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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGCAACCTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcacagcgccgccccatgcagccctgcattgccggtatgttcctcacccacagctttgctgccacgtgcgccgccgcggtgcgccacccctgccttcgtcccgccctaacgcccttcctatccttgactccgcaacccccctaacaccgccaccgcctcgcag

Basic information

species Chlamydomonas reinhardtii
transcript EDO98445
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO98445 (Chlamydomonas reinhardtii), 5'ss of exon 20
lower sequence: EFJ20968 (Selaginella moellendorffii), 5'ss of exon 12
---------GCCGGCAACCTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcacagcgccgccccatgcagccctgcattgccggtatgttcctcacccacagctttgctgccacgtgcgccgccgcggtgcgccacccctgccttcgtcccgccctaacgcccttcctatccttgactccgcaacccccctaacaccgccaccgcctcgcag
         |  || ||| | ||  ||||||||||||| ||||||||||||||||| || || || ||   | || |   |  |||     || |   || | |   |  || |    |  ||||      |||    ||  | | ||   |   ||                                                                               
CTCAAATGTGGTGGTAACTTCCTCTTGCTGGACGAGCCTACCAACGACCTGGACGTGGATACTCTCCG--AACTCTCGAGGAGGCCATCCACAACTTCGC-TGgtgagcttgcttggtagacacattgcctctgg-gtgtctgacaccaacgctggcag-----------------------------------------------------------------------------

upper sequence: EDO98445 (Chlamydomonas reinhardtii), 5'ss of exon 20
lower sequence: EFJ32288 (Selaginella moellendorffii), 5'ss of exon 14
---------GCCGGCAACCTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcacagcgccgccccatgcagccctgcattgccggtatgttcctcacccacagctttgctgccacgtgcgccgccgcggtgcgccacccctgccttcgtcccgccctaacgcccttcctatccttgactccgcaacccccctaacaccgccaccgcctcgcag
         |  |||||| | ||  ||||||||||||| ||||||||||||||||| ||||| || ||   | || |   |  |||     || |   || | |   |  || |    || ||||      |||    ||  |   ||   |   ||                                                                               
CTCAAATGTGGTGGCAACTTCCTCTTGCTGGACGAGCCTACCAACGACCTGGACGTGGACACTCTCCG--AACTCTCGAGGAGGCCATCCACAACTTCGC-TGgtgagcttgcttggtacacacattgcctctgg-gtgtctgaaaccaacgctggcag-----------------------------------------------------------------------------
















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|161816839|gb|FC102989.1|FC102989
EST:     CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTGGACACGCTGCG                         CTGCCTGGAGGAGGCCATCCTGAACTTCGCGGGCACCACACTGCTCATCAG
genomic: CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcaca ... cgcctcgcagCTGCCTGGAGGAGGCCATCCTGAATTTCGCGGGCACCACACTGCTCATCAG
EST: gi|15702278|gb|BI726583.1|BI726583
EST:     CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCG                         CTGCCTGGAGGAGGCCATCCTGAATTTCGCGGGCACCACACTGCTCATCAG
genomic: CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcaca ... cgcctcgcagCTGCCTGGAGGAGGCCATCCTGAATTTCGCGGGCACCACACTGCTCATCAG
EST: gi|14237614|gb|BG856430.1|BG856430
EST:     CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCG                         CTGCCTGGAGGAGGCCATCCTGAATTTCGCGGGCACCACACTGCTCATCAG
genomic: CTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcaca ... cgcctcgcagCTGCCTGGAGGAGGCCATCCTGAATTTCGCGGGCACCACACTGCTCATCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGGCAACCTGCTGCTGCTGGACGAGCCCACCAACGACCTGGACGTTGACACGCTGCGgtgagtcacagcgccgccccatgcagccctgcattgccggtatgttcctcacccacagctttgctgccacgtgcgccgccgcggtgcgccacccctgccttcgtcccgccctaacgcccttcctatccttgactccgcaacccccctaacaccgccaccgcctcgcag

- - - - - TGCTGC
- - - - -  GCTGCT
- - - - - -  TGCTGC
- - - - - - - GCTGCT
- - - - - - - -  GCTGGA