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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgtagggcacccatgccgcccccaaggtaccaggcagcccctct...

Basic information

species Chlamydomonas reinhardtii
transcript EDP09753
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP09753 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 5'ss of exon 4
GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgtagggcacc-catgccgc-ccccaaggtaccaggcagcccctct-----------------------
||| || || || ||  |||| |||||||||||||| |||||||| ||||| ||||||   || | |     |    | |  || |      |     || | |  ||   ||| || ||   |   |  | |     || ||||     | |                         
GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTGgtaagattgatctttacatctcattattaggatctccgcgccttatctgtatacaat-tagcgctccatgttttgtactctgttataacagggttaactttgaacctatgtgtgatattttgcag

upper sequence: EDP09753 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 5'ss of exon 4
GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgtagggcacccatgccgcccccaaggtaccaggcagcccctct-------------------------------------------
||| || || || ||  |||| |||||||||||||| |||||||| ||||| ||||||   || | |  |||     ||    ||  |||        ||      | | ||     | |  | | |     ||| | |  |       ||||                                           
GTCTGGTTCAGTCTGTTTGGATGTCATCAACCAGACATGGAGCCCAATGTTTGgtaagattgatctt-tgcatttcattattaggatcgacaaccagttcattct-ctctgtgccttatctgtacagtta--aagcttcatgttttgtactctgttataacagggttaacttgaacctgtgtgtgatattttgcag

upper sequence: EDP09753 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgt-agggcacccatg-ccgcccccaaggtaccaggcagcccctct
||| || ||||| || || || || || |||||||||||||||||||||||||||| |  |    |           | |    |   | || |   |  |  |      || | |  |   |||          || ||    |          
GTCAGGTTCTGTTTGTCTAGATGTTATTAACCAGACCTGGAGCCCGATGTTCGgtatgatcataacaaatggaacaatatacaagatagttttaactcctgttagtttttgttatgttaattatgatttggatttagttattcag----------

upper sequence: EDP09753 (Chlamydomonas reinhardtii), 5'ss of exon 4
lower sequence: EFJ34378 (Selaginella moellendorffii), 5'ss of exon 4
GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgtagggcacccatgccgcccccaaggtaccaggcagcccctct
||| || || |||||| ||||||| |||||||| || |||||||| |||||||||||    ||   ||| |     ||||   | |  ||  | | | | || |                                                 
GTCCGGCTCCGTGTGCTTGGACGTGATCAACCAAACGTGGAGCCCAATGTTCGgtaaagatga-tttgctcg-aaagtttcaagctctgaaagtt-cgttggtatag----------------------------------------------

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|23365360|gb|BU653180.1|BU653180
EST:     GGGGTCTGTGTGCCTGGATGTCATCAATCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|10788266|gb|AV644938.1|AV644938
EST:     GGGGTCTGTGTGCCTGGATGTCATCAATCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|8400882|gb|BE056516.1|BE056516
EST:     GGGGTCTGTGTGCCTGGATGTCATCAACCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|49466669|gb|BP094582.1|BP094582
EST:     GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|16071742|gb|BI873738.1|BI873738
EST:     GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|22068907|gb|BQ818660.1|BQ818660
EST:     GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
EST: gi|15699843|gb|BI724148.1|BI724148
EST:     GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCG                         ACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA
genomic: GGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcga ... accgccgcagACCTGGTGAACATCTTCGAGGTGTTCCTGCCGCAGCTGCTGCTGTACCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGGGGTCTGTGTGCCTGGACGTCATCAACCAGACCTGGAGCCCGATGTTCGgtaagcgcgagcctgcgcacggggtttgggggtgcgattgatgcctcggcaagcaccgtagggcacccatgccgcccccaaggtaccaggcagcccctct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcccc