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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGACGACCTCCACTCCAACGGCTTCGACGACGCGCTCCTCGCTGATCTCTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccattctatttcgttattccttttttttcttttttagaattctccatagcttactttgtcatgaatttgcatttgtacacgtgacatgtaaagtaatggatggttggattgtgcaattttcag

Basic information

species Oryza sativa
transcript LOC_Os12g03190.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 2
GCCGACGACCTCCACTCCAACGGCTTCGACGACGCGCTCCTCGCTGATCTCTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccattctatttcgttattccttttttttcttttttagaattctccatagcttactttgtcatgaatttgcatttgtacacgtgacatgtaaagtaatggatggttggattgtgcaattttcag
||||| ||  ||||||||| |||| |||| |||||||||||| |  | |||||||||||||||||||| ||||| ||| | || || ||||||   |||||||  |       ||  |   |||    |||   |  || |     | |      |   ||  |||     ||| | ||         |||||||| | | || |||  |||| | ||||  ||| |||
GCCGAAGATGTCCACTCCACCGGCCTCGATGACGCGCTCCTCACCCAGCTCTGCGCCGCCAAGTCCGCAGGCTCTCCCCTCTCCTCCCTGCTCGGCCGAGgtagacaggc---atcccccaatttgactttgcccacttattacgatgt-----acgcgctccgtcg----ttttcgtt---------gacatgtagaatgatcgatacttgggt-gtgcggttt-cag
















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|88427283|gb|CI586831.1|CI586831
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88851700|gb|CI674902.1|CI674902
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88362042|gb|CI607042.1|CI607042
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88587271|gb|CI705007.1|CI705007
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88579428|gb|CI688414.1|CI688414
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAA
EST: gi|88427682|gb|CI689547.1|CI689547
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGT
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGT
EST: gi|88582444|gb|CI699857.1|CI699857
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGG
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGG
EST: gi|88727097|gb|CI750752.1|CI750752
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAANAAACCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88467150|gb|CI696509.1|CI696509
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88903812|gb|CI711514.1|CI711514
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|2310428|gb|C26583.1|C26583
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88306132|gb|CI636510.1|CI636510
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88589443|gb|CI707322.1|CI707322
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
EST: gi|88333928|gb|CI645342.1|CI645342
EST:     CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAG                         GGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA
genomic: CTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACA

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: 70 (upstream exon), 65 (downstream exon)
Score: 72

GCCGACGACCTCCACTCCAACGGCTTCGACGACGCGCTCCTCGCTGATCTCTGCGCCGCCAAGTCCGCCGGCTCGCCCTTATCTTCTCTGCTCTCTCGAGgtatccccat ... caattttcagGGCAATGTCAGCTATTCAACAACCCTGAGGCTAGGAGGAAAGTCATTGACACTGCCAGCGTTCTTGGGAAAACAACTG




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