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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agggagcattttatatatgttttacataaaaatgcataaatgctgtttttgcagtcttatttgccacttattattttgagtttcttctgttctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTC

Basic information

species Oryza sativa
transcript LOC_Os02g18820.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G353548_T04 (Zea mays), 3'ss of exon 4
agggagcattttatatatgttttacataaaaatgcataaatgctgtttttgcagtcttatttgccacttattattttgagttt---cttctgttctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTC
    ||        || | |||  || ||  ||   |     || | ||||||  |  || |  |        |    | | |   || ||   ||||| ||||| || |||||||| |||| | |||| || || ||||| || ||||||||||| || || ||||| ||||| ||||| || ||||||||||||||||| |
---tagttgacagcatttttttatcaaaatgatatttttgatctttctttgcatcccaatattacctcagaagtcagaaatgtaagctgctaacctattgcagGTCAGGTACCATCCTTTACATTCTGACATTCTGGCTAGTGGAAGTTTGGATCATGAGGTTCGTCTGTGGGATGCTAATACTTCAGACTGTATTGGATCAC

upper sequence: LOC_Os02g18820.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 4
agggagcattttatatatgttttacataaaaatgcataaatgctgtttttgca--gtcttatttgccacttattattttgag--ttt---cttctgttctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTC
      |||| | ||| | |||   | || |||  | ||||| | |||||| |  |||||     ||   ||| | ||  |   |||   || ||    |||| ||||| || || |||||||||| | |||| ||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| || |||||||||||||| || |
------cattgtttattt-tttgttacaagaataaacaaatggtctttttgaactgtctttgcatcccaatatcacttaaaaaatttaagctgctaacatattgcagGTCAGGTATCATCCATTACATTCTGACATCCTGGCTAGCGGAAGTTTGGATCATGAAGTTCGTCTATGGGATGCTAATACTTCAGACTGTATTGGGTCAC
















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|58671891|gb|CK060577.1|CK060577
EST:     CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTG                         GTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT
genomic: CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTGgtatgattat ... tctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT
EST: gi|29674170|gb|CB670445.1|CB670445
EST:     CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTG                         GTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT
genomic: CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTGgtatgattat ... tctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT
EST: gi|58671698|gb|CK060384.1|CK060384
EST:     CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTG                         GTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT
genomic: CTGGGAAATGTTTGAAAGTGCTGAGTGGACATCGGCGCACGCCTTGGGTGgtatgattat ... tctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgcagtcttatttgccacttattattttgagtttcttctgttctatttcagGTTAGATACCATCCATTACTTCCTGATATCCTTGCTAGCGGTAGTTTGGATCAGGAAGTCCGTCTTTGGGACGCTAAAACCTCAGACTGTATTGGATCTC
                                   tttcttctgttctatt  CT-rich tract
                      ttattattttgagttt  TA-rich tract