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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcagtccagtccagtccagtccagtgtgtttctgatcttggcgttggctgccactccgcggttgatttgtgtgagctgatttcattaaagttttgcctccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT

Basic information

species Zea mays
transcript GRMZM2G171349_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171349_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g04030.3 (Oryza sativa), 3'ss of exon 11
gtaagtcagtccag---tccagtccagtccagtgtgtttctgatcttggcgttggct--gccactccgcgg---------ttgatttgt---gtgagctgatttcattaaagttttgcctccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT----------
|||||    ||| |   | |  | | ||    ||   |||   |  |    | ||||     ||     ||         |||| | ||    | | |||||| |||||||||||||||| ||||||||||| || ||||| |||||| |  |    |||   |  || | |  ||||||   || |    | ||  ||| | | ||         |  || ||| || |          
gtaaggggctcctgcttttcttttccgttggatgatcttcatcttattatataggcttgattacgttttggaagaactcattgactcgtttcatcatctgattccattaaagttttgccttcaacagcagAATCCATTCCGCTGGTGATGGAC----GGGTTTAAAGCAA-GAAGCGGTGATGGAGCT--CGGTCGTGCGTCTCGTGTGTTGT---TTTGTGTGCGTCGTCGTCGCTGTA

upper sequence: GRMZM2G171349_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g04030.2 (Oryza sativa), 3'ss of exon 11
gtaagtcagtccag---tccagtccagtccagtgtgtttctgatcttggcgttggct--gccactccgcgg---------ttgatttgt---gtgagctgatttcattaaagttttgcctccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT-------
|||||    ||| |   | |  | | ||    ||   |||   |  |    | ||||     ||     ||         |||| | ||    | | |||||| |||||||||||||||| ||||||||||| || ||||| |||||| |  |    |||   |  || | |  ||||||   || |    | ||  ||| | | ||         |  || ||| || |       
gtaaggggctcctgcttttcttttccgttggatgatcttcatcttattatataggcttgattacgttttggaagaactcattgactcgtttcatcatctgattccattaaagttttgccttcaacagCAGAATCCATTCCGCTGGTGATGGAC----GGGTTTAAAGCAA-GAAGCGGTGATGGAGCT--CGGTCGTGCGTCTCGTGTGTTGT---TTTGTGTGCGTCGTCGTCGCT

upper sequence: GRMZM2G171349_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g04030.1 (Oryza sativa), 3'ss of exon 11
gtaagtcagtccag---tccagtccagtccagtgtgtttctgatcttggcgttggct--gccactccgcgg---------ttgatttgt---gtgagctgatttcattaaagttttgcctccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT
|||||    ||| |   | |  | | ||    ||   |||   |  |    | ||||     ||     ||         |||| | ||    | | |||||| |||||||||||||||| ||||||||||| || ||||| |||||| |  |    |||   |  || | |  ||||||   || |    | ||  ||| | | ||         |  |          
gtaaggggctcctgcttttcttttccgttggatgatcttcatcttattatataggcttgattacgttttggaagaactcattgactcgtttcatcatctgattccattaaagTTTTGCCTTCAACAGCAGAATCCATTCCGCTGGTGATGGAC----GGGTTTAAAGCAA-GAAGCGGTGATGGAGCT--CGGTCGTGCGTCTCGTGTGTTGTTT-TGTG----------

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 1 RNA-Seqlibrary.


Block sizes: 48 (upstream exon), 15 (downstream exon)
Score: 2

GACGGAGCTCGACGCCACCAAGAAGCTACTCGAGACGTCGTCCGCCCAGCAGGAGGAGGTCCTGGCGTACATCGAGAAGAAGAAGAAGAAGCGAGGGATGgtaagtcagt ... ccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccgcggttgatttgtgtgagctgatttcattaaagttttgcctccaacagcagAACCCGTTCCGATGGTGACGCGCCAGGGGGGGAAGGGCGATGGCGCGGTGCATGATCCAGTGATCAGGCGGCCCTTGGACCCCCAATACGTATGCATCCT
                    agctgat  putative branch site (score: 2)
                                     ttttgcctcc  putative PPT
                         atttcattaaagtttt  TA-rich tract