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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTATGGGAAAGAAGGGAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaacatccttcttaccatctccacccaacataatgcttatccttattatttctgatagtaatctgagactattgttggttggtttcattttatttatggttttcaaggtgatttggatgttctaaggaaccttacaaattgtgtacaactgcag

Basic information

species Oryza sativa
transcript LOC_Os11g05090.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g05090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G21640.1 (Arabidopsis thaliana), 5'ss of exon 5
AGGCTATGGGAAAGAAGGGAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaacatccttcttaccatctccacccaacataatgcttatccttattatttctgatagtaatctgagacta-ttgttggttggtttcattttatttatggttttcaaggtgatttggatgttctaaggaaccttacaaattgtgtacaactgcag
||  |||||||||||||| | |||||| || || ||||| || || ||||||||  | |||||||| || ||| ||||||||||||||||    || |||||| |  |    |  |   | |||||     |   |  | |   |  |     |  ||  |   | |||  |  ||  ||| |      | | | ||   | |||  ||  |  |                                              
AGCTTATGGGAAAGAAGGAAACTTTTCTTTTCCGAATGTTCCACCTATGGCAGACTTGTTATATGAGGTGGAAGTTATTGGGTTTGATGAAACAAAGGAGgtaagttatttcctataccatcatcttgtttccttaccaagacgactcc----acatccaagctttatcccaacctccttgcttacctctctgacttagatgatgtattgaacag----------------------------------------------

upper sequence: LOC_Os11g05090.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0064g00580.t01 (Vitis vinifera), 5'ss of exon 5
AGGCTATGGGAAAGAAGGGAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaacatccttcttaccatctccacccaacataatgct-tatccttattatttctgatagtaatctgagactattgttggttggtttcattttatttatggttttcaaggtgatttggatgttctaaggaaccttacaaattgtgtacaactgcag
 ||||||||||||||||| || ||||| ||||| ||||| || || ||||||||| |||| ||||||||||| |||||||| ||||||||    ||||||||| |    |  | |  | |   ||   |       || |||| | ||||   ||    | || ||| |  |||   ||| | |         |||  || ||||    |  | |  |   | |||||  |                              
GGGCTATGGGAAAGAAGGAAGTTTTTCTTTCCCGAATGTTCCGCCTATGGCAGATATTTTGTATGAAGTTGAGCTTATTGGCTTTGATGAAACTAAAGAGgtaagttt-ctccttcatgattttccaaagtttctttattgctgtttcctgcctaaacttcattgta-tgcgagctcattataga--------attcaatatatgaacctacaagcaa--cgcatgttacag-----------------------------
















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|112786266|gb|EE590427.1|EE590427
EST:     CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAG                         GGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
genomic: CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaac ... acaactgcagGGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
EST: gi|29663324|gb|CB659599.1|CB659599
EST:     TTGATGATGTCAAAGAG                         GGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
genomic: TTGATGATGTCAAAGAGgtagggaaac ... acaactgcagGGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
EST: gi|27546946|gb|CA765208.2|CA765208
EST:     CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAG                         GGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
genomic: CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaac ... acaactgcagGGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
EST: gi|58693730|gb|CK082417.1|CK082417
EST:     CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAG                         GGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC
genomic: CAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaac ... acaactgcagGGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGAC

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: 74 (upstream exon), 67 (downstream exon)
Score: 11

AGGCTATGGGAAAGAAGGGAGCTTTTCATTCCCAAATGTCCCTCCAATGGCAGATCTTTTATATGAAGTTGAACTTATTGGGTTTGATGATGTCAAAGAGgtagggaaac ... acaactgcagGGGAAAGCCCGAAGTGACATGACAGTAGAGGAAAGGATTGAAGCAGCGGACAGGAGGAAGATTGAGGGCAATGAGTATTTCAAAGAAAAGAAGTTTGAGG




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