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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG

Basic information

species Zea mays
transcript GRMZM5G899123_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G899123_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 8
gtttgtatattccaaaccatggatttgtttttctgattgctggtttgatcaattgc-tcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG
         ||   ||   | | ||   |||||||    | | |||  ||||||   ||||  |    ||   |||  |||||| ||   || |||| ||||||||||| ||| | || ||||| ||||||||||||||||| ||||||||||| |  |||||||| ||
--------gtttgtaat--ttgcttcaattttctggaaacagcttttgtcaattatatctttga----tgaattaaaacaactttctg--ggattatgttgcagACACAGCCATCAAAAATCTGCTCTCAGGTTGGTCTGTGTACTTTTGATGGGAAGCATGGTGTTAG
















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: 27 (upstream exon), 49 (downstream exon)
Score: 338

AATCAATGAAAAGATTGGTGTTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAACAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 635

AATCAATGAAAAGATTGGTGTTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAACAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 420

AATCAATGAAAAGATTGGTGTTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAACAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 388

AATCAATGAAAAGATTGGTGTTGCTGGTGTAGTCAGCCAGGAGTGCAAGACTGTTGTTTCTCAATATGGACAACAGATCCTAGATCTTTTGCTAGCTGAGgtttgtatat ... tattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattgctcttgaagctctgcggtaactcaacttgctattgggttattttgcagACACAACCAGCGAAGATCTGTTCTCAGGTTGGTCTGTGCACTTTTGATGGCACTCATGGTGTCAG
                     cggtaac  putative branch site (score: 388)
                                            ttatttt  putative PPT
                                            ttatttt  TA-rich tract