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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccgccgcggcgctgtttcggggagctcagggaggagctggcgctctgggagctgttacgggcgcgttttctgaaagcaagatatgataacggagggaagggtccggggtcggcagacgcgaaagcacatcgctcactgcttcatctaagttcgtgttcctgtgcatgctttttccattttgcagATGGACCCCAAGTTCCTGCGCAACCAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP03201
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP03201 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 2
-gtaagtgccgccgcggcgctgtttcggggagctcagggaggagctggcgctctgggagctgttacgggcgcgttttctgaaagcaagatatgataacgg--agggaagggtccggggt--cggcagacgcgaaagcacatcgctcactgcttcatctaagttcgtgttcctgtgcatgctttttccattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
   || ||   | |  ||    |||     | |||    || | || | | |  |     |||| |  || | |   ||||      | | |||  | |      || ||  ||   ||  | |  ||  |  | | |        |  ||  ||   |   | |||   |||    ||     |          || |||   || |    ||         
cacaactgttactgttgccaaattttc---atctccac-agcatcttgagat--gcatattgtttcttgctcttaaactgaccttttgctttgaccatgtttgcagATGGACCCCAAGTTCCTGAGGAACCTGAGGTATTCTAGGAAGGGCAACAAAAAGAGTGGTGAGGCTGAAGCTGAGGAGTA--------GGAAGGAAAGCATGGCTTTG---------

upper sequence: EDP03201 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 2
------gtaagtgccgccgcggcgctgtttcggggagctcagggaggagc-tggcgctctgggagctgttacgggcgcgttttctgaaagcaagatatgataacggagggaagggtccggggtcggcagacgcgaaagcacatcgctcactgcttcatctaagttcgtgttcctgtgca-tgctttttccattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
      || | |   |||         | ||    ||||    |||  ||     | | |  |  ||   || | | | ||   |  |  | |  | ||   | |||    | | ||| | |      ||  |  | | |        |  ||  ||   |   | |||   ||| | | |         |   ||    ||   ||                   
acaactgttacttttgccaatttttcatctctaacagctgcttgagatgcaccttggtttttgctctacaactgaccctttgcattga--ccatgtttgcagATGGACCCCAAGTTCCTGAG------GAACCTGAGGTATTCAAGGAAGGGCAACAAGAAGAGTGGTGAGGCTGAGGAGTAGGAAGGAAAGCATGGTTGTGTTTCCT------------------
















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|34994648|gb|CF568565.1|CF568565
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34988353|gb|CF562270.1|CF562270
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34991846|gb|CF565763.1|CF565763
EST:     GACCGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34994520|gb|CF568437.1|CF568437
EST:     GAACGGCATCAAAAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34983440|gb|CF557357.1|CF557357
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCTAAGTTCCTGCGC
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGC
EST: gi|34991289|gb|CF565206.1|CF565206
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34994767|gb|CF568684.1|CF568684
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGGCCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34994827|gb|CF568744.1|CF568744
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993682|gb|CF567599.1|CF567599
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34990139|gb|CF564056.1|CF564056
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34989137|gb|CF563054.1|CF563054
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993472|gb|CF567389.1|CF567389
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34991915|gb|CF565832.1|CF565832
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993468|gb|CF567385.1|CF567385
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34991068|gb|CF564985.1|CF564985
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|16438267|gb|BM003487.1|BM003487
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993946|gb|CF567863.1|CF567863
EST:     GAACGGCATCAAGAAGCCCCAGAAGACCAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34994684|gb|CF568601.1|CF568601
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|10788251|gb|AV644923.1|AV644923
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34990138|gb|CF564055.1|CF564055
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGGCCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993833|gb|CF567750.1|CF567750
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34983176|gb|CF557093.1|CF557093
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34984644|gb|CF558561.1|CF558561
EST:     GACCGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|34993905|gb|CF567822.1|CF567822
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
EST: gi|10784961|gb|AV641633.1|AV641633
EST:     GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGC                         ATGGACCCCAAGTTCCTGCGCAACCAG
genomic: GAACGGCATCAAGAAGCCCCAGAAGAACAAGTTCCCCAGCCGCAAGGGCgtaagtgccg ... cattttgcagATGGACCCCAAGTTCCTGCGCAACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctcactgcttcatctaagttcgtgttcctgtgcatgctttttccattttgcagATGGACCCCAAGTTCCTGCGCAACCAG
 cgctcac  putative branch site (score: 3)
                                    tgctttttccatttt  putative PPT
                                       ttttt  TA-rich tract