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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgccgcgcaggtttcgtggatgccaggggtcaggccttgccatctcactgcatgttgcagatgtgaaacgctcaacgccgttgatagcaatgctgatgccgctgccctctgtctgcgcccatccgccccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAAGGACGTGGCGGCCATGAAGGCCGTGGTGGGTGAGGAGGCGCTGAGCAGC

Basic information

species Chlamydomonas reinhardtii
transcript EDP06821
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP06821 (Chlamydomonas reinhardtii), 3'ss of exon 8
lower sequence: LOC_Os01g51380.1 (Oryza sativa), 3'ss of exon 13
gtgcgtgccgcgcaggtttcgtggatgccaggggtcaggccttgccatctcactgcatgttgcagatgtgaaacgctcaacgccgttgatagcaatgctgatgccgctgccctctgtctgcgcccatccgccccgcctgcagGGACCACTCGGAGGTGTCCAAC-CAGCTGTACGCCAACTACGCCATCGGCAAGGACGTGGCGGCCATGAAGGCCGTGGTGGGTGAGGAGGCGCTG--AGCAGC-------
                                                                         || |    | |||| |||||    ||     |    |   ||  ||   || |           || ||     ||||||| ||||      |||||||| ||||| |||||||| |||||||||||   ||| |||||||| ||||| || ||||| ||||||  | |||        
-----------------------------------------------------------------------gtcggttg--ggcgttcatagc----ctatgttctgcacaaactaccttaaccaagta--tatatatggagtatttactcggatgtgtttgtttcagCTGTATGCCAATTACGCCATAGGCAAGGACGTACAGGCGATGAAGGCAGTGGTTGGAGAGGAAGCGCTGTCATCAGAGGACCTG
















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|22067888|gb|BQ817894.1|BQ817894
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|16435179|gb|BM000399.1|BM000399
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|6541650|gb|AV387434.1|AV387434
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|23367537|gb|BU655355.1|BU655355
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|161796199|gb|FC085388.1|FC085388
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGGGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|161804893|gb|FC089182.1|FC089182
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|23358629|gb|BU646449.1|BU646449
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|161790819|gb|FC081771.1|FC081771
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|49463722|gb|BP091635.1|BP091635
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|161812967|gb|FC098653.1|FC098653
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|10127837|gb|BE726541.1|BE726541
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|161809120|gb|FC095150.1|FC095150
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|23367566|gb|BU655368.1|BU655368
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|23367538|gb|BU655356.1|BU655356
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTG
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTG
EST: gi|10768137|gb|AV618962.1|AV618962
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
EST: gi|239842042|gb|GR283899.1|GR283899
EST:     TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAA                         GGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA
genomic: TCGCTGTCGCGTCTCATGAAGTCCGCCATCGGCGAGGGCATGACCCGCAAgtgcgtgccg ... ccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagcaatgctgatgccgctgccctctgtctgcgcccatccgccccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAAGGACGTGGCGGCCATGAAGGCCGTGGTGGGTGAGGAGGCGCTGAGCAGC
        tgctgat  putative branch site (score: 3)
                                       tccgcccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgccgcgcaggtttcgtggatgccaggggtcaggccttgccatctcactgcatgttgcagatgtgaaacgctcaacgccgttgatagcaatgctgatgccgctgccctctgtctgcgcccatccgccccgcctgcagGGACCACTCGGAGGTGTCCAACCAGCTGTACGCCAACTACGCCATCGGCAAGGACGTGGCGGCCATGAAGGCCGTGGTGGGTGAGGAGGCGCTGAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG