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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtttaggtcagtttttgtgttaaattcctgctcatgagaactcagctaataatgggtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG

Basic information

species Zea mays
transcript AC233887.1_FGT006
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC233887.1_FGT006 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g34000.1 (Oryza sativa), 3'ss of exon 5
gtatttgtttaggtcagtttttgtgttaaattcctgctcatgagaactcagctaataatgggtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG
|||||   || | |    | | |||| |||  |||| |    ||     | || ||||||||||| |||||||||||||||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||||||||| ||||| || || |||||||| |||||||
gtattgtgtttgcttg--tctcgtgtaaaagccctgattgctagggtgaaacttataatgggtgcatgcagGTTTTACGTCTTTCTGCAGCAACTCAAGATCTACCTAGGTCTGTTGTCTGCAACGTTCATGGTGTAAATCCAAAGTTCCTCAAGGTTGGTGAAAAAATAG
















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), 33 (downstream exon)
Score: 98

AAATTACTTGGAATATATCAAGAGAGAGAAAAATGGTGCTATTCAGTCTTTTCTTGTTAAACATATCAATAACTGGGTGACTAGAGCATACTGCCATAAGgtatttgttt ... gtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG


Block sizes: 46 (upstream exon), 33 (downstream exon)
Score: 16

AAATTACTTGGAATATATCAAGAGAGAGAAAAATGGTGCTATTCAGTCTTTTCTTGTTAAACATATCAATAACTGGGTGACTAGAGCATACTGCCATAAGgtatttgttt ... gtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG


Block sizes: 40 (upstream exon), 33 (downstream exon)
Score: 6

AAATTACTTGGAATATATCAAGAGAGAGAAAAATGGTGCTATTCAGTCTTTTCTTGTTAAACATATCAATAACTGGGTGACTAGAGCATACTGCCATAAGgtatttgttt ... gtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 31

AAATTACTTGGAATATATCAAGAGAGAGAAAAATGGTGCTATTCAGTCTTTTCTTGTTAAACATATCAATAACTGGGTGACTAGAGCATACTGCCATAAGgtatttgttt ... gtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgtgttaaattcctgctcatgagaactcagctaataatgggtgcgtgcagGTTTTACGTCTTTCTGCTGCAACTCAAGATCTACCGAGGTCTGTTGTTTGTAACGTACATGGTGTAAATCCGAAGTTTCTTAATGTTGGTGAGAAAATAG
                                 agctaat  putative branch site (score: 31)
       tgttaaatt  TA-rich tract