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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatttcttcatgtgataaaatttcctttcatttggggtgctattatagttaagttgttttttactatgaaattatcttccatgtagctttggagcaggaaatgtatatctgcaaaaggttaatagcaatttatacaacaaaagaaaatatgatttgccctcatgtttcagCACAATGCTTCCACCAGCGCGGCCGTAGAGGCGGAAGCAAGGGGTTGGGCTTCTGTCGGTGTTGGACAGCGCGATGCCAAACGTGCCAGCCACTCTTGCT

Basic information

species Zea mays
transcript GRMZM5G878234_T01
intron # 2
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 2 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 2

GATGATCGCAAAGATTGTTGTGGTTTGTAATGATGCAATCATTGGCCACTCTGAGCATCAATATGTTGCTACAGGGATGCCCACAAAAGCTGCTCTGAAGgtataatttc ... catgtttcagCACAATGCTTCCACCAGCGCGGCCGTAGAGGCGGAAGCAAGGGGTTGGGCTTCTGTCGGTGTTGGACAGCGCGATGCCAAACGTGCCAGCCACTCTTGCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 4

GATGATCGCAAAGATTGTTGTGGTTTGTAATGATGCAATCATTGGCCACTCTGAGCATCAATATGTTGCTACAGGGATGCCCACAAAAGCTGCTCTGAAGgtataatttc ... catgtttcagCACAATGCTTCCACCAGCGCGGCCGTAGAGGCGGAAGCAAGGGGTTGGGCTTCTGTCGGTGTTGGACAGCGCGATGCCAAACGTGCCAGCCACTCTTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggttaatagcaatttatacaacaaaagaaaatatgatttgccctcatgtttcagCACAATGCTTCCACCAGCGCGGCCGTAGAGGCGGAAGCAAGGGGTTGGGCTTCTGTCGGTGTTGGACAGCGCGATGCCAAACGTGCCAGCCACTCTTGCT
 ggttaat  putative branch site (score: 4)
                                     tttgccctc  putative PPT
           aatttatacaacaaaa  TA-rich tract