATAC
















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|10775952|gb|AV632632.1|AV632632
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|16435179|gb|BM000399.1|BM000399
EST:     GCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: GCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|10778196|gb|AV634876.1|AV634876
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|10769041|gb|AV619866.1|AV619866
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161796199|gb|FC085388.1|FC085388
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|10774828|gb|AV625651.1|AV625651
EST:     GTGTCAACATGGAGACTGCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: GTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161804893|gb|FC089182.1|FC089182
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|23362387|gb|BU650207.1|BU650207
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161814739|gb|FC102856.1|FC102856
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161823222|gb|FC110068.1|FC110068
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161803648|gb|FC090560.1|FC090560
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161812967|gb|FC098653.1|FC098653
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG
EST: gi|161809120|gb|FC095150.1|FC095150
EST:     TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCATTTCTTCAAGCAG                         GACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTTTTCCTGAACCTG
genomic: TGTTCGCGGCCATGGGTGTCAACATGGAGACTGCGCACTTCTTCAAGCAGgtgcgcggta ... accaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatatcgtgcttatcgtgtgccggaccccacgccgctgtttctaaccaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTGGCCAATGACCCCACCATTGAGCGCATCATCACGCCGCGTATCGCGCTGA
                                        ttctaac  putative branch site (score: 1)
                                       tttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatgcaccagccgcccgactaagccaattgtcagggccccgcagccatatcgtgcttatcgtgtgccggaccccacgccgctgtttctaaccaccgtagGACTTCGAGGAGAACGGCTCGCTGGAGCGCACGGTGCTGTTCCTGAACCTGGCCAATGACCCCACCATTGAGCGCATCATCACGCCGCGTATCGCGCTGA

acatgca
- - - - - - - - - - - - - - - - - - - - - -agccata
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accccac