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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggccgctgcggtaggctaccgcaatgcccaagagcggactcttgttctgttgctgaccggtacccggcctcgttacgcggctcctccatcgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAGGTGACCACCACCGAGCCGAAGAAGGCCAAGAAGTAAATGTCCTTTACTT

Basic information

species Chlamydomonas reinhardtii
transcript EDP03110
intron # 5
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|9441085|gb|BE441581.1|BE441581
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCG
EST: gi|161802066|gb|FC093775.1|FC093775
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|16073614|gb|BI875610.1|BI875610
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|16071860|gb|BI873856.1|BI873856
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATC
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATC
EST: gi|161796578|gb|FC082388.1|FC082388
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|14225877|gb|BG844693.1|BG844693
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGGTGTGATCCAGGAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|161816445|gb|FC102177.1|FC102177
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|6552075|gb|AV397859.1|AV397859
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|161794670|gb|FC077918.1|FC077918
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|9459700|gb|BE452865.1|BE452865
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCT
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCT
EST: gi|161815712|gb|FC102672.1|FC102672
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|161805951|gb|FC089512.1|FC089512
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|161800461|gb|FC082823.1|FC082823
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|161801948|gb|FC090745.1|FC090745
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGGTGTGATCCAGAAGGAGAAGAACCAAATCA-G
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|14240276|gb|BG859092.1|BG859092
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|6546204|gb|AV391988.1|AV391988
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|10127484|gb|BE726188.1|BE726188
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
EST: gi|9441349|gb|BE441712.1|BE441712
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTC
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTC
EST: gi|23366290|gb|BU654110.1|BU654110
EST:     AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAG                         GTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG
genomic: AGATCAAGTCGGTGGGCACCTACGAGTGCACCATCCGCCTGCACCCCGAGgtgaggagcg ... cgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgttgctgaccggtacccggcctcgttacgcggctcctccatcgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAGGTGACCACCACCGAGCCGAAGAAGGCCAAGAAGTAAATGTCCTTTACTT
      tgctgac  putative branch site (score: 2)
                                    ctcctccatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggccgctgcggtaggctaccgcaatgcccaagagcggactcttgttctgttgctgaccggtacccggcctcgttacgcggctcctccatcgcgccgcagGTTGTGGGCACCTTCTCGGTTGTGATCCAGAAGGAGAAGAACCAAATCAAGGTGACCACCACCGAGCCGAAGAAGGCCAAGAAGTAAATGTCCTTTACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - atgccca