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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_Os01g40840.2
intron # 5
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 43 (downstream exon)
Score: 7

GGGCCAAGCTTGTATGATTTTCTAAAGAGAAATAGATACCAACCTTTCCCTGTGGAACTTGTGCGGGAGTTTGGACGGCAACTGTTGGAATCTGTAGCATgtgtgtgatt ... tctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgctgaaaaggagcatgcttgaccatcttttcctttctttcttctaaaatagATATGCATGAATTACGCCTTATTCACACTGATCTGAAGCCAGAAAACATACTCCTTGTGTCTTCGGAGTATATAAGGGTTCCAGGTTCCAAG
                                            ttctaaa  putative branch site (score: 7)
                  tgcttgaccatctttt  CT-rich tract
                                        tttcttctaaaata  TA-rich tract