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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtgtaatcttatcttttatttttactcgcctgtctacttttaagaaacttttcctctcttactgatacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G068755_T03 (Zea mays), 3'ss of exon 28
gtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
||||| |  |    |  || ||   || | ||   | || | ||  |   | ||| ||    ||   ||||| |   |  ||    ||||||||  | ||||||||||||||||||||||||||||||||| |||||| ||||  || | |||||||| |||||||| ||||
gtatgtttca--tctgcctattccattcattcatatttccatttaatgctgcaacattctaactacaactgaatttattgtttggtgtagGTTGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCTATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G009849_T01 (Zea mays), 3'ss of exon 11
gtatggtgtaatcttatcttttatttttactcgcctgtctactt--ttaagaaacttttcctctcttactga-tacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
||||| |  |     | || ||| ||| | ||  || || | ||  |   | | | ||  | |    ||||| |   |  ||    |||||| |  | |||||||||||||||||||||||||||||||||||||||| ||||  || | |||||||| |||||||| ||||
gtatgtttca--tccacctattactttcattcatctttccatttaatgctgcagcattctcccaacaactgaatttattgtttggcgtagGTGGGAAGGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTATCAGAAAGGCTGAAACTGTCTACTGTACATGAAG
















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|88370934|gb|CI595046.1|CI595046
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTG                         GTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgta ... ttgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
EST: gi|58686785|gb|CK075472.1|CK075472
EST:     CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTG                         GTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA
genomic: CTGCTGAATCCTTTATGAATGAAATTCTCAAGATTTGTGGCCAAGATGTGgtatggtgta ... ttgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgtctacttttaagaaacttttcctctcttactgatacgtcattgatggtagGTTGCGAAGAACTTGAAAGATTTGCCATCACCTACTTTGGCCATTGTAGCAGAGCGGTTAAAACTGTCCACTGTACACGAAG
          ttttaagaaactttt  TA-rich tract