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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT

Basic information

species Oryza sativa
transcript LOC_Os02g47225.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G178822_T01 (Zea mays), 3'ss of exon 5
------------------------------------------gtaac-tttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                                           ||||  ||| || |     |   | | ||  | |  || || ||  |   |    || ||| ||||||||||  |||||||||||||||| || |||||||| |||||||||||||||||||| |||||||| ||||| ||||||
gtaacttttatattgactggctatttaggttgcttttatcttataacacttcttagttctacagattctctattttagattatttttgccttatcgcatgccttcgcagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTTGGGAGTGTATGGCGTGCTATGAATAAACAGAATGGCGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------gtaactttcatattgacttactat---ttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                                              |  | | |  |  ||  | |||   |||||||| |  ||| |||||  |  |     |||||  |||||||||  |||||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||||
gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtcttacaacat-----gtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G17580.1 (Glycine max), 3'ss of exon 1
----gtaactttcatattgacttactatttttaggtcacctttttct--tatcaagtatgtt----gtcttt---------------gcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
    |||  | |   |    | |    ||  ||   | |  |||| |  | |||| ||| ||    || |||                ||| | |||  | ||||||||||||||||| || || || |||||||| ||| | || || ||||| |||| ||||||||||
gtgagtatttgttgcagaagcctgaagttactatacccctcttttttactgtcaaatatctttaaggtttttcttccttccgtgaacacagGTACAAGTTAATTAAGGAAGTTGGTGATGGAACATTTGGGAGTGTTTGGAGAGCCATTAATAAGCAAAGTGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 1
---------------------gtaactttcatattgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                       || || | ||| | |   ||  |||   || |  ||||| |  | || |    ||    | ||| | |||  | ||||||||||||||||| |||||||| |||||||| ||| | ||||| ||||| ||||  |||||||||
gtgatttctttctctttttgcagaagttac-tatagtcccccttgtttattgttagttttttttattaaaattacctgcaaatacagGTACAAGTTAATTAAGGAAGTTGGTGATGGGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT

upper sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
----------------gtaactttcatattgac-ttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
                | ||||| | | || |  ||  |||||| | ||     | |   |   |  | ||  | || | ||| |  |  || || |||||||||||||| |||||||| || ||||| ||||| || |||||||| || | ||||||||||
gtgagtgggcttgtatggaacttgcttgttaatatttgtattttaatgtgttgatatgtctgagagttttg--gcctctacagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT

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: 73 (upstream exon), 74 (downstream exon)
Score: 87

ATGGACAGgtaactttca ... gtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgacttactatttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT
   gacttac  putative branch site (score: 87)
                                           ttgtcttt  putative PPT
      ttactattttta  TA-rich tract