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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g40840.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G366935_T07 (Zea mays), 3'ss of exon 5
----gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
    ||  || |||| ||||||||||||||||||| ||| | |||| ||||||||| | ||||  ||  | |||||  ||| |  ||   |||||||||||  ||||||||| |     || |||||||||||| ||  | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||  |||||| || | |||
gtgtgttagttattgcttgattctgcatatcaattattagctaatttggtagctgcagcttca--ctattattgctccaaaaggccagtgttgaccatctt--cctttctttttgt---aacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 5
gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
             |||||||||||||||||| ||| | |||| ||||||||| | ||||  ||  | |||||  ||| |  ||   |||||||||||  ||||||||| |     || |||||||||||| ||  | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||  |||||| || | |||
-------------tgattctgcatatcaattattagctaatttggtagctgcagcttca--ctattattgctccaaaaggccagtgttgaccatctt--cctttctttttgt---aacagATATGCATGACTTGAGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTGTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G094039_T01 (Zea mays), 3'ss of exon 4
gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
            ||||||||||| ||||||| ||| | |||| ||||||    | |||| | |||| |||||  ||||| |||   || ||||||||||| ||| |         || |||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||  |||||| || | |||
-----------cttgattctgcacatcaattattagctaatttggtagcattggcttcacttttctattgcttcaaaggggcagtgttaaccatcttttcttttgt---------aacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 5
----gtgtgtgattgtttgattctgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
    ||  || |||| ||||||||||| ||||||| ||| | |||| ||||||    | |||| | |||| |||||  ||||| |||   || ||||||||||| ||| |         || |||||||||||| || || ||||| ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||  |||||| || | |||
gtgtgttagttattgcttgattctgcacatcaattattagctaatttggtagcattggcttcacttttctattgcttcaaaggggcagtgttaaccatcttttcttttgt---------aacagATATGCATGAGTTGCGGCTTATCCACACTGATCTGAAGCCAGAAAACATACTACTTGTCTCTTCTGAGTATATAAAAGTTCCAAGTACAAAG

upper sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G08480.2 (Glycine max), 3'ss of exon 5
------------------------------------gtgtgtgattgtttgattc------tgcatatcaattcttaacaaattcggtagctgctgattcattcttctgttgctgaaaaggagcatgcttg---------accatcttttcctttctttcttctaaaata----gATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
                                     ||| | ||| ||   |        | || || ||  | |  |   |||  | ||  ||| ||  ||  ||    | || |  | | | || |||         ||  |   ||| ||  | |  | ||  |||    |||||||||||| ||||||| || |||||||| || ||||||||||| ||||| ||||| || || || ||| ||| | | ||  | |  |||
gtctgtggattattcttggccttcagtttatttctcatgtttcattcttaagtctcttgcttacaaattaaaccatggctttttccttggc--ctgctttctttgtccagggatgcagtgtatcttggttgtgtctgcttactttaacttctttcttgttctttatcatattcagATATGCATGAACTACGCCTAATCCACACTGACCTAAAGCCAGAAAATATACTTCTTGTTTCCTCTGAATATGTAAAGCTCCCTAGCTATAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
                                            ttctaaa  putative branch site (score: 2)
                  tgcttgaccatctttt  CT-rich tract
                                        tttcttctaaaata  TA-rich tract