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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacctgagttcgtagtaagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag

Basic information

species Oryza sativa
transcript LOC_Os05g50750.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G128748_T01 (Zea mays), 5'ss of exon 13
GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacctgagttcgtagtaagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag
|||||| ||||| ||  | ||||| ||||| |||| |||||||||||||| |||||| |||||  | ||||| ||||||||||| || || || || |||||||||| | |||| |||| |  ||||  |  | |      |   |  |  |       | |   |||||||  |  ||  ||  | |  |  ||||
GATCTTGAGGACGCTGCTTTCAAAGGAGAAAGTTGATGAAGATATTGATTTCAAGGAACTTGCGGCCATGACGGAAGGATACAGCGGCAGTGATCTCAAGgtttgtgcactgctctgaaacgaagtttatgttcataggaagcagtattccacagctgctctgaaactgaaagctgttgttttcctctctgccccag

upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 5'ss of exon 13
---GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacc--tgagttcgt-agtaagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag
   |||| | | ||| || ||| | |||||  | |   | || ||| |||| |  |||||||||||||| ||||| ||||| || | |||||| || ||||||||||||   |    | | |    ||| ||  | |  || |  |||||||||     |  | ||  |  | ||||||                        
GATGATCCTGAAGACTCTCTTGGCTAAAGAACAAG---CCGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGTTATACTGGAAGTGATCTTAAGgtttgtacttctgatggcaatgatgaattgattaagaatcagctgtgttgactc--ttgggattaacaattgaaacag----------------------

upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 5'ss of exon 12
---GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacctgagttcgtagtaagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag
   ||| || | ||| || ||| ||||||| || |   | || ||| |||| |  |||||||||||||| ||||| ||||| || | |||||| || ||||||||||||        ||  ||     |   | || |  |      || |  |||||||  |||     |||  ||| |      |  |||   | |||
GATGATATTGAAGACTCTCTTGGCAAAAGAAAAAG---CAGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGTTATACTGGAAGTGATCTTAAGgtttgta------cttctactgacatcaatggtgaattg----attaa--gaatctgc-tgttgtgttgactcttgggattaatcgttga--aacag

upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv02s0025g00650.t01 (Vitis vinifera), 5'ss of exon 13
GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacctgagttcgtagtaagcttctgtgttgatagaatctga-atgtatgactgaaactttgtgcctttttttgggtaccag
|||| | | ||| || ||||||||||| || ||||| ||||   | |||| ||||||||||||||| ||||| |||||||| |||||||| || ||||||||| ||  ||| ||  ||||  |  |  ||     ||||   ||     | |||| |   |   |||||| | |||      |||  |   |      
GATCATGAAGACTCTTTTGTCAAAAGAAAAAGTTGCAGAAGGATTAGATTTCAAGGAGCTTGCAACCATGACAGAAGGATATAGTGGAAGTGATCTTAAGgttggt--atttctcagaacggggttctgt-----gctttgatgc----ataatcaggtgttcttgactgcagcttaacttttttaatacag------

upper sequence: LOC_Os05g50750.3 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 5'ss of exon 14
---GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggat-tgctttgaacctgagttcgtag--taagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag
   |||||| | ||| ||  || ||||||| || |   | || ||| |||| |  |||||||||||||| ||||| |||||||| | |||||| || ||||||||||||   | | ||     |    ||   | |  ||||  || |   || |    |  | ||  |  | ||||||                        
GATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAG---CAGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGATATACTGGAAGTGATCTTAAGgtttgtacttctactgatggcaatggtgaattgattaagaatcagctgtgttgaccttggcattaactattgaaacag----------------------

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTTAAGGACACTATTGTCAAAAGAGAAGGTTGCTGAAGATATTGATTACAAGGAGCTTGCAACAATGACCGAAGGATACAGTGGAAGCGACCTTAAGgtttgtggattgctttgaacctgagttcgtagtaagcttctgtgttgatagaatctgaatgtatgactgaaactttgtgcctttttttgggtaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG