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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttactttcttaccttctttggtttaagatgttagtgtgatgatactgttgacacatatttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG

Basic information

species Zea mays
transcript AC196144.3_FGT002
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC196144.3_FGT002 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g01240.1 (Oryza sativa), 3'ss of exon 25
gttactttcttaccttctttggtttaaga--------tgttagtg----tgatgata--ctgttgacaca--tatttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG
||||| ||  |  | | | |     ||||        | ||| ||    || |||||  ||| ||| ||   || ||  | |||||||||||||| ||||| ||||||||||| ||||     || | |||||  || |  || ||| |||| |||| ||| ||  ||| || |||||||
gttacatttctgacatgtgttaagaaagaattgttgttattaatggagctgttgatatcctgctgatacttttactttgtcaagGATTATGCACTGGAGTCAGATAACAATACCATAAAATCTTCTGTACATTCAATAGCCAGGACAATAGCTGGAAATCTAGCCTATGCTAATTGCAAG
















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 4 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 137

GGATTTGGCTTTGGATAAGGCTAACAGGGAGATAATACTCCCTGTTATTCAAAGAAGTGTGACCATAGCAAGCCGAACTACAAAAGAACTTATTCTGAAGgttactttct ... tttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 51

GGATTTGGCTTTGGATAAGGCTAACAGGGAGATAATACTCCCTGTTATTCAAAGAAGTGTGACCATAGCAAGCCGAACTACAAAAGAACTTATTCTGAAGgttactttct ... tttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 39

GGATTTGGCTTTGGATAAGGCTAACAGGGAGATAATACTCCCTGTTATTCAAAGAAGTGTGACCATAGCAAGCCGAACTACAAAAGAACTTATTCTGAAGgttactttct ... tttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 46

GGATTTGGCTTTGGATAAGGCTAACAGGGAGATAATACTCCCTGTTATTCAAAGAAGTGTGACCATAGCAAGCCGAACTACAAAAGAACTTATTCTGAAGgttactttct ... tttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttggtttaagatgttagtgtgatgatactgttgacacatatttcttgaagGATTATGCACTAGAGTCTGATAACAATACGATAACTCGATCCGCACATTTGATGGTTAGAACATTAGCCGGAAGTCTGGCACATGTTACTTGCAAG
                                 tgttgac  putative branch site (score: 46)
                                           tatttctt  putative PPT
                                          atatttctt  TA-rich tract