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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgcctgcattactgcaacttcgtttggtagttaaggtgtgaccggaccccaatcctgcctgaccctgcgctgctgctgttatcgctgcgtcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACATTGACAAAACCCTGGAGCGCTCGGAGCGCATCGTGGAGGACACGAAAGC

Basic information

species Chlamydomonas reinhardtii
transcript EDP04002
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|15699344|gb|BI723649.1|BI723649
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTNCATGCAGCAGCTGATG
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATG
EST: gi|6542430|gb|AV388214.1|AV388214
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTAGGAAG                         GCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGAAATCCAGG
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGG
EST: gi|15699343|gb|BI723648.1|BI723648
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTCCATGCAGCAGCTGAT
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGAT
EST: gi|14239537|gb|BG858353.1|BG858353
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTCCATGCAGCACCTGATGAAGAAGGGCCGGACGGACATCCAGGACA
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACA
EST: gi|15699342|gb|BI723647.1|BI723647
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGNACGGACATCCAGGACA
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACA
EST: gi|16432160|gb|BI997386.1|BI997386
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACA
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACA
EST: gi|15694620|gb|BI718925.1|BI718925
EST:     GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAG                         GCATGTCCATGCAGCAGCTGATGAAGAAAGGGCCG-ACGGACAT
genomic: GGCAGACCTGCTGAACGGTGCCGCGCCGGAGGCGGAGCAGGCGTTGGAAGgtgggagggg ... tcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAA-GGGCCGGACGGACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccccaatcctgcctgaccctgcgctgctgctgttatcgctgcgtcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACATTGACAAAACCCTGGAGCGCTCGGAGCGCATCGTGGAGGACACGAAAGC
            gcctgac  putative branch site (score: 3)
                                           cgtcccct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgcctgcattactgcaacttcgtttggtagttaaggtgtgaccggaccccaatcctgcctgaccctgcgctgctgctgttatcgctgcgtcccctgcagGCATGTCCATGCAGCAGCTGATGAAGAAGGGCCGGACGGACATCCAGGACATTGACAAAACCCTGGAGCGCTCGGAGCGCATCGTGGAGGACACGAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - -actgcaac
- - - - - - - - - -ttcgttt
- - - - - - - - - - - - - - - - - aggtgtg
- - - - - - - - - - - - - - - - - - - - - - - accccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt