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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgtcgccgcgccaagctccctttctttccccaacaaccaccctctcctccctccctccctccctccctgccccctcccttccttccctccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTTCGGCCACATGCTCTCCAACGCCCTGTACGAGCGCCGCTTCGGGCCCTAC

Basic information

species Chlamydomonas reinhardtii
transcript EDP08231
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP08231 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: LOC_Os02g08520.1 (Oryza sativa), 3'ss of exon 2
---------------------aacgtcgccgcgccaa-gctccctttctttccccaacaaccaccctctcctccctccctccctcc-ctccctgccccctccc-ttccttccctccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTTCGGCCACATGCTCTCCAACGCCCTGTACGAGCGCCGCTTCGGGCCCTAC
                      |  | ||      |  |     ||   || |     |   |   | |          |   |   | || ||      |   | ||  |     |   |||||||||| |||||| ||||| |||||||| | ||||||||||||    | ||||    | |  |||||     ||| |||                     
gtgggtgtcccggaactctcggattttgctctagaaccggcgtattgagttgcttgttagttagggttttgggggggttttgatgtgcgccgtgtgtttgcagGTACCAGCGGCTGGTGTTCAGGCACAAACTGTACCAGCTGAGGGAGGAGAGGGACATGAAGCCCCAGGCATTCGCTAGCCTCGTCTCCGCGCTCCTCTAC---------------------

upper sequence: EDP08231 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GRMZM2G092975_T01 (Zea mays), 3'ss of exon 2
----aacgtcgccgcgccaagctccctttctttccccaacaaccaccctctcctccctccctccctccctccctgccccctccc-----ttccttccctccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTTCGGCCACATGCTCTCCAACGCCCTGTACGAGCGCCGCTTCGGGCCCTAC
      ||  |  ||   |  ||||| | || | | ||    |      || |       |  | |       ||   ||  |      | ||  |  |  |   |||||||||| |||||  |||||||||||||| | ||||||||||||   ||||| | |  | |  ||||      ||| |||                     
gtgagtcgcagttgccgaattctcccctcctctacacacgggctgttgccttcgtttcggcagcttaggattttgggtccctctgcagGTACCAGCGGTTGGTGTTCAGGCACAAGCTGTATCAGCTGCGGGAGGAGAGGGACATGAAGCCCGAGACCTTTGCCAGCCTTGTCTCTGCGCTCCTCTAC---------------------
















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|16073100|gb|BI875096.1|BI875096
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|161807776|gb|FC098889.1|FC098889
EST:     TCAGGACTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|15371985|gb|BI531411.1|BI531411
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|9458406|gb|BE452224.1|BE452224
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|15369050|gb|BI528476.1|BI528476
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|10126170|gb|BE724874.1|BE724874
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
EST: gi|15697559|gb|BI721864.1|BI721864
EST:     TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCG                         GCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT
genomic: TCAGGCCTGCAGACGGATGCCACCACGCTGCACCAGAAGCTCCAATTCCGgtgagtttag ... ccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctccctccctccctccctccctgccccctcccttccttccctccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTTCGGCCACATGCTCTCCAACGCCCTGTACGAGCGCCGCTTCGGGCCCTAC
       ctccctccctccctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgtcgccgcgccaagctccctttctttccccaacaaccaccctctcctccctccctccctccctccctgccccctcccttccttccctccgccctcagGCACAACCTGTACAAGCTGCGGGAGGAGCGCGACATGAAGCCCTCCACCTTCGGCCACATGCTCTCCAACGCCCTGTACGAGCGCCGCTTCGGGCCCTAC

- - - - - - - - - - - tttcttt
- - - - - - - - - - - - - - - - - acaacca