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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g08340.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G004799_T01 (Zea mays), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
||||||   |||||||||||||||| || ||||||||||| || ||||||||||| || ||  ||||| |||||  |||||||||||||||| | ||||||| |||| || |  |  || ||            |||     | ||||||||||||||  ||  ||||| || | |||||  |||
AATTGGTGTTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTGGGAAATGTGTGGATGTTTGGTAGCCGTTCTTCTGCCCATGACGCTCCTAACCTATACAGgtatgtgttgattggttgcaat------------cctctagccacaacttagatgttttatctcttgtttgtaaccatttc-cag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA17G30020.1 (Glycine max), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|| |  || | ||||| || |||||||| |||||||||||||| ||||| ||||| || ||||| | | | ||| |  | || |||||||| |||||||||  |    |   |  ||  | |   || |   |     | || | |  |   |||       || || |    |||  ||  |||
AAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCTGTTGAAGAAGCTCCTAATTTGTACAGg--tagcctttcattcattcttg--catttaatcttcagattttaagatattatgaaattatatctgcttcatatctcttggcag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT1G80400.1 (Arabidopsis thaliana), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|  ||||  | |||||||||||||| |||||||||||||| |||||||| |||||||| || || |   | ||||    |||  |||||||  |||||||||    |      |     |||   | || | |  |    |    |||| | ||  | || |      |  || |  | || |||
AGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCTCCTTCTGATTCTCCTAAACTGTACAGgtacacgccttcgact--tcatccgctat-tatgtcccaatgaggaactgaaattctaacac------tcatgtttttcttgcag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgt--------ctgtgatgctaagcagccatagacaatgtgttccttgc--ttctcaacttagatgtttactcatttgttagtgatcatttttcag
|| ||||||||||||| |||||||| ||||||||||| || || ||||| |||||||| || || | | | |||      || |||||||||||||||||||         |  |||    ||||   | |  |||         |||  ||  |||    ||    || |  ||||||       || ||  ||
AAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCTGCTGCCGAGGCTCCTAACTTGTACAGgtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatt--tttgttctcttgtatgttctag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagat--gtttactcatttgttagtgatcattttt-cag
|  ||||  |||| || |||||||| |||||||||||||| || |||||||||||||| || || |   |||||| |  ||| ||||| || ||||||||||   |  |  ||   |   ||| |     | |   ||     || ||     |      |||||  |||   |   | ||  | |||
AGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCTCCCTCTGATGCTCCCAAATTGTACAGgta-atagttgtagttatgtatatagtccatttctattagaattccaccccttttgagccactcaagtgtctcttgcccttcctgcag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctg---tgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|  ||||||||||||| ||||||||||| |||||||| || || || |||||||| || || || |   | ||   |  ||| ||||| ||||||||||||| |    |  | | |   | |           | | | || || |      |      | |  |  || || |   |   |  ||||
AGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCATCCTCTGAGGCTCCCAACTTGTACAGgtattgtttagtaccatttatcacattttgtcatttccattactcccttctgtgagaactcaacctattctttgcatttcctcatcag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 5'ss of exon 3
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|  |||| |||||||| |||||||||||||||||||| ||||| ||||| ||||| || || || |   | ||| |    |  ||||| || |||||||||| |  |    |        | | |       ||  ||    |||  | |  |  |  |  |  ||  | | |||   ||  |||
AGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCTTTTACCGCAGCTCCAAATTTGTACAGgtattagtcaattcttgcttacatattgaccctttattttcactctgcatgaaaatccaacctgtttcttgggattgcttg-cag

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ36853 (Selaginella moellendorffii), 5'ss of exon 2
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|  | ||  ||||||| ||||| || |||||||| || |||||||| ||||||||||| || || |   | ||   ||  || || || ||  ||||||||| ||               | | |    |  || ||||   |||| | |   ||||| ||  || |  ||              
AGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAAGCGCCAAATCTGTACAGgtatggag------------acacattgcgctttgcttgtgcctcatcatttttgtttcctgtttcggcag--------------

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ27808 (Selaginella moellendorffii), 5'ss of exon 2
AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatgctaagcagccatagacaatgtgttccttgcttctcaacttagatgtttactcatttgttagtgatcatttttcag
|  | ||  ||||||| ||||| || |||||||| || |||||||| ||||||||||| || || |   | ||   ||  || || || ||  ||||||||| ||               | | |    |   |  |||   |||| | |   ||||| ||  ||    ||              
AGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAAGCGCCAAATCTGTACAGgtatggag------------acacattgcgctctgtttgtgcctcatcatttttgtttcctgtttctgcag--------------

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: 24 (upstream exon), 28 (downstream exon)
Score: 2

AATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCTCTCCATGACGCTCCTAACTTGTACAGgtctgtgatg ... catttttcagGCTGTGCATAGTATTCCTTGCATTCGGCTTCATCGGCTATGCCCTGCCTTTCATCCTATGTACAATGATATGCTGCTGCCTACCCTGCATTATCTCCATG




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