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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacagtgaaccattttaccagaatatatcagtagtttgcttcatattttgacaggggaccacgtgacaaaatatactaatcttctcctatttctggcagGTTACAGGAATACCAGTTGTGTTTATGTCTGCATTGGAGGGTAGGGGGCGGATTGCTGTCATGCGCCAGGTTATAGATACTTATGAGAAATGGTGTTTAA

Basic information

species Oryza sativa
transcript LOC_Os01g12540.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12540.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G848602_T01 (Zea mays), 3'ss of exon 7
-----ttacagtgaaccatttta--ccagaatatatcagtagtttgcttcatattttgacaggggaccacgtgacaaaatatactaatcttctcctatttctggcagGTTACAGGAATACCAGTTGTGTTTATGTCTGCATTGGAGGGTAGGGGGCGGATTGCTGTCATGCGCCAGGTTATAGATACTTATGAGAAATGGTGTTTAA
       | |   |||   |  |  |  |||||| |   |  |||| |||||||| |    | |   ||  |  |||| | |  | || | |  ||  || |||||||| ||||||||||||| ||| ||  |||| ||  ||||||| ||||||||||||||||| |||||||||||||||||||| |||||||| ||||||||||
gctgaaaagaaataactgctacattctggaatatgt---tgttttgtttcatattcttgtggagtggcagattgcaaagtgt--tgatatcc--ctccttttggcagGTGACAGGAATACCAGCTGTTTTCGTGTCAGCGCTGGAGGGGAGGGGGCGGATTGCTGTGATGCGCCAGGTTATAGATACCTATGAGAAGTGGTGTTTAA

upper sequence: LOC_Os01g12540.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G39960.1 (Arabidopsis thaliana), 3'ss of exon 7
-ttacagtgaaccattttaccagaatatatcagtagtttgcttcatattttgacaggggaccacgtgacaaaatatactaatcttctcctattt-ctggcagGTTACAGGAATACCAGTTGTGTTTATGTCTGCATTGGAGGGTAGGGGGCGGATTGCTGTCATGCGCCAGGTTATAGATACTTATGAGAAATGGTGTTTAA
 | | | | ||  |||  | |    | ||| | |   |   ||| | ||||| ||     |  |||         |  |       |  ||||| || |||| | || |||||||||||||||||||| |||||||| ||||| || || || || |  || |||    | || |  ||||| ||  ||| |||||||| ||
gtaataataaaa-attgcatct---tttattaatt-ctcatttcttcttttgccatt---cttcgtatttcccggtgatggaaacataatatttgcttgcagATAACTGGAATACCAGTTGTGTTTATCTCTGCATTAGAGGGAAGAGGACGTATGGAAGTAATGAAAGAAGTCACTGATACATACAAGAGATGGTGTTCAA

upper sequence: LOC_Os01g12540.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv16s0022g01890.t01 (Vitis vinifera), 3'ss of exon 7
ttacagtgaaccat---tttaccagaatatatcagtagtttgcttcatattttgacaggggaccacgtgacaaaatatactaatcttctcctatttctggcagGTTACAGGAATACCAGTTGTGTTTATGTCTGCATTGGAGGGTAGGGGGCGGATTGCTGTCATGCGCCAGGTTATAGATACTTATGAGAAATGGTGTTTAA
  | ||   |  |    | | |||     | || ||  | | |  ||||   |  |||      |  | |     | |     || | || | | |||| ||||||||||||||||||||||| || || || ||||| ||||| |||||  | ||  |||| ||||||||||| || ||||| ||||| |||||||||||||
-aaaagaacattacagatcttccattgcctttctgttatgtaccacataacctt-cagaaatataaattaattggtttcgggttcatatcgtttgtctg-cagGTTACAGGAATACCAGTTGTATTCATTTCAGCATTAGAGGGAAGGGGAAGAATATCTGTGATGCGCCAGGTCATTGATACATATGAAAAATGGTGTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgacaggggaccacgtgacaaaatatactaatcttctcctatttctggcagGTTACAGGAATACCAGTTGTGTTTATGTCTGCATTGGAGGGTAGGGGGCGGATTGCTGTCATGCGCCAGGTTATAGATACTTATGAGAAATGGTGTTTAA
                             tactaat  putative branch site (score: 1)
                                   tcttctcctatttct  CT-rich tract
                       aaaatatactaatctt  TA-rich tract