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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttccatccccaaccaatcctgttactatcccatcgctctccatgcctctgacctttccatctgccccccggcccctcccgcgcgcgcgcggcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCAAGATCGCCGCCAAGCTGGAGATCATGGAGCCCTGCTGCTCCGTTAAGGA

Basic information

species Chlamydomonas reinhardtii
transcript EDP04425
intron # 2
splice site 3'
intron type U2

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|22070936|gb|BQ820274.1|BQ820274
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|49459183|gb|BP087096.1|BP087096
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|22070937|gb|BQ820275.1|BQ820275
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|23366869|gb|BU654688.1|BU654688
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|9028232|gb|BE238272.1|BE238272
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|6544161|gb|AV389945.1|AV389945
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|6544497|gb|AV390281.1|AV390281
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|14226588|gb|BG845420.1|BG845420
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|10772277|gb|AV623100.1|AV623100
EST:     AAGGCGTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: AAGGC-TGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|14237451|gb|BG856267.1|BG856267
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
EST: gi|14227106|gb|BG845922.1|BG845922
EST:     GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTG                         GCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA
genomic: GAAGGCTGCTGTTAAGATGAACATCGCCACCGATGTCACCGAGCTGATTGgtgagcgggc ... gcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgacctttccatctgccccccggcccctcccgcgcgcgcgcggcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCAAGATCGCCGCCAAGCTGGAGATCATGGAGCCCTGCTGCTCCGTTAAGGA
 ctctgac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttccatccccaaccaatcctgttactatcccatcgctctccatgcctctgacctttccatctgccccccggcccctcccgcgcgcgcgcggcgcctgcagGCAAGACCCCTATGGTCTACCTGAACAAGGTGGCCACGGGCACGCACGCCAAGATCGCCGCCAAGCTGGAGATCATGGAGCCCTGCTGCTCCGTTAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT