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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttatctatatgaaatctgcttaagcaaaattgtggtaccctttcactgtgtctacaagctaatagtttctgtaactacctttattattgctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG

Basic information

species Zea mays
transcript GRMZM2G470292_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G470292_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 4
cttatctatatgaaatc-tgcttaagcaaaattgtggtaccct---ttcactgtgtctacaagctaatagtttctgtaactacctttattattgctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG
 ||||  |  |  | |  |   |         ||||  |   |   ||   || ||  |  |   | | | |||    |  ||   || | |    |||||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| |||||||||
gttatgcacttacacttgtatgttgtttgccctgtgagattttatattttttgggttgatcattcagtggattc----atgacacctaatctgtacttttatagGGACATCCAGAAATAGTTGTCCAACTCGTTGACCTGATTGGCATCACATCAATAATGGAG
















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), 49 (downstream exon)
Score: 157

GTGGTAATATGTTTGGTGCTGCGGAAGACTGCTCCACTTATGAGTTATGTTCAGgtattcccca ... ctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GTGGTAATATGTTTGGTGCTGCGGAAGACTGCTCCACTTATGAGTTATGTTCAGgtattcccca ... ctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

GTGGTAATATGTTTGGTGCTGCGGAAGACTGCTCCACTTATGAGTTATGTTCAGgtattcccca ... ctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GTGGTAATATGTTTGGTGCTGCGGAAGACTGCTCCACTTATGAGTTATGTTCAGgtattcccca ... ctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgtctacaagctaatagtttctgtaactacctttattattgctttttatagGGGCATCCAGAGATAGTTGTCCAGCTTGTTGACCTGATTGGCATCACATCGATAATGGAG
                        ctgtaac  putative branch site (score: 128)
                                          ttgcttttt  putative PPT
                                   tttattattgcttttt  TA-rich tract