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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcccttttctcggttcggtttggttggtgggggaagggggtaattctaattctgggcttgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC

Basic information

species Oryza sativa
transcript LOC_Os01g56890.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132978_T01 (Zea mays), 3'ss of exon 1
--------gtgcgttcccttttctcggttcggttt-ggttgg--tgggggaagggggtaattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
           |    |||   | | | | | ||  ||||||  ||| ||    || |||||||     | || |   ||||| |||||||||| ||||||||||||||||| |||||||||||||  | | ||| || |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
gtacgcatacacccctcctcccccctgcttgattgaggttgggttggtggggaaggctaattctggaggttggttggttgctccgcagCATCCGAATCCGATAGGGGAGGGGCTGGCCATGGAGGCGTTCGCGGAAGCCGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTCA

upper sequence: LOC_Os01g56890.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G127453_T02 (Zea mays), 3'ss of exon 1
----gtgcgttcccttttctcggttcggtttggttggtg--ggggaaggggg-taattctaattctgggct---tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
    || ||  ||  |  | | | | | || || | |||  || || |  || |||||||     | || |   ||||| |||||||||||||||||| || |||||| |||| ||||||||  | | |||||| |||||||||||||||||||||||||| ||||| ||||| ||  ||||  
gtacgtacgcacctgtcccccagcttgattggggttgtgttggtgaggaaggctaattctggaggttggttggttgctccgcagCATCCGGATCCGATTGGCGAGGGGCTGGCTATGGAGGCGTTCGCGGAGGCAGCCGGGCCGGAGTGCATCGTGCCCGGACAGCAAGCGCCTCTAAGGCTTA
















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|88827005|gb|CI777570.1|CI777570
EST:     TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAG                         CATCCGGATCCGATAGGGG
genomic: TCCGCGTCGCGCAGGACGATTATTCCGCCTACGCCCTCGCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGG
EST: gi|33797362|gb|CF324543.1|CF324543
EST:     GCCGTCATGAAG                         CATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG
genomic: GCCGTCATGAAGgtgcgttccc ... tgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggtttggttggtgggggaagggggtaattctaattctgggcttgctctgcagCATCCGGATCCGATAGGGGAGGGGTTGGCCATGGAGGCTATGGTGGAGGCGGCCGGGCCGGAGTGCATCGTGCCCGGGCAGCAGGCGCCGCTGCGGCTGC
                              ttctaat  putative branch site (score: 2)
                                           cttgctct  putative PPT
                           taattctaatt  TA-rich tract