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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggctgtttaattttgtgagcaattatgtgataatttctggttgacgctaattgtctatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCACCAAATTTCAGAGGGAAGGCCAATTACAGGTTCTTTTGATGGCAACATGA

Basic information

species Oryza sativa
transcript LOC_Os08g34950.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34950.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G153722_T02 (Zea mays), 3'ss of exon 7
-------gtaggctgtttaattttgtgagcaattatgtg--ataatttctggttgacgctaattgtctatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCACCAAATTTCAGAGGGAAGGCCAATTACAGGTTCTTTTGATGGCAACATGA
       | ||      | | | | |||||   | ||||  || ||| ||   |||  || ||||   ||||||||||||| |||||||||||||||||||||| ||||||| ||||| ||||||||| |||||||||  ||||||||||||||||||||||||||||||||| |||
gtagtgtgaagatgtacttaatgtatgagcctgtgtgtgcaatcattcctcactgatactgattgctaatgattcagGTGGATGACTCAGCTGAACTTCTGTTCTCTGAAGTTCTGAACGCACTCCACAAAATTTCAGGAGGAAGGCCAATTACAGGTTCTTTTGATGGCAACTTGA
















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|29622970|gb|CB627981.1|CB627981
EST:     TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAG                         GTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
EST: gi|33676698|gb|CF304937.1|CF304937
EST:     TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAG                         GTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
EST: gi|33678298|gb|CF306537.1|CF306537
EST:     TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAG                         GTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
EST: gi|33796202|gb|CF323967.1|CF323967
EST:     TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAG                         GTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
EST: gi|569650|gb|D40499.1|D40499
EST:     TTGATTTCACTTCTCAGCACCAGGAATNGGTAGAGCAAGAAGCAAATNAG                         GTGGTTGACTCAGCTGAACTTNTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
EST: gi|88363129|gb|CI616286.1|CI616286
EST:     TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAG                         GTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC
genomic: TTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 51 (upstream exon), 68 (downstream exon)
Score: 21

CCGATATGCATCGATCAAGGTTCATTCAGTGTATTTGCCACCACCGAAACTTGATTTCACTTCTCAGCACCAGGAATGGGTAGAGCAAGAAGCAAATGAGgtaggctgtt ... tatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCACCAAATTTCAGAGGGAAGGCCAATTACAGGTTCTTTTGATGGCAACATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgagcaattatgtgataatttctggttgacgctaattgtctatgattcagGTGGTTGACTCAGCTGAACTTCTGTTCACTGAAGTACTGAATGCACTCCACCAAATTTCAGAGGGAAGGCCAATTACAGGTTCTTTTGATGGCAACATGA
                                  cgctaat  putative branch site (score: 21)
          aattatgtgataattt  TA-rich tract