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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcggcaacatggtgcgggctgctgatggagggtttgttgcggacctccacgcgcgtgaggtccacacacatattcactcgtatatgttgaccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCGGCTCTGGATCTGGGCGCTGAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP07882
intron # 4
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|34981501|gb|CF555418.1|CF555418
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|6544162|gb|AV389946.1|AV389946
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|7615939|gb|AW721379.1|AW721379
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCACGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|34991270|gb|CF565187.1|CF565187
EST:     CACTGAGTTCGAGGGCTATGACGAAGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10781219|gb|AV637899.1|AV637899
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10775330|gb|AV632010.1|AV632010
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|15368596|gb|BI528022.1|BI528022
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|15372623|gb|BI532049.1|BI532049
EST:     GCTGGCTGCCACTGAGTTCGAGGGGTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCTCAAGGGTGTGGAGATCACGCAAGCG
genomic: GCTGGCTGCCACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10774936|gb|AV625759.1|AV625759
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|49462012|gb|BP089925.1|BP089925
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCA
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCA
EST: gi|34982918|gb|CF556835.1|CF556835
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|34983136|gb|CF557053.1|CF557053
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|14231927|gb|BG850743.1|BG850743
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10790668|gb|AV628034.1|AV628034
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|34982917|gb|CF556834.1|CF556834
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10778795|gb|AV635475.1|AV635475
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|14235722|gb|BG854538.1|BG854538
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|15372587|gb|BI532013.1|BI532013
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|15372909|gb|BI532335.1|BI532335
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGNTGTGGAGATCACGCAAGC
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGG-TGTGGAGATCACGCAAGC
EST: gi|34983127|gb|CF557044.1|CF557044
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
EST: gi|10792297|gb|AV629663.1|AV629663
EST:     CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGT                         GTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG
genomic: CACTGAGTTCGAGGGCTATGACGAGGAGGAGACCGTGCGTgtgagtccct ... ccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccacgcgcgtgaggtccacacacatattcactcgtatatgttgaccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCGGCTCTGGATCTGGGCGCTGAG
                                       tgttgac  putative branch site (score: 3)
                                   tatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcggcaacatggtgcgggctgctgatggagggtttgttgcggacctccacgcgcgtgaggtccacacacatattcactcgtatatgttgaccgcgcgcagGTGATCATGTCGGGCAACCAGGAGCCCAAGGGTGTGGAGATCACGCAAGCGGCTCTGGATCTGGGCGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- ggcaaca
- - - - - - - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgttg