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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAAATTAGGCTGGAGCAGGAGGATGAGGGCGTGCCTAGCACAGCCATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtcttcgcacgacactctgcgctggtgacgtgtgggcagtcataagaggactcgagcccgacgatatcgccccctacag

Basic information

species Chlamydomonas reinhardtii
transcript EDP08130
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP08130 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 2
TGAAGAAAATTAGGCTGGAGCAGGAGGATGAGGGCGTGCCTAGCACAGCCATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtcttcgcacgacactctgcgctggtgacgtgtgggcagtca-taagaggactc--gagcccgacgatatcgccccctacag------------
||||||| ||| |  ||||||||||||||||||| || || ||||| |||||||| || |||||  || | |||||  |||  |||   ||  ||||  |||      | |     | |     | |    |  | |||| ||   ||| |     || ||  | ||    | | | |   | ||                
TGAAGAAGATTCGCTTGGAGCAGGAGGATGAGGGGGTTCCCAGCACCGCCATTCGCGAGATTTCTCTCTTGAAAGAAATGCAGCACAGGAACATTGTTAGgtatattatatctctgctaagtgtttctgaag-aatgtgttggtcttcaattgtgtgattcatgtgctgagcaacaacattctctgggcgtagagatagag

upper sequence: EDP08130 (Chlamydomonas reinhardtii), 5'ss of exon 2
lower sequence: AT3G48750.1 (Arabidopsis thaliana), 5'ss of exon 3
TGAAGAAAATTAGGCTGGAGCAGGAGGATGAGGGCGTGCCTAGCACAGCCATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtcttcgcacgacactctgcgctggtgacgtgtgggcagtcataagaggactcgagcccgacgatatcgccccctacag
||||||| || ||||| |||||||||||||| || || ||||||||||| ||  | ||||| ||  || | |||||  |||  |||  |||  |||||  ||  |  ||     | |     |     ||| |   |  ||   | ||     |  | |   |   || | | |   |  | ||||
TGAAGAAGATCAGGCTAGAGCAGGAGGATGAAGGTGTTCCTAGCACAGCAATCAGAGAAATCTCCCTCTTGAAAGAAATGCAGCACAGCAACATTGTCAAgtatgatgttaatac-cattgttgaaaactgattcagcatgatgactctggtaaacaattttgattgatgttttttgctac-acag
















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|23366705|gb|BU654524.1|BU654524
EST:     ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCG                         GCTCTATGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
genomic: ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtc ... ccccctacagGCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
EST: gi|16434131|gb|BI999357.1|BI999357
EST:     ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCG                         GCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
genomic: ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtc ... ccccctacagGCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
EST: gi|15701513|gb|BI725818.1|BI725818
EST:     ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCG                         GCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
genomic: ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtc ... ccccctacagGCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
EST: gi|15694668|gb|BI718973.1|BI718973
EST:     ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCG                         GCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT
genomic: ATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtc ... ccccctacagGCTCTACGACGTGCTCTACAGCGACCGCCGATTGTACTTGGTGTTCGAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAAATTAGGCTGGAGCAGGAGGATGAGGGCGTGCCTAGCACAGCCATTCGGGAAATTTCGTTCCTTAAAGAGCTGCGCCACGACAATGTTGTCCGgtgagcagtcttcgcacgacactctgcgctggtgacgtgtgggcagtcataagaggactcgagcccgacgatatcgccccctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC