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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaagtagaccccaaaagctcttgtccttgcgcccctcactgatctcaagatcaaccagaaattcgactagtgagtagtgacattcttttactaacgcagGTTTTATCGCACATTATGCTACCCTCGCTAGCAGGGACGTG

Basic information

species Zea mays
transcript GRMZM5G816636_T01
intron # 8
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 3 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 8

GCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAGGTCTCGTCAAGCTAATGGGCCGGCACAGTGgtaagcttct ... actaacgcagGTTTTATCGCACATTATGCTACCCTCGCTAGCAGGGACGTG


Block sizes: 38 (upstream exon), 41 (downstream exon)
Score: 4

GCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAGGTCTCGTCAAGCTAATGGGCCGGCACAGTGgtaagcttct ... actaacgcagGTTTTATCGCACATTATGCTACCCTCGCTAGCAGGGACGTG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 78

GCAGTTGAGGAGGCTCAACGTGCAATAAATGCTGCTCATGTGGAAGCTGTAAGTGCTGAGAATGGTATAGGTCTCGTCAAGCTAATGGGCCGGCACAGTGgtaagcttct ... actaacgcagGTTTTATCGCACATTATGCTACCCTCGCTAGCAGGGACGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagatcaaccagaaattcgactagtgagtagtgacattcttttactaacgcagGTTTTATCGCACATTATGCTACCCTCGCTAGCAGGGACGTG
                                            tactaac  putative branch site (score: 78)
                                      ttcttttact  CT-rich tract
                                     attctttta  TA-rich tract