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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaatgtaaacaattcaatggtgtataccttttctggcagtttcttgttctttgattccataatataataaaaggagctgagaatttcctcctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACCTTGATGGGAAATTTTTAGCAACAGAGAATTTCTACCATACTTCCAAG

Basic information

species Oryza sativa
transcript LOC_Os08g33850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g33850.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152457_T05 (Zea mays), 3'ss of exon 5
-----gcaatgtaaacaattcaatggtgtataccttttctggcagtttcttgttct---ttgattccataatataataaaaggagctgagaatttcctcctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACCTTGATGGGAAATTTTTAGCAACAGAGAATTTCTACCATACTTCCAAG
         | |||    || ||||       | |||  |   |  ||||  ||||   || ||| |||   |||||  | |    ||||  ||    | | ||||||||| |||||  || |||||||||||  | ||||||||||||||||||||  | || ||||||||||| || ||||| || || ||||||||||| |||
atgtttatgtttaatttgttgaatgcctacagcttttgttaatacattctcattctcaatttatttcatggcataattgagg----tgagtgtt----ctttttgcagAGGGATGTACATATCATGAATGCCGCCTTGGAGCAGCATTTGTACCAGAGTTGGAAGGGAAATTTTTGGCGACAGAAAACTTTTACCATACTTCAAAG

upper sequence: LOC_Os08g33850.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G152457_T06 (Zea mays), 3'ss of exon 5
-----gcaatgtaaacaattcaatggtgtataccttttctggcagtttcttgttct---ttgattccataatataataaaaggagctgagaatttcctcctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACCTTGATGGGAAATTTTTAGCAACAGAGAATTTCTACCATACTTCCAAG--
         | |||    || ||||       | |||  |   |  ||||  ||||   || ||| |||   |||||  | |    ||||  ||    | | ||||||||| |||||  || |||||||||||  | ||||||||||||||||||||  | || ||||||||||| || ||||| || || ||||||||||| |||  
atgtttatgtttaatttgttgaatgcctacagcttttgttaatacattctcattctcaatttatttcatggcataattgagg----tgagtgtt----ctttttgcagAGGGATGTACATATCATGAATGCCGCCTTGGAGCAGCATTTGTACCAGAGTTGGAAGGGAAATTTTTGGCGACAGAAAACTTTTACCATACTTCAAAGGT
















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|38482258|gb|CF966306.1|CF966306
EST:     CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAG                         AGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACC
genomic: CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAGgtatatatct ... cctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACC
EST: gi|568839|gb|D39688.1|D39688
EST:     CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAG                         AGGAATGTAGGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGAC
genomic: CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAGgtatatatct ... cctgttgcagAGGAATGTAGG-TACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGAC
EST: gi|58691243|gb|CK079930.1|CK079930
EST:     CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAG                         AGGAATGTAGGTACCATGAATGCCGTATGGGAGC
genomic: CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAGgtatatatct ... cctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGC
EST: gi|58691215|gb|CK079902.1|CK079902
EST:     CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAG                         AGGAATGTAGGTACCATGAATGCCG
genomic: CTTCTCCGAATGTAGATCTGCAGCACTAACACTATTGCAGAAAGGAAGAGgtatatatct ... cctgttgcagAGGAATGTAGGTACCATGAATGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctttgattccataatataataaaaggagctgagaatttcctcctgttgcagAGGAATGTAGGTACCATGAATGCCGTATGGGAGCAGCATTTGTACCAGACCTTGATGGGAAATTTTTAGCAACAGAGAATTTCTACCATACTTCCAAG
    ctttgat  putative branch site (score: 5)
                                       tttcctcctgttgc  putative PPT
     tttgattccataatat  TA-rich tract