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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatctcattggtttatatctaaagattatttagttcatggctgttttgctaaatcatatcttagtattaccaatgtttagagctgcaaaattcct...

Basic information

species Oryza sativa
transcript LOC_Os03g50850.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50850.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G178227_T01 (Zea mays), 5'ss of exon 10
TGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaata----tctcatt--ggtttatatct----aaagattatttagttcatggctgttttgctaaatcatatcttagtattaccaatgtttagagctgcaaaattcct
||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||| ||||| || ||||| ||||| ||||| ||||||| ||    ||  |||  ||  ||||| |      || || ||   |  |    |  |  |  | ||   |    ||||  ||||||| ||  |              
TGACGAAGAGCAACAAATCTACAATCCTCTCAAGTTGCCGATGGGTTGGGATGGCAAACCTATCCCCTACTGGCTGTACAAGCTACATGGCCTTGGGCAGgtaactagttgtcatatttgggagtatatttcctagtagcttgttacctctagtcttagtcagtgagatggcacggcagtagcaccaatgctttcactca----------
















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|25806388|gb|CA762349.1|CA762349
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58030390|gb|CX727933.1|CX727933
EST:     GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|88966922|gb|CI379806.1|CI379806
EST:     TATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGATATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: TATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58030389|gb|CX727932.1|CX727932
EST:     GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|87039441|gb|CI194063.1|CI194063
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58683962|gb|CK072649.1|CK072649
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29625135|gb|CB630146.1|CB630146
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29664559|gb|CB660834.1|CB660834
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|86602502|gb|CI264830.1|CI264830
EST:     ATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29675683|gb|CB671958.1|CB671958
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29664555|gb|CB660830.1|CB660830
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|88228807|gb|CI226658.1|CI226658
EST:     ATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|58674178|gb|CK062864.1|CK062864
EST:     ATAAGCTCCATGGTCTTGG-CAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29639904|gb|CB644913.1|CB644913
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|29629058|gb|CB634069.1|CB634069
EST:     GGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: GGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
EST: gi|86253465|gb|CI058390.1|CI058390
EST:     ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAG                         GAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT
genomic: ACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCT

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: 69 (upstream exon), 74 (downstream exon)
Score: 31

TGATGAAGACCAACAAATCTACAATCCTCTTAAGTTGCCGATGGGTTGGGACGGCAAACCTATACCCTATTGGCTATATAAGCTCCATGGTCTTGGTCAGgtaaatatct ... tttttgtcagGAATTCAAATGTGAGATATGTGGAAACCACAGCTACTGGGGGCGACGGGCTTATGAGCGGCATTTCAAGGAGTGGCGCCATCAGCACGGGATGCGCTGTC




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