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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttagcttttctgtgtttgcacatgtatgttgctttgcgcatgcatgtaattgctcatgtatccattcgtttgaacacttgacggaacagttgctgactatttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG

Basic information

species Zea mays
transcript GRMZM2G098236_T02
intron # 9
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), 49 (downstream exon)
Score: 31

AGATAAGAGAGTTGTTATTCCGGGAGATACTGGAATATCACCCACAACTGCTGAGTAGCTACATTAATGGCACAGAGAGGACAACCTTTCTCTACCCAAGgttttagctt ... ttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 20

AGATAAGAGAGTTGTTATTCCGGGAGATACTGGAATATCACCCACAACTGCTGAGTAGCTACATTAATGGCACAGAGAGGACAACCTTTCTCTACCCAAGgttttagctt ... ttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 26

AGATAAGAGAGTTGTTATTCCGGGAGATACTGGAATATCACCCACAACTGCTGAGTAGCTACATTAATGGCACAGAGAGGACAACCTTTCTCTACCCAAGgttttagctt ... ttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 107

AGATAAGAGAGTTGTTATTCCGGGAGATACTGGAATATCACCCACAACTGCTGAGTAGCTACATTAATGGCACAGAGAGGACAACCTTTCTCTACCCAAGgttttagctt ... ttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatccattcgtttgaacacttgacggaacagttgctgactatttttatgcagTGCTGTTGATCAATTTAAGAAGCAGTTTTCTCATCTTGAAGAGAGTGGTGGTAACGGCCCATCAGTTCCAACAGACAGGAAACATGCATCTCTTCCCAG
                                   tgctgac  putative branch site (score: 107)
                                         ctattttt  CT-rich tract
                                        actatttttat  TA-rich tract