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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcaaattttatttctacaacttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT

Basic information

species Zea mays
transcript GRMZM2G591258_T01
intron # 7
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: 49 (upstream exon), 48 (downstream exon)
Score: 478

GGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAGgttcgttatt ... ttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 295

GGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAGgttcgttatt ... ttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 217

GGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAGgttcgttatt ... ttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 492

GGCACCCCTAAAGTTGTTGCTGCATTTGCTGAAAGGAGGGAGTTTGACAAGATACTGATATACTCAAAGCAGgttcgttatt ... ttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagttgttgtaactcatttgagcttcaaattttatttctacaacttgggtccagGTTGGGTACACTCCAGATTATCTCTTCCTCCTCCAGACCATCTTGCGTACAGATCCACAGGCGATTGATTGTTTGAACATAATCGGTCATTT
       ttgtaac  putative branch site (score: 492)
                        ttcaaattttatttct  TA-rich tract