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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatctcttatctttatattttttctgttctcatttgttttttaccattttgatatgtattttttttttcatattgtagGTGATGGAAATGTCCGCATATGGAGAAACTATACTCAAAAGGGAGGACAAAAACTTGTAACTGCTTTTTCATCAGTTCAAGGCTATCGAAGTGCTGGTCG

Basic information

species Oryza sativa
transcript LOC_Os12g01922.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G460090_T01 (Zea mays), 3'ss of exon 9
gtatatctcttatctttatattttttctgttctcatttgttttttaccattttgatatgtattttttttttcatattgtagGTGATGGAAATGTCCGCATATGGAGAAACTATACTCAAAAGGGAGGACAAAAACTTGTAACTGCTTTTTCATCAGTTCAAGGCTATCGAAGTGCTGGTCG
||| | ||||| ||| ||| ||    || | || ||          |||||    | | || |||||     | |||| ||||||||||||||| |||||||||| ||| | | ||   |||||||| || ||||||||||||||||||||||||||||| ||  |||||  |||||||||
gtacacctcttttctctatgtt----ctatacttat---------gccattgcactgtctaattttt-----acattgcagGTGATGGAAATGTACGCATATGGAAAAATTTTGCTTGTAAGGGAGGGCAGAAACTTGTAACTGCTTTTTCATCAGTTCAGGGACATCGAGCTGCTGGTCG

upper sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G048067_T02 (Zea mays), 3'ss of exon 17
gtatatctcttatctttatattttttctgttctcatttgttttttaccattttgatatgtattttttttttcatattgtagGTGATGGAAATGTCCGCATATGGAGAAACTATACTCAAAAGGGAGGACAAAAACTTGTAACTGCTTTTTCATCAGTTCAAGGCTATCGAAGTGCTGGTCG
||||  ||||  ||| ||| |||||  | ||  || || | ||||||||||    | | ||      ||||||| ||| ||||||||||||||| ||  |||||| ||| | |||||||||||||||||||||||||||||| ||||| ||||| ||||| ||  |||||| |||||||||
gtatgcctctgttctatatgtttttcat-tttacacttatcttttaccattgcattgtctaa-----ttttcatgttgcagGTGATGGAAATGTACGTGTATGGAAAAATTTTACTCAAAAGGGAGGACAAAAACTTGTAACGGCTTTCTCATCCGTTCAGGGACATCGAACTGCTGGTCG
















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), 50 (downstream exon)
Score: 17

CCAGTGAATACTTTTGAAAACCACAAGTTATCTGACAGAGGCCTATCTAAACTTTTGCTGATCAATGAGCTTGATGATAGCTTGTTGTTAGTTGGCTCAAgtatatctct ... catattgtagGTGATGGAAATGTCCGCATATGGAGAAACTATACTCAAAAGGGAGGACAAAAACTTGTAACTGCTTTTTCATCAGTTCAAGGCTATCGAAGTGCTGGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttctcatttgttttttaccattttgatatgtattttttttttcatattgtagGTGATGGAAATGTCCGCATATGGAGAAACTATACTCAAAAGGGAGGACAAAAACTTGTAACTGCTTTTTCATCAGTTCAAGGCTATCGAAGTGCTGGTCG
                       ttttgat  putative branch site (score: 17)
                                   ttttttttttcatatt  putative PPT
             ttttttaccattttga  TA-rich tract