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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcacggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGGTTCGTCGCTACCGACATCACTTACATATAT

Basic information

species Oryza sativa
transcript LOC_Os05g41110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044137_T02 (Zea mays), 3'ss of exon 3
gtaagtttgt-ttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcacggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGGTTCGTCGCTACCGACATCACTTACATATAT
|||||      |||| |||| |       |||| | |||   ||| |  | |  ||| |  ||  ||  |       |  || |||||  ||   |||   | | | |||          |||||||||||||||||||||| ||||||||||||||||||||| |||||||||||||||| ||||||||||| |                               
gtaaggccaccttcaccctttcagg---attatctattgcaagat-gtgttttgatttagttatttgctag------tatgtaatata--ttaacact---tttttgact----------tttcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACAGGGTGTGCTGCCTCAGTATCATCGACCCAG-------------------------------

upper sequence: LOC_Os05g41110.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 3
-------------gtaagtttgtttcatccttccgaaccatttatgttttgtgtgatagcatctgtattcatctacatgtcac--ggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGGTTCGTCGCTACCGACATCACTTACATATAT
              | | | || || || | |    |  |      ||   || |       |  |   ||| ||  |||      |     || |       |    | ||     ||   | |||||||| | | ||||||| ||||| || || ||||||||||||||||||||||| ||  ||   ||   ||||| |||||| |                               
gtaagtggcggtcctcaatatgcttgatgcctagtcaataccggc-ttccatggggctttggcgctgcgcatttatttgttgttgagcgcacccattgcccgctgctttcctcaccttccctccgtgccttc-cctccagACAACGTTGACCTGGGCACTGCCTGCGGCAAGTACTACCGCGTCAGCGTGCTGGCCATCACCGACCCCG-------------------------------
















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|88400326|gb|CI591016.1|CI591016
EST:     TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAA                         ACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC
genomic: TGAGTATTACGCCATGTTGGGAAAAGTTAGCGTTCACCATTTCCATGGAAgtaagtttgt ... tcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttccgtgatatagtttggtactgtatgtcttactgtgccttcgctttcagACAATGTTGATCTTGGAACTGCCTGCGGCAAGTACTACCGGGTGTGCTGCCTCAGCATCATCGACCCTGGTTCGTCGCTACCGACATCACTTACATATAT
                               gtcttac  putative branch site (score: 3)
                                          ccttcgctttc  putative PPT
            atatagttt  TA-rich tract