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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagcaacaggaaatactgttcaaatttaccgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG

Basic information

species Oryza sativa
transcript LOC_Os03g52340.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G108115_T01 (Zea mays), 3'ss of exon 8
-agagcaacaggaaatactgttcaaatttaccgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
  ||  || |    | |    |||   |  |  |||| | |||||   ||||||  | |||  ||  || | |||||   || |        | |  |||| | ||||||||||||||||||||||||||| |  | || |||||||| ||||| ||||| |||||||| |||||||||||||||||| |||||||||| |
atgaaaaatattctaaaaccatcagcataccttttgagttcattttgtatgttta-agtggatatttgtttaacaatacttccttctttgcgactgatcagTTGCAGCTGCAGCGAAATGAGGTCATTGCATTGTTCAATCTTCTGAACAGGCTCTCAGAGTCTGTCAAATTTGTACATGAAAAAGGATCATCAATTGAAG

upper sequence: LOC_Os03g52340.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G521844_T01 (Zea mays), 3'ss of exon 8
agagcaacaggaaatactgttcaa------atttac-cgttgaatacatttaagatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
  |    |   ||||| | |  ||      || |||   |||| | |||||   ||||||  | |||  ||  || | |||||    ||||| ||  | || ||||| | ||||||||||||||||||||||||||| |  | || |||||||| ||||| ||||| |||||||| |||||||||||||||||| ||||| | || |
--attggcgaaaaatattctaaaaccatcaatatacattttgatttcattttgtatgttta-agtggatatttgtttaacaata---cttcttggcga-ttgttcagTTGCAGCTGCAGCGAAATGAGGTCATTGCATTGTTCAATCTTCTGAACAGGCTCTCAGAGTCTGTCAAATTTGTACATGAAAAAGGATCATCAGTCGAAG
















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|88539718|gb|CI469698.1|CI469698
EST:     GAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: GAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|29619060|gb|CB624072.1|CB624072
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58593304|gb|CF991612.1|CF991612
EST:     CATTGAAGATTCGTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|58606099|gb|CK034132.1|CK034132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCGTTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88485242|gb|CI422513.1|CI422513
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|86500373|gb|CI143006.1|CI143006
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|88472627|gb|CI409898.1|CI409898
EST:     CATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|29657857|gb|CB654132.1|CB654132
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
EST: gi|33679109|gb|CF307348.1|CF307348
EST:     CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCA                         CTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG
genomic: CATTGAAGATTCTTTTCTCTGTTGATGGAGAGAACCATTTGAATCAATCAgtacgtatct ... aattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtttgcaatggtgatgagtctgacaatttgtcttctgggtaaattattcagCTCCAGCTGCAGCGAAATGAGGTCATTGCACTAGTAAACCTTCTGAATAGGCTGTCAGAATCTGTCAACTTTGTACATGAAAAAGGACCATCAATTGAGG
                     gtctgac  putative branch site (score: 3)
                                           taaattattca  TA-rich tract