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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtcagggacttgtgtggcttgcatggccctcctggtcgctgtggtcgctcgctgactgggagcccgcgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAGATGATTGGTGACATTATTCCCGTGGAGATTACCGTCTACGAG

Basic information

species Chlamydomonas reinhardtii
transcript EDP06359
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDP06359 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: PP1S204_118V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------gcaagtcagggacttgtgtggcttgcatggccctcctggtcgctgtggtcgctcgctgactgggagcccgcgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAAC--GCTCAGACCTCCAAGATGATTGGTGACATTA-TTCCCGTGGAGATTACCGTCTACGAG------
                            ||  ||  | || |  ||  | ||| |||        | |||| ||||| |  |      || ||  | | ||  |  ||| ||  ||   ||   || |  || |   |||   |  ||||     || ||     |       ||   ||   |    || |||  |  |          
aattcagcgatttttcggtttcgtgtttgct-gttggagattgatggag-ttgaatgatgtggaggatcgcagtggttgggc-----ttgtgaagctg-gcattagagGCTGGAAAGGCTAC--CCCTGCGCCACCTGTAGGTCCAGCTCTCGGGTCGAAAGGAGTCAACATTATGGCTTTTTGCAAGGAGTACAATGCAAAGACCGCAG
















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|9460047|gb|BE453037.1|BE453037
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|22061479|gb|BQ814276.1|BQ814276
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|14228058|gb|BG846874.1|BG846874
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|10776277|gb|AV632957.1|AV632957
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|14242515|gb|BG861331.1|BG861331
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|14232323|gb|BG851139.1|BG851139
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|22076132|gb|BQ824908.1|BQ824908
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCAAAATTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|15703713|gb|BI728018.1|BI728018
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|16072714|gb|BI874710.1|BI874710
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|14228059|gb|BG846875.1|BG846875
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|15373308|gb|BI532734.1|BI532734
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|16436205|gb|BM001425.1|BM001425
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|10776269|gb|AV632949.1|AV632949
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|6544356|gb|AV390140.1|AV390140
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|15369242|gb|BI528668.1|BI528668
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
EST: gi|14232134|gb|BG850950.1|BG850950
EST:     CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAG                         GGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG
genomic: CTGGCAAGGCCAACCCCGCTCCTCCTGTGGGCCCCGCTCTTGGTTCCAAGgcaagtcagg ... cgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggccctcctggtcgctgtggtcgctcgctgactgggagcccgcgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAGATGATTGGTGACATTATTCCCGTGGAGATTACCGTCTACGAG
                            cgctgac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtcagggacttgtgtggcttgcatggccctcctggtcgctgtggtcgctcgctgactgggagcccgcgcgctgcagGGTGTGAACATTATGGCCTTTTGCAAGGAGTACAACGCTCAGACCTCCAAGATGATTGGTGACATTATTCCCGTGGAGATTACCGTCTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT