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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggctccaaatttaaatagattcacatggttctagtctttttgccattgatctcatgtaatctgccatatgcttcttcaattggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAAGCCATACA

Basic information

species Oryza sativa
transcript LOC_Os02g35870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G070708_T04 (Zea mays), 3'ss of exon 2
------gtgggctcca----aatttaaatagattcacatggttctagtctttttgccattgatctcatgtaatctgccatatgcttcttcaattggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAAGCCATACA-----------------------------------------
      ||||| ||||    |||||   |   ||  |||| ||      |  ||    ||||    |   |||||   ||||   | ||    |||||  |||||||||||| ||||||||||| |||||||| |||||||||||||| || |||||||||||                                         
gtgggtgtgggttccatttcaatttgtgtgatttgccatgatttcttattacttagttttgactgaa---aatctctaatatatctttt----tggat--gcagAAGCATGGGGAAGACAAGGATATAATGGGAGAGGTAACCAAGACTCATGAAGCCATACAGTGAGCTCCTTCAACTTCATATGGGGTTCAACTTAACCATG

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G013079_T01 (Zea mays), 3'ss of exon 2
gtgggctcca----aatttaaatagattcacatg-gttctagtctttttgccattgatctcatgtaatctgccatatgcttcttcaattggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAAGCCATACA
||||| ||||    || ||   |   ||| ||||  ||||  |  ||| |   ||||    |   |||||   ||||   |      ||||||  |||||||||||| ||||||||||| |||||||| ||||||||||||||||| ||||| |||||
gtgggttccatttcaacttgtgtgatttcccatgcattcttattatttgggttttgactgaa---aatctctaatataact------ttggat--gcagAAGCATGGGGAAGACAAGGATATAATGGGAGAGGTAACCAAGACCCATGAAGCTATACA

upper sequence: LOC_Os02g35870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G070708_T02 (Zea mays), 3'ss of exon 2
------gtgggctcca----aatttaaatagattcacatggttctagtctttttgccattgatctcatgtaatctgccatatgcttcttcaattggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAAGCCATACA
      ||||| ||||    |||||   |   ||  |||| ||      |  ||    ||||    |   |||||   ||||   | ||    |||||  |||||||||||| ||||||||||| |||||||| |||||||||||||| || |||||||||||
gtgggtgtgggttccatttcaatttgtgtgatttgccatgatttcttattacttagttttgactgaa---aatctctaatatatctttt----tggat--gcagAAGCATGGGGAAGACAAGGATATAATGGGAGAGGTAACCAAGACTCATGAAGCCATACA

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|58601085|gb|CK011613.1|CK011613
EST:     GGCAGGATAGGGAGTTGCAACTCATATCAGAGGATTGCAATACAAAGAGG                         AAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAA
genomic: GGCAGGATAGGGAGTTGCAACTCATATCAGAGGATTGCAATACAAAGAGGgtgggctcca ... ggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAA
EST: gi|58678637|gb|CK067324.1|CK067324
EST:     GGCAGGATAGGGAGTTGCAACTCATATCAGAGGATTGCAATACAAAGAGG                         AAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAA
genomic: GGCAGGATAGGGAGTTGCAACTCATATCAGAGGATTGCAATACAAAGAGGgtgggctcca ... ggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgccattgatctcatgtaatctgccatatgcttcttcaattggatttgcagAAGCATGGAGAAGACAAGGACATAATGGGTGAGGTAACCAAGACCCACGAAGCCATACA
       cattgat  putative branch site (score: 4)
                 atgtaat  TA-rich tract