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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcaaatttacagcatctttgtctgacataatttgcaaagtgtttaattaactgtctgacatgatggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 7
gttagttcaaatttacagcatctt--tgtctgacataatttgcaaag---tgtttaattaactg-----tctgacat-------------gatggtt----cattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC
|||||| || ||| ||| || ||   |||   | | |  |    | |   | ||| ||  | ||     ||| |||               ||||||    |   |||| |||||||| ||||   | || ||||| |||||| | |||||   ||| ||| ||||| |||||||||||||||||||||||  |||||||||||| |
gttagtacacattaacaacacctgggtgttcaaaaaagatcttgagggtttatttgatctattgatgattctaacactattagatgtttgaatggttgcctctccagGACAGGAATTTAAATCAGCTGGCGTCATCTGAATCATCTAGTTCTGGTACGAGGAATTATGTTCCAGGAAGCAGTGATCCTCATAGCAGTGGTTTGCGGC
















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|29672696|gb|CB668971.1|CB668971
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATA
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCGTTG                         GAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA
genomic: GATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACA

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: 75 (upstream exon), 74 (downstream exon)
Score: 163

GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTGgttagttcaa ... ggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgacataatttgcaaagtgtttaattaactgtctgacatgatggttcattagGAGAGGAATTTTAATCGCTTTGCTTCATCGGAATCAGCAAGTTCAAATACAAGGCATTATCTTCCAGGAAGCAGTGATCCTCATGCCAGTGGTTTGCGCC
                aaagtgtttaattaa  TA-rich tract