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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA

Basic information

species Oryza sativa
transcript LOC_Os03g27780.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G077960_T01 (Zea mays), 3'ss of exon 2
------------gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttg---ttcatattctcccccttttgg-acaaatatctttctgatttatgaatacatgatca--gtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
            | ||      |   |    ||  |||| ||  | | |      || |  |  |  |  ||  | | |||   |      | |   |   |  |||       ||  | |  || |       || ||   ||  |  |  | | || ||| ||||||| |||||||||| |||||  ||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || || || ||||||||||||||
gtattataaatgggatgccaggtctgcctgtcttttaaccatccaaaagcaaattatttc-tcaatggatttgcaatgttcacaggagcatacaccatttgctgtttactgtggattgcatggtgttagcctcctatattgccatgggatcttcagactctttcactgcgatgtaaactgactgttataatgttttcagCTGCACGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCACGATGCATTCTAGAATCTGCTGA

upper sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G150213_T04 (Zea mays), 3'ss of exon 2
-------------------------------gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
                                  |||  | ||||  ||||  || |    | || |||||| ||     |  ||  || |  ||  ||   |||| |              |||| | |      | | |       ||| || ||  | ||  | | ||  || ||||| | ||||||||||    ||  ||||||||||| || || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||
gtattataaatgggttgtcagatctgcctgtccgttaaccattcaa-aagcaaattatttctcagtggatgtccaatgtttacaggagcatacagcatttgctgtttac-----------catggatagaggatgattttagcctcctatatatcat-ggagtcctcagactgtttcactgtgatgtaaactga---ctataatgttttcagCTGCACGTTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCACGATGTATTCTAGAATCTGCTGA

upper sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA17G36150.2 (Glycine max), 3'ss of exon 2
gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatc--tttctgatttatgaatacatgatcagtg--ttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
                                                                                       | |   ||  ||||||  || || ||  | |   |     | | ||  |||| ||  |       |    |    | | | | ||    ||||    ||       || || || ||||| || ||||| || ||||| ||||||||||| || || ||||||||||| |||||||| ||  |||| |||||| ||||
------------------------------------------------------------------------------------aaacatgatgaagaatatcaattactaatggaagttaatggtgtaactgacttgtgattgatagtttttatacttctgaattaatatttttttgttacagGCCA-AAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTCCTTGAATCTTCTGA

upper sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G09020.1 (Glycine max), 3'ss of exon 3
gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
                                                                            ||    | |   |    |  ||   | |  |||| || ||| |  |   |   | |  || |    |   | |    ||| |    ||| |     |  || |||        || || || ||||| || ||||| || ||||| ||||||||||| || || ||||||||||| |||||||| ||  | || |||||| ||||
----------------------------------------------------------------------------atcaattactaatggaagttaatggtgtaactgacttgtgattg-acagtttttatacttctgatttaatatttttttgttattatatttt----gttgttgcagGCCAAAAATCTGGAACAACTGTCACCTTTGTCATTATAGAAGGATGGGTTGTAACAGTTGCATCAGTTGGTGATTCCCGTTGCGTACTTGAATCTTCTGA

upper sequence: LOC_Os03g27780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g10700.t01 (Vitis vinifera), 3'ss of exon 3
gtattattctttcactaagctgataacgatttagaggatgtgcatgtaatttagaggcttttagttttctttgttcatattctcccccttttggacaaatatctttctgatttatgaatacatgatcagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
                                                                           | |  | | | |  |     |   |   ||     ||| | || |     |   | |  || || |  || |||    || ||| |   | |  | |  ||||||||       ||||| || ||||| || |||||||||||||| |||||||| || ||||| || || ||||| ||||| || || || || |||||||||||
---------------------------------------------------------------------------cttgattttctctctgcatgctgctgcattctcctttttttaagagtcttttcatctcatt-taaatgtg-act----tgaaaatttgatatggctactttttcagCACGAACTTCAGGAACAACTGTTACCTTTGTTATAATAGAAGGATGGGTGGTAACTGTTGCTTCCGTTGGTGATTCACGGTGCATACTTGAATCTGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgttgttatacacttgcactgcggtgtaaactgattgttaccatgttttcagCGGCGCGCTCAGGGACCACTGTGACTTTTGTTATAATAGATGGATGGGTTGTCACTGTAGCATCAGTTGGCGATTCCCGCTGTATCCTAGAATCTGCTGA
                               aactgat  putative branch site (score: 3)
                                              tgttttc  putative PPT
     ttgttata  TA-rich tract