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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtatgtcgacgacggctttcttccctcgttatctccccaactcctgactcgtgctctcgtgccctacgcatccctgcttcacctcctcaacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGGAGTGCCGTGCACTGCGGGAGCCTCACTCTTGCAAATGCGTGTTAGGACA

Basic information

species Chlamydomonas reinhardtii
transcript EDP04368
intron # 2
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|6545757|gb|AV391541.1|AV391541
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGTCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAAGAAGCAGCT-GTCTGTGGA-TGCTGN
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161817517|gb|FC104967.1|FC104967
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|9027611|gb|BE237651.1|BE237651
EST:     ACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: ACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|6542406|gb|AV388190.1|AV388190
EST:     AGCTGGAGCAGGCGGCGCAGCAGACACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCG
EST: gi|14230459|gb|BG849275.1|BG849275
EST:     AGCTGGAGCAGNCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|22067351|gb|BQ817492.1|BQ817492
EST:     ACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: ACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|16437014|gb|BM002234.1|BM002234
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|12251794|gb|BF861657.1|BF861657
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|23365486|gb|BU653306.1|BU653306
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161804457|gb|FC092750.1|FC092750
EST:     AGTTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161817516|gb|FC104966.1|FC104966
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGAGGACGATGACGAG                         TTGTTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161804308|gb|FC089676.1|FC089676
EST:     AGCTGGAGCAGGCGGGGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTTAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161804309|gb|FC089677.1|FC089677
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|14230460|gb|BG849276.1|BG849276
EST:     AGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161814538|gb|FC102343.1|FC102343
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161824160|gb|FC107769.1|FC107769
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|15704471|gb|BI728776.1|BI728776
EST:     CGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: CGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161811563|gb|FC098041.1|FC098041
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|15704472|gb|BI728777.1|BI728777
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGNGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|15692193|gb|BI716498.1|BI716498
EST:     ACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: ACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161804458|gb|FC092751.1|FC092751
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCG
EST: gi|10126796|gb|BE725500.1|BE725500
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161795839|gb|FC087641.1|FC087641
EST:     AGCTGGAGCGGGCGTCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161801218|gb|FC087064.1|FC087064
EST:     AGCTGGAGCANGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161796870|gb|FC083226.1|FC083226
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161812831|gb|FC095111.1|FC095111
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGNGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161820035|gb|FC109708.1|FC109708
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|22055470|gb|BQ811839.1|BQ811839
EST:     GCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACTGATGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTG
genomic: GCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGAC-GATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTG
EST: gi|161794436|gb|FC080765.1|FC080765
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161795840|gb|FC087642.1|FC087642
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
EST: gi|161820034|gb|FC109707.1|FC109707
EST:     AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGATGACGAG                         CTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG
genomic: AGCTGGAGCAGGCGGCGCAGCAGCCACTGCCCGCGGACGACGACGATGAGgtgaggggtc ... caacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgactcgtgctctcgtgccctacgcatccctgcttcacctcctcaacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGGAGTGCCGTGCACTGCGGGAGCCTCACTCTTGCAAATGCGTGTTAGGACA
 tcctgac  putative branch site (score: 2)
                            tccctgcttcacctcc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcgtatgtcgacgacggctttcttccctcgttatctccccaactcctgactcgtgctctcgtgccctacgcatccctgcttcacctcctcaacccacagCTGCTGGACTAAGCGTTGCGGCGAGGAAGCAGCTTGCCTGGGGAATGCTGGAGTGCCGTGCACTGCGGGAGCCTCACTCTTGCAAATGCGTGTTAGGACA

- cgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctacgca