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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtatagctttgctttacctgtttacctcaagttgcagctgattttcacaaaattcataacagGATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG

Basic information

species Oryza sativa
transcript LOC_Os01g72870.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72870.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G133959_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------------------------------------------------------gtaatgtatag---ctttgctttacctgtttacctcaa-gttgcagctgattttcacaaaattcataacagGATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG
                                                                                                                             |  ||| |||   | ||      | | ||||  |       | | |||||||| | | |  | || |||||||   |||| ||| ||||||||||||||| ||||||||||||| ||||||
gtaacttacacagcttaactgatgtttgtttcacattcaatgcaactatgagtgccaacaacccgacaggaaaccttgtaatgcatgtacattagaggcccttaagtgtctgggttacaatttaattctgtctagattccttatccagcatatttatattgccagcggaactgattttaatacatcttatgacagGATTGCGAGCATGGGCGATTGTTTTCGTTGTATGAACAAATTGACCACAAG
















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|27576528|gb|CA999222.1|CA999222
EST:     CGATTGGGCATATTTCACATAGCAAAAAG                         GATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG
genomic: CGATTGGGCATATTTCACATAGCAAAAAGgtaatgtata ... ttcataacagGATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG
EST: gi|58677445|gb|CK066132.1|CK066132
EST:     CGATTGGGCATATTTCACATAGCAAAAAG                         GATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG
genomic: CGATTGGGCATATTTCACATAGCAAAAAGgtaatgtata ... ttcataacagGATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctttacctgtttacctcaagttgcagctgattttcacaaaattcataacagGATGCAGAGCGTGGACGATTGTTTTCGTTGCATGAACAAATTGATCACAAG
                            agctgat  putative branch site (score: 4)
                                 attttcacaaaatt  TA-rich tract