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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAAGTTCAACACGAGTTGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacatttctaaatgagctttttggacatttaaattgaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcag

Basic information

species Oryza sativa
transcript LOC_Os01g34620.5
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34620.9 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G880300_T02 (Zea mays), 5'ss of exon 3
CTCAAGTTCAACACGAGTTGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacatttctaaatgagctttttggacatttaaatt-------gaagaacttattttgtggcaaagctaggcatgtcttaaagtttcatgatgtatttctgccatttgttaatgctgcctcataattgttgggcag
||||| | |||||||| | |||||||||||||||||||||||||||||| |||| |  | || || |||  ||||| ||||  |||||  | || |||||||||| ||||    | ||||| ||   | | ||||| |||       |||| || ||  |||||  ||| ||||||||  | | ||| ||  |||||||| | |   |  ||  |   || | |   | ||  | || ||
CTCAACTACAACACGAATAGCTGCTGATCCTGATACACATCAAGATTTCGAGCCAAAGAGCAGAATTTCAGACATGACTTTGCATGACGCTATTGCTCAGgtatttacatgcagagatgagattcaagaatatttatattaaacattgaagcacctaacttgtgataaaactaggcataacctgaagcttattgatgtatcttt-ttagctgccatctcttcttatcattttcttggtag
















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|218500313|gb|FG954965.1|FG954965
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218483000|gb|FG956128.1|FG956128
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218489064|gb|FG948407.1|FG948407
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33688088|gb|CF316327.1|CF316327
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|86510934|gb|CI153567.1|CI153567
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|58675402|gb|CK064089.1|CK064089
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38482485|gb|CF966520.1|CF966520
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38478580|gb|CF962713.1|CF962713
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33680954|gb|CF309193.1|CF309193
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|218505071|gb|FG947171.1|FG947171
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|58693371|gb|CK082058.1|CK082058
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|86901749|gb|CI310511.1|CI310511
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|88427128|gb|CI586676.1|CI586676
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33662134|gb|CF293101.1|CF293101
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|38477159|gb|CF961292.1|CF961292
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|86431345|gb|CI084956.1|CI084956
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|33808808|gb|CF330289.1|CF330289
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
EST: gi|88316503|gb|CI622749.1|CI622749
EST:     AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAG                         GATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT
genomic: AGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCT

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: 68 (upstream exon), 75 (downstream exon)
Score: 29

CTCAAGTTCAACACGAGTTGCTGCTGATCCTGATACACATCAAGATTTCCAGCCTACAACCAAAAGTTCCAACATGTCTTTTGATGACATTGTTTCTCAGgtattaacat ... tgttgggcagGATATCAAGGAGAACCCAGTCCTGATCTACATGAAGGGTTATCCTGATGCTCCTAGGTGTGGGTTCAGTGCGTTGGCAGTTAGAGTCCTCAAGCAATATG




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