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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag

Basic information

species Oryza sativa
transcript LOC_Os03g10940.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA01G39950.1 (Glycine max), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |||||       | |   ||| |  |  |||  |  || ||||    |   ||||    | |  ||||   |||   |  |  ||||    ||      ||  || |  |   |||||                    
ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAGgt-------aatatccatcgtggtttgc--aattgcttat---aaatgtttggttatcttgctgtcactgtacacagtaatttc---atgtgttagttcgagactatgatatatt--------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G22250.1 (Glycine max), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcat-ttgcacttgtatctgtatatgtct-gctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
||||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||||   |     |  |  |  |    ||   |    |  |   | | | | |||    |||    ||  ||| || | | |  |||||| || | ||||||                                     
ATATTTCGCAAGGAACCTTTCTTTTATGGTCACGACAACCATGACCAGCTTGTCAAAATAGCTAAGgta-acatttatggaggttcagcagtgtctaaaattgcaaaattatcttgttgatgctgtgcaagttaatgccttgttttagtttctgact-ataatatttt-----------------------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA11G05340.2 (Glycine max), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgt-----ttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaa-atattgcaggcattagcatattgatgaactatacctgagcag
||||||||||| ||||| ||||| ||||| || || |||||||| ||||||||||||||||| |||||       |  |  |||  ||   |   ||  |  | || ||||  ||     |  |||      | |||  |   || | || || | |  |   | |||||                                     
ATATTTCGCAAAGAACCTTTCTTTTATGGTCATGACAACCATGATCAGCTTGTCAAAATAGCTAAGgtaacatccgtcatggtttgcaattatttataagtgtttggttatcttg----ctgtcaccatacacagtaatttcatgttttggttccagattatgatatatt-------------------------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA17G17790.1 (Glycine max), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcat-ttgcacttgtatctgtatatgtc-tgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
||||||||||||||||| || || ||||| ||||| |||||||| ||||||||||||||||| |||||   |     |  |  |  |   |||   |    |  |   | | | | |||    |||    ||  ||||| || | |  |||||| || | ||||||                                     
ATATTTCGCAAGGAACCTTTTTTTTATGGTCACGACAACCATGATCAGCTTGTCAAAATAGCTAAGgta-acatttatggaggttcagtaatgtatagaattgcaaaattatcttgttgatgctgtgcaagttaatgtcatgttttagtttctgact-ataatatttt-----------------------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0129g00410.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
|| |||||||||||||||||||| ||||| || || || ||||| ||||||||||| || |||||||| ||      ||    || | | ||    |  | || | ||  ||  ||| ||  |  ||    |  |     | ||         | | |  |||| || | | |||                          
ATCTTTCGCAAGGAACCATTCTTTTATGGTCATGACAATCATGATCAGCTTGTCAAGATTGCCAAGgtatg------tttggctaaatg-atcttaaaat-ttaaggcatagtcttttcatat-cattcaaaggttctgccactttgccaaaacagcatgtatttcaagtactag--------------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv18s0001g09320.t01 (Vitis vinifera), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
|| ||||||||||| |||||||| ||||| || ||||| |||||||||||||| ||||| ||||||||     ||| |                 | |||||||| ||| |          || | |       ||   |  ||| ||| |   |   |||   | | ||| |  |||   | |  | | |||   |    
ATTTTTCGCAAGGAGCCATTCTTTTATGGTCATGATAATCATGACCAGCTTGTAAAAATTGCCAAGgta-atgacaat-----------------cgtgtgttta-gctaaa---------ttatgttatctcctggtggtcctgttttttcttt---aatccagtaagcaatgccat---ggttgagtgtactcaattg-

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgtttatgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
||||||||||| ||||||||||| |||||||| || || || || ||||| || || || ||||||||||       |  ||  |||   |||    | | ||  || |    |  |   |||||   ||| ||                                                                   
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttt-------taaacgcaga---atgtctgtttcttgctgtttttgacgttggcttgtgg-tgtttag------------------------------------------------------------------

upper sequence: LOC_Os03g10940.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ28543 (Selaginella moellendorffii), 5'ss of exon 6
ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctacagttcacatagacgcatgcgcatgtgttt-atgctgagcatttgcacttgtatctgtatatgtctgctctgctttctgcctgaaaatattgcaggcattagcatattgatgaactatacctgagcag
||||||||||| ||||||||||| |||||||| || || || || ||||| || || || ||||||||||  || |      ||    |  ||    ||| ||| | | ||     | |   ||                                                                              
ATATTTCGCAAAGAACCATTCTTTTATGGCCATGACAATCACGATCAGCTGGTGAAGATTGCCAAGgttt--taaacccagaatgtctgtttgttgctgtttttgacgttggcttgtggtgtttag----------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|15852784|gb|BI805580.1|BI805580
EST:     CATGACCAGCTTGTCAAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: CATGACCAGCTTGTC-AAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
EST: gi|87016659|gb|CI275661.1|CI275661
EST:     CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
EST: gi|66923472|gb|CX110320.1|CX110320
EST:     CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
EST: gi|25806912|gb|CA762873.1|CA762873
EST:     CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
EST: gi|86261473|gb|CI017215.1|CI017215
EST:     CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: CATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
EST: gi|86425593|gb|CI070690.1|CI070690
EST:     TATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAG                         GTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA
genomic: TATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCA

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: 64 (upstream exon), 53 (downstream exon)
Score: 14

ATATTTCGCAAGGAACCATTCTTCTATGGCCACGATAACCATGACCAGCTTGTCAAAATAGCCAAGgtttgctaca ... acctgagcagGTTCTAGGTACAGACCAGCTTAATGCTTACCTGAATAAATACAGGATTGCACTTGATCCCCAGCTTGAGGCTCTGATTGGGAG




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