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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaacaacattgcagttagtatgtttggacagcttcatgtttcagattcaagagtgtaagcgtgtaataaatgtttgattcattcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC

Basic information

species Zea mays
transcript GRMZM2G408305_T03
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408305_T04 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g15540.1 (Oryza sativa), 3'ss of exon 7
gtttgaacaacattgcagttagtatgtttggacagcttcatgtttcagattcaagagtgtaagcgtgtaataaatgtt-tgattcattcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC
||| | ||      | |  || ||| |||| | |  ||||  ||||| | |  ||||||   |  |   |   ||  | || || |||||||  ||| ||||| || ||||||||||||||||| ||||||||||||||||||||||| |||  ||||||| | || |||||   |||||||||||| |||||||
gttggcactctgcagtacataatat-tttgcataatttcagatttcaaacttcagagtgctggtctaatacgcattctgtgcttgattctta--gGTACTTCCGGTGTTTATCAAAGCTTTGCCGCTAAAAGAAGATCATGAAGAATCCATGGTTGTCTATAGCTGTGTCTGTAATTTATTATTATCTTCACATC
















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: 105

GTTTAGTAACTCAGAATCAGATGATGCAGTAAGAGATAACGCTGCTGGTGCTATTGCTAGGATGATAATGGTGCAGCCTCAGTCGATTCCTCTCAACCAGgtttgaacaa ... attcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTTAGTAACTCAGAATCAGATGATGCAGTAAGAGATAACGCTGCTGGTGCTATTGCTAGGATGATAATGGTGCAGCCTCAGTCGATTCCTCTCAACCAGgtttgaacaa ... attcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

GTTTAGTAACTCAGAATCAGATGATGCAGTAAGAGATAACGCTGCTGGTGCTATTGCTAGGATGATAATGGTGCAGCCTCAGTCGATTCCTCTCAACCAGgtttgaacaa ... attcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 101

GTTTAGTAACTCAGAATCAGATGATGCAGTAAGAGATAACGCTGCTGGTGCTATTGCTAGGATGATAATGGTGCAGCCTCAGTCGATTCCTCTCAACCAGgtttgaacaa ... attcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttcagattcaagagtgtaagcgtgtaataaatgtttgattcattcttatagGTTCTTCCAGTTTTTATCAAAGCTTTGCCACTAAAAGAAGATCATGAAGAATCAATGACTGTCTATGGTTGCGTCTGCGGTTTATTATTATCATCACATC
                                    gtttgat  putative branch site (score: 101)
                                          ttcattctt  CT-rich tract
                            taataaatgtttgatt  TA-rich tract