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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttagagcgaccgagcagggcggcggagggctgcgaacacatttcggcagcgactgggaaagcctcggtccctagcaagctccatatgcctattacggtcgtggtgccatcaaataaccgcgttacaaattgccggtcgcccttgtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGAAGGGTAGCTTCAAGAAGAGCCGGAAGCCCCGGTTCTCGGTGGTCTTCCA

Basic information

species Chlamydomonas reinhardtii
transcript EDP01709
intron # 1
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|9027899|gb|BE237939.1|BE237939
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34994814|gb|CF568731.1|CF568731
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34983333|gb|CF557250.1|CF557250
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6551450|gb|AV397234.1|AV397234
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|22072614|gb|BQ821952.1|BQ821952
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6547622|gb|AV393406.1|AV393406
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34987787|gb|CF561704.1|CF561704
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6548274|gb|AV394058.1|AV394058
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGGCTGTGAAC
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAA-GGCTGTGAA-
EST: gi|34983741|gb|CF557658.1|CF557658
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6543358|gb|AV389142.1|AV389142
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34983740|gb|CF557657.1|CF557657
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|7427134|gb|AW661306.1|AW661306
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6549034|gb|AV394818.1|AV394818
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34993436|gb|CF567353.1|CF567353
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34983365|gb|CF557282.1|CF557282
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34991513|gb|CF565430.1|CF565430
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34991590|gb|CF565507.1|CF565507
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34993277|gb|CF567194.1|CF567194
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34991796|gb|CF565713.1|CF565713
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34983443|gb|CF557360.1|CF557360
EST:     ATGGCCCCGAAAG                         GCAACGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|49462611|gb|BP090524.1|BP090524
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34991066|gb|CF564983.1|CF564983
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6548876|gb|AV394660.1|AV394660
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|10783710|gb|AV640382.1|AV640382
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34982046|gb|CF555963.1|CF555963
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|6549466|gb|AV395250.1|AV395250
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|34991855|gb|CF565772.1|CF565772
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|49467236|gb|BP095149.1|BP095149
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
EST: gi|22064005|gb|BQ815547.1|BQ815547
EST:     ATGGCCCCGAAAG                         GCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA
genomic: ATGGCCCCGAAAGgtgcgttaga ... gtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtggtgccatcaaataaccgcgttacaaattgccggtcgcccttgtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGAAGGGTAGCTTCAAGAAGAGCCGGAAGCCCCGGTTCTCGGTGGTCTTCCA
            aaataac  putative branch site (score: 2)
                                        cccttgt  putative PPT
         atcaaataa  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttagagcgaccgagcagggcggcggagggctgcgaacacatttcggcagcgactgggaaagcctcggtccctagcaagctccatatgcctattacggtcgtggtgccatcaaataaccgcgttacaaattgccggtcgcccttgtgcgtgcagGCAAGGCTGACGCCAAGGCGGTGGCCGCCAAGGCTGCTAAGGCTGTGAAGAAGGGTAGCTTCAAGAAGAGCCGGAAGCCCCGGTTCTCGGTGGTCTTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG