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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcttacatgtccaagaaaataaaacatgctgaaactgaaataactatataccctcatggactgctgttcttacacttgtttgcttatttgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT

Basic information

species Zea mays
transcript GRMZM2G700828_T01
intron # 4
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: 13 (upstream exon), 48 (downstream exon)
Score: 5

GGATGATGGTTCGTTTCATTATGATCAAGATTTATTTAACAGgtagaactct ... tgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 3

GGATGATGGTTCGTTTCATTATGATCAAGATTTATTTAACAGgtagaactct ... tgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 6

GGATGATGGTTCGTTTCATTATGATCAAGATTTATTTAACAGgtagaactct ... tgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT


Block sizes: 26 (upstream exon), 25 (downstream exon)
Score: 2

GGATGATGGTTCGTTTCATTATGATCAAGATTTATTTAACAGgtagaactct ... tgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatataccctcatggactgctgttcttacacttgtttgcttatttgtggcccagCAAAATTACAGTATATTGAATGAAGTTGATATCAAGCGGCGCCAAGAGGATGACATAAATAGGGTTTCAACTGTTCTTTCAATTTCCAAACCAGAGGCAT
                       ttcttac  putative branch site (score: 2)
                                       cttattt  putative PPT
                                        ttatttgt  TA-rich tract