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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatagaatttcctttactggattcacattttgtttgcttactgttctcattgaaaaatattcacatttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG

Basic information

species Zea mays
transcript GRMZM2G110109_T01
intron # 6
splice site 3'
intron type U2

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: 47 (upstream exon), 47 (downstream exon)
Score: 37

TTCTGCCAGAGTTAGAAGGGATGCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGCCTTCTCACAAATGGCACTTATGGGGATAACATTTTGAAGgtaatagaat ... atttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 15

TTCTGCCAGAGTTAGAAGGGATGCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGCCTTCTCACAAATGGCACTTATGGGGATAACATTTTGAAGgtaatagaat ... atttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 10

TTCTGCCAGAGTTAGAAGGGATGCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGCCTTCTCACAAATGGCACTTATGGGGATAACATTTTGAAGgtaatagaat ... atttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 28

TTCTGCCAGAGTTAGAAGGGATGCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGCCTTCTCACAAATGGCACTTATGGGGATAACATTTTGAAGgtaatagaat ... atttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattcacattttgtttgcttactgttctcattgaaaaatattcacatttctgcagGACAAAGATACAATGCCACTTCCAAATCGTGATAAAAACCTAAGCTTTG
               tgcttac  putative branch site (score: 28)
                                            catttct  putative PPT
                                 aaaaatattcacattt  TA-rich tract