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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC

Basic information

species Oryza sativa
transcript LOC_Os02g53130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 1
-----------------------------gtaattaaccaaccatatcttcctcgaacgcactgcacg---agacacacattgttgcatctttgtg-atcttaacttgtgtgttttttttttggattat---gtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                              |   | | |||  |     || | |      ||| |||   |    | ||  | |   | | ||||  | |     ||||||| | | ||||| ||  |   ||||||| |||||||||  |||||||||||| ||||||||||| ||||| ||||||||||||||||||||||||||||| |||||||| |||||||| || |||||
gtatgttatgtatctgcctcgctcgctcgctcgctcatcaaatacggtctctttgtttcttctggacgccgacgtgcgcaaggctaagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttttgaatggtttcgtgcagCGTGGTGGTACCGGCCGGAGTACATAATAAACGAGCTCAACATCAACTCGGTGATCACCACGCCGGGACACGACGAGGTGCTGCCCATCAACGCCCTGAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 1
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
    ||     | |         | |    | |||| ||     ||   |||   |       ||   |||  |   |||| | | | |      ||| |||| ||||||||||||||||||| ||||||||||||||||||||| ||||||||||||||||| || |||||||| |||||||| |||||||| || || ||
---gtttgtacatcggtctagttttgtttcctctgctcg----ccaacgtgtgcgagggcgacgacgctaa--taaatgttctctctgt------tgtacagCGTGGTGGTACAAGCCGGAGTGCATGATAAACGAGCTGAACATCAACTCGGTGATCACCACACCAGGACACGACGAGGTGCTGCCCATCAACGCCCTCAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G33490.1 (Glycine max), 3'ss of exon 1
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgc---atctttgtgatcttaacttgtgtgt---tttttttttggattatg--tgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
        |||||  |   |   |  |         | || |      ||  | |   || ||  ||  |  ||  | |   |   || | ||||||  | |   ||||| |||||||||||||| |||||| | ||| |||||| |||  |||||||| ||||| || |||||    ||||| ||| |  |  |||||||  |    ||
--------ccaactttgcatgtgt--agtctgtcatatgacatgtttcttcctacgaaattttcatggacacaaactataattacattctattttggtgtgtccctgcagGTTGGTGGTACAAGCAGGAGTATAAGATCAACGAGTTGAGTATAAACTCAGTGATAACTACGCCTTCTCACGAGGAGATCTTGTCCATCAACTCATATAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G02510.1 (Glycine max), 3'ss of exon 1
----------------------------------gtaattaaccaaccatatcttcctcgaacgcactgcacgagac-----acacattgttgcatctttg--------------tgatctta---------acttgtg-tgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                                   |||||     ||    | || |        | |||| |||       |   |  || | |  |||               | || | |         | |  ||  |||||||||   |  |   || || ||||||||||||||| || ||||| || |||||| |||| |||||||| ||||| || |||||  | ||||| ||| |  | ||||||||  |   |||
gtataatatgtctttcttcgaactcttatggtttttaattttgttacttctttttgcctaggaatattgcatgaggttgaaaatgaacagtggtacttttacagtgagatttagataatttcatggacagaaattaatgacgttttttttggtgtctccttgtagGTTGGTGGTACAAGCCAGAATACATCATCAACGAGTTGAATATAAACTCAGTGATAACTACGCCTTGTCACGAGGAGATCTTGCCCATCAACTCATGGAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G33480.1 (Glycine max), 3'ss of exon 1
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
  || | |   |         | |  |||    | |     |   |  || |     |       |  | || ||| || | || ||   |  |   ||||| ||||||||| |||||||| || || || |||||| ||||||||||||| ||||| || |||||| | ||| | ||| |  | ||||||||  |   |||
-caacttagagatgtgtgtaacatataacatgtttcttccaaggaattttttcatggcacaa-attaattacatgtttgatattcttggtgtgtccctgcagGTTGGTGGTATAAGCCGGAATATATCATCAACGAGTTGAACATAAACTCAGTGATAACGACGCCGTGTCACCAGGAGATCTTGCCCATCAACTCATGGAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G11430.1 (Glycine max), 3'ss of exon 1
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgc-agCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
||| |  || |  |    |||     |      ||| |    || | ||| |   |   ||    | | || |  ||| || | | |||  ||| | |   ||||||||||||||||||||| || || || |||||||| ||||||||||| ||||| ||||||||  | ||||| ||| |  | ||||||||  |   |||
gtattctactattc---ccttttcttatttttttgctct---cataaattctaatagactttgattataaaataatgttttctctgtttcaatttttttttagCTTGGTGGTACAAGCCGGACTATATTATCAACGAGCTTAACATAAACTCCGTGATAACCACGCCTTGCCACGAGGAGATCTTGCCCATCAACTCATGGAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G37130.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------gtaattaaccaaccatatcttcctcgaacgcactgcacgagacac--acattgttgcatctttgtgatct---taacttgtgtgtttt----ttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                                                                            ||    |  ||| | | |       |    |    | || | ||  |  ||| || ||  |       |   | ||||   |   ||    ||   ||| ||   |  || ||||||||| ||||| |||||||| || |||||||| ||||||||||| ||||| || |||||  | ||||| ||| | || |||||||| ||  | ||
gtacataaaatctttttgcttcaataaatctcattaagatgaactaattgatatgtttaaaaagtctccgaacctataggagaaaaacaaaaacagaaatcatattaaaaaatgaaaaactaatgttggtggatgatgtcagcttctgtgacttacataaattcaaattcaatggttttgttttagGTTGGTGGTATAAGCCAGAGTACATAATCAACGAGCTAAACATAAACTCCGTGATTACGACGCCATGTCACGAGGAGATTCTTCCCATCAACGCTTTCAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G77760.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                          |||  | |     |  |     || ||  |  |||  | |    |      | || |||  |||  ||   | ||||||||||||| ||||| || ||||| || |||||||| || |||||||||||||| || || || || ||||  ||| |  | || || |||||  | ||
-----------------------gtaaac-tattaacttacccttgtcttcttttacattttagttaccgatgctaatattatttacttgtttttgttacagCTTGGTGGTATAAGCCTGAATACATAATCAACGAGCTTAATATAAACTCGGTGATTACAACACCTGGTCACGCAGAGATTTTACCGATTAATGCATTCAC

upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g03910.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------gtaattaaccaaccatatcttcctcgaacgcactgcacgagacacacattgttgcatctttgtgatcttaacttgtgt-gttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                                |||||   || ||  ||  ||  |      |    |    | | || |  | |  |  | ||||| |  |  |||   | ||||  | ||    | |||||||||||||| |||||||||||||| || || ||||||||||| ||||| || ||||| || ||  | ||||| ||  |  | ||||||||  |   |||
gtacactgcgccccacatccccccacccccctattaatagac-atgactctctatattttgtttttggttttataaatgggcgaagatgag-gatctgaggtaatgttactattttggttgacatggagcagCTTGGTGGTATAAGCCGGAGTACATCATTAATGAGCTGAACATTAACTCCGTCATCACTACACCATGCCACGAAGAAATCTTACCCATCAACTCCTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgttgcatctttgtgatcttaacttgtgtgttttttttttggattatgtgcagCTTGGTGGTACAAGCCGGAGTACATGATAAACGAGCTGAACATAAACTCGGTGATCACCACGCCGGGACACGATGAGGTGCTCCCCATCAATGCGCTGAC
                  tcttaac  putative branch site (score: 2)
                                ttttttttttggatta  TA-rich tract