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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG

Basic information

species Oryza sativa
transcript LOC_Os05g44560.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM5G845682_T02 (Zea mays), 3'ss of exon 4
gtaatcaattatttagttgaaa--aatcatgcatgtgg-agttagatttatg---gtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
|||||||| |||||| ||   |  | | |   |  |   |  ||||||||||    | |||  ||   |  |  ||     |  | |||| |||||||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||| |||||||||||| ||||||||||||||||||| |||||
gtaatcaagtatttatttactaccagtaaactagatcttaaatagatttatgtgaatattttaaatatttgtactaccttttgctttcttccagGTGGACAAGCAAAAACTCTAATGTTCGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGCACTTTAAAGTTTGCTGAAAGGGTGTCTGG

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtt--tttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
|||||||| |||||| ||   |   | |  ||||  | | | ||| ||| ||   ||  || | | || | |     || | |||| |||||||||||||||| || |||||||||||||| ||||||||||||||||||||||||||||| |||||||| ||| ||||||||||||||||||| |||||
gtaatcaaatatttatttacta---cctagatgttaaat-atattaatgtttatcttccaaattttatgt-accttttattttcttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 15
gtaatcaattatttag---ttgaaaaatcatgcatgtggagttagatttatg--gtttttgtaactat-----aatcttataaaataatctcttgca--gGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
||||    ||||| |    |||  |  |||      | || |    | ||||  | |||| | |  ||     | |||| |     | | | |||||  ||||  ||||| |||||||| |||||||||||||| ||| | || ||    |||||||| || ||  | |||||| |||||||||||||||||||||||||
gtaaatctttattcatcatttgttatgtcacatgccttgaatcttttctatgtagattttcttatgatctttgactcttgtctttgattttattgcacagGTGACCAAGCGAAGACACTCATGTTTGTTCAAATTAATTCAGACGTAAGTTCATATTCTGAAACACTGAGCACTTTAAAGTTTGCTGAAAGGGTTTCTGG

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
----------------------------------------gtaatcaatt--atttagttgaaaaatcatgcatgtggagttagatttatggtttttgtaactataat--cttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
                                         || |   ||  ||||  ||| |   | ||  | |   | ||  | | |||| ||    || |  |||  |||      |  | | |   |||||| ||||| || || || |||||||| ||  | |||||||||||||  |||||||| || ||| |||||||  | |||||||||||| ||||||||||
gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttgatttaagcata-ttgcagtcatggcttactaaattgcaatagctttgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
||| |  |  ||  | || || ||  |   |  |     | ||| | || |  |||   || || || | |    |||| | ||  ||| || ||||| || || || |||||||||||||| ||||||||||  || |||||| | |||||| |||| ||| | || ||||| ||||| ||||||||
gtactataagatagacttcaataaaaa---aaatattacttgatat-tgttgcttgcttctttactcctctttt-taatttttt--agGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG

upper sequence: LOC_Os05g44560.1 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G18410.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaatcaattatttagttgaaaaatcatgcatgtggagttagatttatggtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
    | ||   |  |  |         ||  | |  | |     |     ||||   |  |||     | | |  |||  ||   ||||||| | ||||||||||||||||||||||||| | ||||||||| ||   |||||||||||| | || || ||| | || || || ||  | || |||||
---gttaac--tccaaatcttctgctctgttttttcaatcgtgatcgaaattttctaacttatctctgtgtgatttaacatc--acagGTGGTCGAGCAAAGACACTAATGTTTGTTCAACTGAATCCTGATATTACTTCATATTCAGAGTCAATGAGTACTTTGAAATTCGCAGAGCGTGTCTCTGG

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: 67 (upstream exon), 43 (downstream exon)
Score: 12

CTGTCTGCTTTGGGTGATGTGATTTTTGCTTTGGCGCAAAAGAATGCTCATGTGCCATACAGGAACAGCAAGCTAACACAAGTTCTTCAAAGCTCTTTAGgtaatcaatt ... tctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggagttagatttatggtttttgtaactataatcttataaaataatctcttgcagGTGGACAAGCAAAGACACTAATGTTTGTTCAAATAAATCCTGATGTTGAGTCATATTCAGAGACTATAAGCACTCTAAAGTTTGCTGAAAGGGTTTCTGG
                    ttgtaac  putative branch site (score: 12)
                                             tctcttgc  putative PPT
         atttatggtttttgta  TA-rich tract