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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattacatattgacctactactcagattccttttttatgtaatcaaatcttcttttgatgaattttatgttctgtttttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA

Basic information

species Zea mays
transcript AC217385.3_FGT009
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217385.3_FGT009 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g11120.1 (Oryza sativa), 3'ss of exon 4
gtattacatattgacctactactcagattccttttttatgtaatcaaatcttcttttgatgaattttatgttctgtttttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA
||| || |  || |||| ||||| |  | |||| |     || | ||    | |||||||| || | | ||| | ||| || ||  ||||||||| |||||||| |||||||| || ||||||||  |||||||||||||||||||||| || || |||||||||||||| || ||||| ||||||||
gtaatatagtttcaccttctactgaagtgccttctcc-catagtgaatctattttttgatgtatgtaa-gttttatttgtt-ctaaagAGGGCGCAAGAACTGCACTTAACCTTGGTGGCACAATGCTTGGTTTCTACCCTGTTAGAGTCTTACCTTCAAAGACAGCTATATTGCCTGTGAATCCAAA
















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: 30 (upstream exon), 49 (downstream exon)
Score: 104

GGCACCCTATTCTGCCGCTCCACCGCCAAGCGCCTGCAGTTCTGTTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 128

GGCACCCTATTCTGCCGCTCCACCGCCAAGCGCCTGCAGTTCTGTTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA


Block sizes: 29 (upstream exon), 49 (downstream exon)
Score: 98

GGCACCCTATTCTGCCGCTCCACCGCCAAGCGCCTGCAGTTCTGTTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA


Block sizes: 30 (upstream exon), 49 (downstream exon)
Score: 118

GGCACCCTATTCTGCCGCTCCACCGCCAAGCGCCTGCAGTTCTGTTTTGCATTTATTGAGTTCTCTGATGAAGgtattacata ... ttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgtaatcaaatcttcttttgatgaattttatgttctgtttttttctgtagAGGGCGCCAGAACTGCGCTTAACCTGGGAGGCACAATTTTTGGTTTCTACCCTGTTAGAGTTTTGCCGTCAAAGACAGCTATGTTACCTGTTAATCCAAA
                    ttttgat  putative branch site (score: 118)
                              ttttatgttctgtttt  putative PPT
                            aattttatgttctgtt  TA-rich tract