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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttatgaggtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC

Basic information

species Oryza sativa
transcript LOC_Os11g01140.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G001457_T01 (Zea mays), 3'ss of exon 1
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttatgaggtggtg-gtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
                                                                                                                    || |  ||| ||  || | | |  |   | |  || |  | ||    |||  | | ||| ||  |   |||| | ||||  ||||| |||||||||||||| ||||| |||||||||||||| || ||||| ||||| || ||| ||||||||||||||||  ||||||||||||||||||||||
-------------------------------------------------------------------------------------------------------------------gtaactaatcttg--tgctaaaagaaacatgtatgatacagctac---tatatgatagtgagttctctttctactggttgtgtcagGAATTCTTCTATATGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCC

upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20
lower sequence: GLYMA12G07890.2 (Glycine max), 3'ss of exon 21
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatggttacattactgtatcagacatggttatggttatgag-gtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
                                                                                               |||  || |     | ||  ||| | |||    |    | |||| |    |  | ||| || ||   | |  |   |  |   | || ||   ||  ||  |||||| |||||| ||||||||||||| ||||| |||||||| || || ||||| || |||||| | |||||| | |||||  | ||||||||  | | ||||||
-----------------------------------------------------------------------------------------------gaatttaatggccgaaac--ttaacctattggtctctttcacataa----aagacacacggatacactaaaaaacatactttgactgcatgccttacttttttcagGAATTCTTTTATATGAAATGTTTTATGGGTATACACCATTCAGGGGAAAGACTAGGCAAAGAACATTTACAAATATTCTCCACAAGGACCTTAAATTTCC

upper sequence: LOC_Os11g01140.3 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 20
gtaattcttccaccaacaatatagttatcttgttagacagtccttgtagtctattcaattactgtgaataaataaagtattgaaaattaaaaggtgaaaatagtttagaacaccattatcatatcatgcatg-gttacattactgtatcagacatggttatggttatgaggtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
                                                                                                 ||||| | || |      |     |  | |   ||   || |   ||  ||   |  |   ||  ||| |    |  || |     || | |||| |  || ||| |||||||||||||||||| | ||||| |||||||| ||||| ||||| || ||||||  ||||||||| || ||  | ||||| ||| | | ||||||
-------------------------------------------------------------------------------------------------aaatactatatatgtgtgtgtgtgttccctttgtgcactaaaactcttaattttaactcaatactgtttt----ttctgattgattatatgtttgctcttttagGCATTCTTCTATATGAAATGCTTTATGGATATACACCATTTAGGGGAAAGACAAGGCAAAAGACATTTGCCAACATTCTTCACAAAGATCTTAAATTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagacatggttatggttatgaggtggtggtaatgaatctatttgttgattcagGGATTCTTCTATATGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCC
                                            tgttgat  putative branch site (score: 4)
                               taatgaatctattt  TA-rich tract