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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggcccaactaatttgttaatattacttaatattctatacttcttttgggatgaagtcaatactctacttggttcgctgacgtttgttgttattgttcaatttttag

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37210.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G032222_T03 (Zea mays), 5'ss of exon 13
GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggcccaactaatttgttaatattacttaatattctatacttcttttgggatgaagtcaatactctacttggttcgctgacgtttgttgttattgttcaatttttag
||||||||||| ||||| ||||| || || |  ||||||||||||||||||||||| ||  ||   ||   || ||||| | | |||    | |        |||  | |      |||| |   ||| ||||    |||   || | || || ||||||
GCATTTGAATACGGATTAATTCCGGGTATGGTTTTGTCTGCACTGGAACGgtgaggtcc--ctg--ttaagaaaattacctgagattagtcatt--------gatatatt------tctattccattcactgagtcatgtctatact-tttaacttttag
















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|218502645|gb|FG955089.1|FG955089
EST:     GCATTTGAATCTGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29615151|gb|CB620164.1|CB620164
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29657656|gb|CB653931.1|CB653931
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29675569|gb|CB671844.1|CB671844
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29662394|gb|CB658669.1|CB658669
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTTTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|218486085|gb|FG956984.1|FG956984
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29637767|gb|CB642776.1|CB642776
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|86859459|gb|CI278866.1|CI278866
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCANGGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29669361|gb|CB665636.1|CB665636
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29667105|gb|CB663380.1|CB663380
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29676401|gb|CB672676.1|CB672676
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29659147|gb|CB655422.1|CB655422
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
EST: gi|29681493|gb|CB677768.1|CB677768
EST:     GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACG                         ATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA
genomic: GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGA

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: 50 (upstream exon), 67 (downstream exon)
Score: 21

GCATTTGAATATGGATTTATTCCAGGCATTGCCTTGTCTGCACTGGAACGgtgaggccca ... caatttttagATACGTATTCAAAGGAAAGTCCCCCTTTACCTTAAAGCACGGGATACCTGACCATGAAGCAACAGAT




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