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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttttactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtag

Basic information

species Zea mays
transcript GRMZM2G313536_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 16
GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttt-tactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtag
|||||||||| ||||||||| | ||||| ||| |||||||||||||||||||||||||||| ||||||||||||||| | || ||  |  | |  || |  | || |||  |    |||  | || |  | |        | ||||  ||| ||    |||||  | |    |                                                            
GTTGGGACACCGATCAGTTCCTTACAGATATTTCAGAGGCTACTTTGGTTATGTCAAGTGTGGTTAAGAATgtgagttgaattaataatatgttgccttgatatattcaggta---attatcaatatgatact-------attcat--gagttgtaatgttttgatatggttgtag---------------------------------------------------------

upper sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 17
GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttttactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtag
                                                              | |  |  ||    |||   ||  || || |    |    |  |    ||| |  || |  |||  ||     |||      | | |  || |    | |  || ||| |  |     |  || |||    ||| | | ||    ||                       
--------------------------------------------------------------GGTGGGCTTGCACCTGGTG-GATTCAACTTTGATGCCAAATTgttggttcc-cgctgacattgttttttttttttgtgtgtgtgtaaattggt---ctctgattcaactgaatttcaattgacttggaa--ttctattatgtcaacag----------------------

upper sequence: GRMZM2G313536_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA17G07380.1 (Glycine max), 5'ss of exon 17
GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggcatgaaccagctctctccctttttactcaaatccacattgcctatgtacttcccagttgcactcatatgagctgctgcgtttttgtttaacagggtggacttgcacctggtggtttcaactttgatgccaaattgtcagtaccttttgtgtag
                                   ||||  ||||       ||  | |  | ||      |  | || ||    ||  |||| ||  | | ||||   || |   ||   | | | |  |||   |    |  | |     ||   ||| | |                                                                    
----------------------------------GGAGG--ACTTGCACCCGGTGGATTCAACTTCGATGCGAAATTgtca--gtccttctctatctttatatacttgtattcctgtttgttttattcccccc--ctcagtttctgtacttagcaatgttatag--------------------------------------------------------------------

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: 36 (upstream exon), 45 (downstream exon)
Score: 301

GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggca ... ttttgtgtagGTTGTAACATTGCTCTATGGCTTCAATCAGGCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGG


Block sizes: 38 (upstream exon), 48 (downstream exon)
Score: 269

GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggca ... ttttgtgtagGTTGTAACATTGCTCTATGGCTTCAATCAGGCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGG


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 239

GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggca ... ttttgtgtagGTTGTAACATTGCTCTATGGCTTCAATCAGGCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 401

GTTGGGACACAGATCAGTTCATGACAGACATTGCAGAGGCTACTTTGGTTATGTCAAGTGTAGTTAAGAATgtgagtggca ... ttttgtgtagGTTGTAACATTGCTCTATGGCTTCAATCAGGCTAGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGG