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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgggtttgacgagcagttcattcacgctacggtactcggtgccgcactgccgccgccgcctctcactgggacctgccgccctcctgtctatgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP03835
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03835 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 3'ss of exon 3
-acgggtttgacgagcagttcattcacgctacggtact-cggtgccgcactgc-cgccgccgcctctcactgggacctgccgc-cctcctgtctatgaccgc---------agGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG---------
     | ||||||  ||  | | | ||  |  |||  |   |      | |||   | | |     || ||| |      |   ||| ||    || | ||          |||| ||  | ||||| |||||||||| ||| ||||||||||| || || || |||||||| ||||||||          
gtaatgcttgacgttcacctaactgactttttggttttattgcattcaaatgcatactgtcaatattccctgtgcttcctcatgccttctactaataagcgtccttctgcaagGTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAG

upper sequence: EDP03835 (Chlamydomonas reinhardtii), 3'ss of exon 4
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 3
acgggtt--tgacgagcagttcattcacgctacggtactcggtgccgcactgccgccgc-cgcctctcac---tgggacctgccgccct--cctgtctatgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG---------
    |||  |  |   ||| |  | ||  || |   ||  | |  ||  |        | ||  | |  |    |||   |     | |    | |  ||    |||||| ||  | || || ||||| |||||| |||| ||||| ||| |||| |||||||||||||| ||||||         
gttagttaatcccagccaggttgt-caaacttctcgacatgatctcgtgcatttcttactcgtatttagcagacgggtggtaataacttaatttattaattgtggcagGTTGCCAGGTGTACAAAGATAATCAACGCCAATACGGATGACTCCAAATACGTCATCAACGTGAAGCAGATTGCCAAG
















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|22076975|gb|BQ825751.1|BQ825751
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|14226250|gb|BG845066.1|BG845066
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|23365334|gb|BU653154.1|BU653154
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|22065629|gb|BQ816456.1|BQ816456
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|14228702|gb|BG847518.1|BG847518
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|14226251|gb|BG845067.1|BG845067
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|22076877|gb|BQ825653.1|BQ825653
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
EST: gi|10789963|gb|AV627328.1|AV627328
EST:     GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAG                         GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC
genomic: GGGACCTGGTGTCGGACAAGCAGATGCAGCAGGAGGAGCAGCCGCTGCAGgtgggggcgg ... atgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgccgccgccgcctctcactgggacctgccgccctcctgtctatgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG
               ctctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgggtttgacgagcagttcattcacgctacggtactcggtgccgcactgccgccgccgcctctcactgggacctgccgccctcctgtctatgaccgcagGTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAG

- gggtttg
- - - - -acgagca
- - - - - - - - - tcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctcact