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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgtattcagttctttatactgtatgaatgcttgtttgtcaatcctggaacatatcgttatgtgccacacaagcaggatttgccatttaacttttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG

Basic information

species Oryza sativa
transcript LOC_Os01g59930.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 3
gtaaattgtattcagttc--tttatactgtatgaatgcttgtttgtcaatcctggaacatatcgttatgtgccacacaagcaggatttgccatttaacttttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG
|||||   |||| || ||  |||    |||  | || ||| ||    |  | | | ||   || |    || ||||| ||            |||||   || | || |  |||||||| || ||||| |||||||| || |||||||| || |||||||||||||||||| ||||||||||||||||||||
gtaaa---tatttagatcgattttccttgttcggatacttttt----atgctttgcac---tcatatgttgacacaccagt---------tctttaatccttttgatcacacagATGTATCCCCAAGGGAGAATGTCCCATCATTTCCGCGAGATGAAAGTTGGTGATTATTTGTCTGTGAAGGGACCTAAG

upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G29720.1 (Glycine max), 3'ss of exon 3
gtaaattgtattcagttctttat-actgtatgaatgcttgtttgtcaatcctgga----acatatcgttatgtgccacacaagcaggatttgccatttaacttttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG
      | |||||||  |    | |||  ||   | ||| ||| | | |  ||      |  | | ||  | | ||         || ||| |  | |||  | |    | ||  |||||||||| |||||||| |||||||||||||||||||| |||   |||||||| ||  | |||||||| ||||| |||
-----gtatattcagaacccattgacttcatccttacttttttctaacttatgtgcattattttttgtcttctcccttgatgattgggttttctgtctaaaatatgcattcat-tagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCTGTGAAAGGACCCAAG

upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 3
gtaaattgtattcagt-tctttatactgtatgaatgcttgtttgtcaatcctggaacatatcgttatgtgccacacaagcaggatttgccatttaactt----ttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG
      | |||||||  ||  |  |||  |    |   | |||   ||     |  |||    || |||      |    |  |||||   ||     |    |   ||||    |||||||||| |||||||| |||||||||||||||||||| |||   |||||||| ||  | || ||||| |||||||||
-----gtatattcagaatccattgacttcacccttatgttttttctaacttatgtgcattattttttgtcttctcccttgattatttggttttcggtctaaaatatgcatacattagATGTACCCACAAGGAAGGATGTCACACCATTTCCGTGAGATGCGTGTTGGTGACTACCTTTCCGTGAAAGGACCTAAG

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|58685456|gb|CK074143.1|CK074143
EST:     CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG                         ATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
genomic: CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAGgtaaattgta ... cataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
EST: gi|58684839|gb|CK073526.1|CK073526
EST:     CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG                         ATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
genomic: CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAGgtaaattgta ... cataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
EST: gi|58595179|gb|CF993487.1|CF993487
EST:     CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG                         ATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
genomic: CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAGgtaaattgta ... cataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
EST: gi|427743|gb|D23879.1|D23879
EST:     CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG                         ATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
genomic: CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAGgtaaattgta ... cataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
EST: gi|117244284|gb|CT843075.1|CT843075
EST:     CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAG                         ATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT
genomic: CCCCTACTACATTGGATTCTGATCTAGGGCATTTTGAGCTTGTTATTAAGgtaaattgta ... cataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgttatgtgccacacaagcaggatttgccatttaacttttctcataatgcagATGTACCCTCAAGGAAGAATGTCACACCATTTCCGTGAAATGAAAGTTGGTGATTATATGTCTGTGAAGGGACCTAAG
                                atttaac  putative branch site (score: 3)
                                      cttttctcat  CT-rich tract
                                atttaactttt  TA-rich tract