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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcgcgcgtgaccagcagagggggtcaggggttgaatccttgttgctgggtggggcaaacatggtaatgctggaagaggccggcagtgcgcctgcttccttactggctacgttcgccggctgaccttctcctatgtcttcacccccccccccccctccccgctcctcgcctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTCAACAACCAGCACCTGGGCATGGTGGTGCAGTGGGAGGACAGGTTCTACA

Basic information

species Chlamydomonas reinhardtii
transcript EDP01876
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP01876 (Chlamydomonas reinhardtii), 3'ss of exon 11
lower sequence: EFJ12072 (Selaginella moellendorffii), 3'ss of exon 3
gtgcgtgcgcgcgtgaccagcagagggggtcaggggttgaatccttgttgctgggtggggcaaacatggtaatgctggaagaggccggcagtgcgcctgcttccttactggctacgttcgccggctgaccttctcctatgtcttcacccccccccccccctccccgctcctcgcctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTCAACAACCAGCACCTGGGCATGGTGGTGCAGTGGGAGGACAGGTTCTACA
                                                                                                                       | |||    |   ||   | || ||||   | |              |||| | | |  | ||||||||| || || ||   | | || || ||   ||| ||  | ||| || | |||||||||||| |||| ||||| || ||||||||||| || |||||||
-----------------------------------------------------------------------------------------------------------------------gtcggt--gcgagctttaacgttttcatttcacgt-----------actccgctcgtaatttcagGAGCTAGCGACGATTCACGTGGAAAAACTCCCCGTGAAAATCATGGTGTTAAACAACCAGCACTTGGGAATGGTTGTACAGTGGGAGGATAGATTCTACA
















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|8576814|gb|BE129451.1|BE129451
EST:     AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTGAAGGTGATGCTGCTC
genomic: AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
EST: gi|161805706|gb|FC093674.1|FC093674
EST:     AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
genomic: AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
EST: gi|16435578|gb|BM000798.1|BM000798
EST:     AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
genomic: AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
EST: gi|16073006|gb|BI875002.1|BI875002
EST:     AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
genomic: AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
EST: gi|15702979|gb|BI727284.1|BI727284
EST:     AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
genomic: AGACCGTGGTGGACATTGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
EST: gi|15372067|gb|BI531493.1|BI531493
EST:     TGACGGCGACGGCTCCTTCCTCATGAACGTGCAG                         GAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC
genomic: TGACGGCGACGGCTCCTTCCTCATGAACGTGCAGgtgcgtgcgc ... ctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcctatgtcttcacccccccccccccctccccgctcctcgcctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTCAACAACCAGCACCTGGGCATGGTGGTGCAGTGGGAGGACAGGTTCTACA
           tcttcacccccccccc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcgcgcgtgaccagcagagggggtcaggggttgaatccttgttgctgggtggggcaaacatggtaatgctggaagaggccggcagtgcgcctgcttccttactggctacgttcgccggctgaccttctcctatgtcttcacccccccccccccctccccgctcctcgcctgctctcagGAGCTGGCCACCATCTTCATTGAGAAGCTGGACGTCAAGGTGATGCTGCTCAACAACCAGCACCTGGGCATGGTGGTGCAGTGGGAGGACAGGTTCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA