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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactgatgcttatcttgctaaaagcataattatttctaggagatcatcttagaacaataatccattttctattatctaaactcttactgcattgaag

Basic information

species Oryza sativa
transcript LOC_Os08g10150.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA09G15200.1 (Glycine max), 5'ss of exon 17
---ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactgatgcttatcttgctaaaagcataattatttctaggagatcatcttagaacaataatccat-tttctattatctaaactc-ttactgcattgaag
    | ||||| |||||||| |||||||||||||| |||||||| || ||    | |||    ||||||||    || |||||  | ||||              ||| |       |  |||      ||| ||  | | |  | || |  | | ||   |  |   | ||| |  ||| |   ||  | | |  | | |  
TATCTAGAGATCCATCTCTTTTGGGCTGGAAAAGGGACTTGTTGTATACCAGTTCAAGGTACTTATGGGCCCCTGATTTCAGCCATTAGTGCTATCCCAGgtaaaacttaaaagagacaggcttttcatatatttggtccaaacacat-acgtgaaaatgttgttttttatttttcctatttttgctagtcattatagtaa--

upper sequence: LOC_Os08g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G25590.1 (Glycine max), 5'ss of exon 20
---ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactgatgcttatcttgctaaaagcataattatttctaggagatcatcttagaaca-ataatccattttctatta-----tctaaactcttactgcattgaag---------------------------
    | |||||||||||||| |||||||||||||| ||||||||||| || || | |||    |||||||| |  ||   |||| |   ||   || || | |||| |  |    |      |   |   ||  | |||       | | | | |  |   ||||||| || ||   ||     || ||| |  ||     ||  |                            
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATG---CTATTCCAGgtaatactatgaaaaaaattggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatttttttaatttgatacattgttttgtgttgtacag

upper sequence: LOC_Os08g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA08G25600.1 (Glycine max), 5'ss of exon 17
---ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactg------atgcttatcttgctaaaagcataatta-------tttctaggagatcatcttagaacaataatccattttctatt-atctaaactcttactgcattgaag-----------------
    | |||||||||||||| |||||||||||||| ||||||||||| || || | |||    |||||||| |  ||   |||| |   ||             ||||       |   ||       || | |  ||||||       ||  |     || |||    | ||   |   |||    ||| || || | | ||| |    | ||                  
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATCCCAGgtaatactatgaaaaaaatttggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatatttttaatttgataaattgttttgtgttgtacag

upper sequence: LOC_Os08g10150.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT1G56120.1 (Arabidopsis thaliana), 5'ss of exon 17
---ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactgatgcttatcttgctaaaagcataattatttctaggagatcatcttagaacaataatccattttctattatctaaactcttactgcattgaag
    | ||  | ||||| ||||||||||||||||| || ||||| ||||||| || ||||   ||||||||||  ||  | ||  | ||||   |          ||  | | ||    |  |          | ||||  |       ||||    | | || |   |    | | |  ||  ||  | | |        
CATCTCGAAGTCCATCTTTTCTGGGCTGGAAAAGGAACATGTTGTATTCCTATCCAAGGGGCTTATGGGCCATTAATAGCGGCCGTCAGTGCGACACCAGgtaacacaaacggttgatatattttttttcctctgattttca-----ctatctcccgatactagttagtgccgtgtcacatattcttgttcag--------

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: 27 (upstream exon), 63 (downstream exon)
Score: 2

ATGGAGATTCATCTCTTCTGGGCTGGAAAAGGCACTTGTTGCATTCCTACCCTAGGGTTCTATGGGCCATCTATCTCAGCATTAAGTGTCTCTTTTTCGGgtactgatgc ... tgcattgaagGGGATCCTGGTCTAAACATAAACAACACGACTAACGGTGAGAATACAAGCAGCGGTAGAAGAGGTTTGGTTGTTGGAGTTGTAGTCAGTGCTGTTATTGT




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