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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtaatgtctaaatttaggtagtttggtttggttgatgtgcgctagcagtttgatgatagttttgccaatttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAGGGACACGGCTGGTATCTTCAGAGTCCACCAATTCGAAAAGATTGAGCAA

Basic information

species Oryza sativa
transcript LOC_Os01g37837.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37837.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 6
gtgggtaatgtctaaatttaggtagtttggtttggttgatg-tgcgctagcag-tttgatgatagttttgcca-----atttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAGGGACACGGCTGGTATCTTCAGAGTCCACCAATTCGAAAAGATTGAGCAA
||| ||||| || |  || || |  |||   ||  ||  ||   | ||| ||  ||| || |||  |     |     || |||||||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||| ||||||||||||||||||||||| || ||||| || || |||
gtgagtaatttcgatcttcagtttctttatctt--ttagtgacacactatcaaatttaatcataaataaattacatacatatagATATGCTGGGTACTCCACATGCTTCCGGAAGGAAGCTGGTTCGCATGGAAGGGACACAGCTGGTATCTTCAGAGTCCACCAGTTTGAAAAAATCGAACAA
















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|163920929|gb|EG710103.1|EG710103
EST:     TGTGCGTATCATCTAGGTGATCGAATTTATCCTGCTGAATTGCCAATTAG                         ATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG
genomic: TGTGCGTATCATCTAGGTGATCGAATTTATCCTGCTGAATTGCCAATTAGgtgggtaatg ... gccaatttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG
EST: gi|33796179|gb|CF323955.1|CF323955
EST:     TGTGCGTATCATCTAGGTGATCGAATTTATCCTGCTGAATTGCCAATTAG                         ATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG
genomic: TGTGCGTATCATCTAGGTGATCGAATTTATCCTGCTGAATTGCCAATTAGgtgggtaatg ... gccaatttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG
EST: gi|27577321|gb|CB000016.1|CB000016
EST:     TGTGCGTATCATCTAGGTGANNNNNNNNNNCCTGCTGAATTGCCAATTAG                         ATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG
genomic: TGTGCGTATCATCTAGGTGATCGAATTTATCCTGCTGAATTGCCAATTAGgtgggtaatg ... gccaatttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttggtttggttgatgtgcgctagcagtttgatgatagttttgccaatttagATATGCTGGATATTCCACCTGCTTCCGGAAAGAAGCTGGTTCACATGGAAGGGACACGGCTGGTATCTTCAGAGTCCACCAATTCGAAAAGATTGAGCAA
                             gtttgat  putative branch site (score: 5)
                                         ttttgcc  putative PPT
                                     atagtttt  TA-rich tract