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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatgacatactctgaaatgaaggatttgaaccttgaataatgttcttacagtttgttttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC

Basic information

species Zea mays
transcript GRMZM2G179732_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179732_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g74460.2 (Oryza sativa), 3'ss of exon 8
---gtaatcatgacata--ctctgaaatgaaggatttgaaccttgaataatgttcttac-agtttgttttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC
    | |||| |||| |  ||||||||||    || |  || ||||   | |||||||| |  || | ||| |||||| ||||| |||||||||  |||||||||  | |||||||||||| ||||||| | |||  |||||||||||||||||||||| 
gtaatcatcacgacacacactctgaaatggta-atctttactttgag--acgttcttactacattttctttaatgcagGACTTCGGAGTCTTTTTCACCCATATGCCTTCCAAGATACAATTCTATGGCTTTCTTATATGCTTATGTTCATTTTTTTGAT
















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: 101

ATTTCCAGGTTATTAGTCTTGTTGGAGCACAAAAGGCAACTTTGCATCCTGATGATATTTTATTACTTGCGAATTTCATTCTGTCCTCTGGATCTTTTAGgtaatcatga ... ttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 102

ATTTCCAGGTTATTAGTCTTGTTGGAGCACAAAAGGCAACTTTGCATCCTGATGATATTTTATTACTTGCGAATTTCATTCTGTCCTCTGGATCTTTTAGgtaatcatga ... ttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 121

ATTTCCAGGTTATTAGTCTTGTTGGAGCACAAAAGGCAACTTTGCATCCTGATGATATTTTATTACTTGCGAATTTCATTCTGTCCTCTGGATCTTTTAGgtaatcatga ... ttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 96

ATTTCCAGGTTATTAGTCTTGTTGGAGCACAAAAGGCAACTTTGCATCCTGATGATATTTTATTACTTGCGAATTTCATTCTGTCCTCTGGATCTTTTAGgtaatcatga ... ttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatgaaggatttgaaccttgaataatgttcttacagtttgttttttatgcagAACTTCAGAGTCTTTTGTACCCATATGTTTGCCAAGATACAATCCTATGGCCTACTTGCATGCTTATGTTCATTTTTTTGAC
                              ttcttac  putative branch site (score: 96)
                                       tttgtttttt  putative PPT
                                     agtttgttttttat  TA-rich tract