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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcttcatcgacatctattgcgtacggcgctggtcagcgcagctgcggcagtttagggctctggggtatcccgatctttgacatcgcgcgcctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGGCCGCTCGCTGACCAACACCGTCTACAACCTGGGTCTGGAGGGCGAGTAT

Basic information

species Chlamydomonas reinhardtii
transcript EDO98385
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|10793205|gb|AV630571.1|AV630571
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49471002|gb|BP098863.1|BP098863
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTA
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTA
EST: gi|10792185|gb|AV629551.1|AV629551
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGAT
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGAT
EST: gi|49469498|gb|BP097359.1|BP097359
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10792139|gb|AV629505.1|AV629505
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|15373138|gb|BI532564.1|BI532564
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10788939|gb|AV626659.1|AV626659
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10784372|gb|AV641044.1|AV641044
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTA
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTA
EST: gi|10792275|gb|AV629641.1|AV629641
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGAT
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGAT
EST: gi|10789214|gb|AV626934.1|AV626934
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49468541|gb|BP096402.1|BP096402
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTCCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10788268|gb|AV644940.1|AV644940
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATG
EST: gi|49465034|gb|BP092947.1|BP092947
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10785929|gb|AV642601.1|AV642601
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49465732|gb|BP093645.1|BP093645
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10793021|gb|AV630387.1|AV630387
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|15692438|gb|BI716743.1|BI716743
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49467688|gb|BP095549.1|BP095549
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10791311|gb|AV628677.1|AV628677
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTAC
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTAC
EST: gi|6551266|gb|AV397050.1|AV397050
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10787105|gb|AV643777.1|AV643777
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49466180|gb|BP094093.1|BP094093
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49466649|gb|BP094562.1|BP094562
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCC
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCC
EST: gi|239840758|gb|GR282448.1|GR282448
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|10787802|gb|AV644474.1|AV644474
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGG
EST: gi|49468329|gb|BP096190.1|BP096190
EST:     GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAA                         GAAGGAGGACCCCAAGTTCATCTACTACCTG
genomic: GTCCGCGAGAAGCTCATTGACTCGTTCAACAAGACCCACGAGCACTGGAAgtgagcaggg ... cctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcagtttagggctctggggtatcccgatctttgacatcgcgcgcctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGGCCGCTCGCTGACCAACACCGTCTACAACCTGGGTCTGGAGGGCGAGTAT
                              ctttgac  putative branch site (score: 4)
                                           cgcctttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcttcatcgacatctattgcgtacggcgctggtcagcgcagctgcggcagtttagggctctggggtatcccgatctttgacatcgcgcgcctttcgcagGAAGGAGGACCCCAAGTTCATCTACTACCTGTCTGCTGAGTTCCTGATGGGCCGCTCGCTGACCAACACCGTCTACAACCTGGGTCTGGAGGGCGAGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - atcgaca
- - - - - - - - -ttgcgta