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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcaagattgtttgaaccctggttttgctagtccacgaaactaatcagctctttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA

Basic information

species Chlamydomonas reinhardtii
transcript EDO97462
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: LOC_Os03g57940.3 (Oryza sativa), 3'ss of exon 3
--------gtcagcaagattgtttgaaccctg--gttttgctagtccacgaaactaatcagctctttg---------cgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
             | |  |   ||| || |||  | | || ||||  |   |  |  | || | | ||         |  | |||| ||  | |||||||||||||| ||||||||||| || |||||||| || || |||||||||   || ||| |
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagttt-ttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCA

upper sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: LOC_Os03g57940.4 (Oryza sativa), 3'ss of exon 3
--------gtcagcaagattgtttgaaccctg--gttttgctagtccacgaaactaatcagctctttg---------cgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA--------------------------
             | |  |   ||| || |||  | | || ||||  |   |  |  | || | | ||         |  | |||| ||  | |||||||||||||| ||||||||||| || |||||||| || || |||||||||   || ||| |                          
gtttcatttcttaccacctcaattggacactgaagctctgttagtttagttagttt-ttagatatctgaatgaatatcctgtagGTTGCGCTTAAATTTGAGCACCGAAGCAGTAAAGGATGTAACTATGGCCCTCCATACGAGTGGCAGGTTTACCAGTAAGAATTTCACACAATCTATCCCT

upper sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: GLYMA08G47680.2 (Glycine max), 3'ss of exon 2
gtcagcaagattgtttgaaccctg--gttttgctagt---ccacgaaactaatcagctcttt-gcgcg-cagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
|| |       | ||   |||     ||||    | |   | |||  | | |     ||||| | |   ||||||||||| |||||||||||| | | ||| |||||||| |||||||| || || |||||||||   ||||||||
gtaaaagcttctcttgttacctcactgtttgaacaattttctacggcattgactgattctttcgtgtttcagGTGGCTTTGAAATTTGAGCACAGGAACAGCAAAGGCTGTAACTATGGCCCTCCTTACGAGTGGCAAGTGTACAA

upper sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
-------gtcagcaagattgtttgaaccctggttttgctagtccacgaaactaatcagctctttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
       ||  | ||||||   | |       |    ||  ||   |   || ||||    |  |    ||||| ||||| || ||||| ||| | ||||||||||| |||||||||||||| || || ||||||   || |||| 
gtagactgttcg-aagatttgctcagttggattggctcttttctcagcggctgatcaaagat--gttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: EDO97462 (Chlamydomonas reinhardtii), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
-------gtcagcaagattgtttgaaccctggttttgctagtccacgaaactaatcagctctttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
       ||  | |||||| | | |     | ||   ||  ||   |   || ||||    |  |    ||||| ||||| || ||||| ||| | ||||||||||| |||||||||||||| || || ||||||   || |||| 
gtagactgttcg-aagattttctcagttg-gattgctcttttctcagcggctgatcaaagat--gttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|14226523|gb|BG845355.1|BG845355
EST:     CCGCAGAGTGTCGTCAACATAGCAAAAGGACGGCCCCCAGGCGAACCCAG                         GTGCCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCGACTATGGGGC
genomic: CCGCAGAGTGTCGTCAACAAAGCAAAAGGACGGCCCCCAGGCGAACC-AGgtcagcaaga ... ttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGG-C
EST: gi|23366719|gb|BU654538.1|BU654538
EST:     GCCGCAGAGTGTCGTCAACAACGCAAAAGGACGGCCCCCAGGCGAACCAG                         GTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCC
genomic: GCCGCAGAGTGTCGTCAACAAAGCAAAAGGACGGCCCCCAGGCGAACCAGgtcagcaaga ... ttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttgaaccctggttttgctagtccacgaaactaatcagctctttgcgcgcagGTGGCTTTAAAATTTGAGCACCGCAGCAGTAAAGGCTGCAACTATGGGCCCCCCTACGAGTGGTCCGTGTACAA
                               aactaat  putative branch site (score: 2)
                                         ctctttgc  putative PPT
                              aaactaat  TA-rich tract