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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaaaattgtgatttgaccttattttagtgcatatgctttaccttcatgcgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag

Basic information

species Oryza sativa
transcript LOC_Os02g07760.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 16
GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaa---------------------aattgtgatttgaccttattttagtgcatatgctttaccttca--tgcgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag
|||||||  ||||||| ||||||||||| |||||||| || |||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||  ||| | |                     ||||   |   |||||| || |||||||||   | ||| ||||  |||||  ||||| || |  |||||| |||| | |||||      |  |||||  |||||      |||   |||||
GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGAATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaagtttacagttagaccttctaatcttaacaatttcaaccagaccttgttgtagtgcatagaatctactttcacgtgcgagtaaatggtctaatattgaggaattgtctgacact----tcatagttgttaacatctttttttcatttcag

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G128114_T01 (Zea mays), 5'ss of exon 16
GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaa-------------aattgtgatttgaccttattttagtgcatatgctttaccttcatg--cgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag
|||||||  ||||||| ||||||||||| |||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||   || | |             ||||   ||   |||||  | ||||||||||  | ||| ||||||  |||| ||||  ||   ||||||| || | | |||||      |   ||||  ||||| ||   |||   |||||
GAGCAAATGTCATGCTAGGTGGTAAAAGACACAGCCTGGGGATGTCATTTTATGAGCCAACTGTAGTAGGGAATGTCAGCAATGATATGCTTCTTTTCAGgtaaactttacagttggaccttagcaatttcaatcaaaccttgatatagtgcatatattctactttcatgtgcgaataaatagtcttacattgagcaactgtctgacact----tcaaagttgttaaca-tcttttttcatttcag

upper sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AT1G79440.1 (Arabidopsis thaliana), 5'ss of exon 16
GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttcaaaaattgtgatttgaccttattttagtgcatatgctt-taccttcatgcgaagaaatgttcaatcattgagaaattctttgacatccttgttctagtttctaacaatcacatttggcttcag
||||||| |||||  ||||||| ||||||||||| || |||||| | ||||||||||| |||||  |  |  | ||     || | ||| |  | |  | ||| |     |||| | | |  | |  ||    |  | ||  | ||| || ||  |    | ||  | |  || ||| | |   ||| | | |||  ||||  |       |  |||    |||   |  ||
GAGCAAAAATCATCATTGGTGGCAAAAGGCACAGTCTAGGGATGACTTTCTATGAGCCTACTGTTATCCGCGATGTTTCGGATAACATGATCATGTCTAAgtaagtactgaaaaatttcacataa--ttgcagtgttacagcttcttgtatctctaaagaacgagttatagaaacatagtg---ttcctcg-catttttgtgatcagaagaactaatttacttt--ttctag

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|86496493|gb|CI139126.1|CI139126
EST:     TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAG                         GGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
EST: gi|218485663|gb|FG949794.1|FG949794
EST:     TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAG                         GGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
EST: gi|88227449|gb|CI226929.1|CI226929
EST:     TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAG                         GGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
EST: gi|218498992|gb|FG968229.1|FG968229
EST:     TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAG                         GGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
EST: gi|218482143|gb|FG968613.1|FG968613
EST:     TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAG                         GGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA
genomic: TATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGA

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: 71 (upstream exon), 73 (downstream exon)
Score: 54

GAGCAAACATCATGCTTGGTGGTAAAAGGCACAGCCTTGGGATGTCATTCTATGAGCCAACTGTAGTAGGGAACGTCAGCAATGATATGCTTCTTTTCAGgtagggttca ... ttggcttcagGGAAGAAGTCTTTGGTCCAGTTGCACCACTTGTACCATTCAAAACTGAGGAAGATGCAATCCGTATGGCCAATGATACCAACGCAG




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