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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g44330.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G151236_T03 (Zea mays), 5'ss of exon 8
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttt-tctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatac-tacatgtggtctgatgcacaatttttcttgcag--------------------------------
|||||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| ||||||||||| ||||||||| ||  ||  ||| |   ||| | | |   |||    | |||  ||||  |||  |||||  |||  || || |      ||  | |  | |   |  |                                 
AATGTGCTCAAGCTATGTGATTTTGGGAATGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTTAGCCGTTTCTATCGGGCACCTGAGATCAgtgagttctttcatcctgcaatgtttttagattttctttct---tacttagtactcatatgttgtctgtatatatatatatatatatatatatatatatatatatatatatatgtgacaactaacatgttttcttgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G147811_T01 (Zea mays), 5'ss of exon 9
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgcacttcattttgttgtgtattcaatatt--cttcctactgttattctgtctccatactacatgtggtctgatgcacaat-----ttttcttgcag
|||||||| ||| | |||||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| |||||||||||||| |||||||||||  |||||||| ||       || |    |  || |  ||||  |     |||  | ||  |||  |||||  || |  | |     |  ||  |  |      |||||||||||
AATGTGCTCAAGGTATGTGATTTTGGCAACGCTATGCTTGCTGGTATGAATGAAGTTACGCCTTATCTTGTCAGCCGTTTCTATCGGGCACCTGAGATCGgtgagttctttcatctttacctgggatgtttttagattcctttcctactttatgctcatatgttgtctgtatgcatcttacctacctatatatgaaacatgttttcttgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G42220.1 (Glycine max), 5'ss of exon 14
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgc---acttcattttgttgtgtattcaatattcttcctactgttattctgtctc-catactacatgtggtctgatgcac-aatttttct-tgcag
|||||  ||||||| ||||| ||||||||||| ||| ||||||| |  || || |||||||| ||||||||||| ||||| |||||||| || || |||||| |||||| ||  | ||     || ||  | |  |     |||  |  ||  | ||  |    || |||    |   ||  || | ||       ||| ||||| |||||
AATGTTTTGAAGCTTTGTGACTTTGGCAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATCGTGCCCCGGAAATAAgtaagttccattcattgctatgatttatgatttcataatcccaaactgtttttttcttgttgaatgcctcatggatgccaactgttttggcttttgaatgtttctatgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA01G20810.1 (Glycine max), 5'ss of exon 11
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttc----tcgcactt-cattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcac-----aatttttct-tgcag
|||    | ||| | ||||| ||||| ||||| ||| ||||||| |  || || |||||||| ||||||||||| || || |||||||| ||||| || ||| |||| |||| |      | | || ||| ||     ||  | |  ||| |||    ||| ||| ||  |   || |   | |   ||| ||  |     || |||||| |||||
AATACTTTTAAGTTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGCTTTTATCGTGCCCCTGAAATCAgtaagttactttgcagtacagtaattgcatattcccaagtcctaaccatttttct---tgtcattttgaatatttaatgggtttttactgttgggctttcaaacttttctatgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G24820.2 (Glycine max), 5'ss of exon 11
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcag
|||||  ||||||| ||||| ||||| ||||| ||| ||||||| |  || || |||||||| ||||||||||| ||||| |||||||| || || |||||| ||| || |   |  ||       |   ||| | ||   | |||     | |||      ||  ||| |||   | | | ||  || |    |||   |||||
AATGTTTTGAAGCTTTGTGACTTTGGTAATGCCATGTTTGCTGGTAAAAATGAAGTTACACCATATCTTGTGAGTCGTTTTTATCGTGCCCCGGAAATAAgtaagtcccatagatttcataatccctaactgtttttttcttgttc-----aatgtctcatggttgcca-act--gttttggcttttgaatg--tttctatgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G25840.1 (Arabidopsis thaliana), 5'ss of exon 9
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgcacttcattttgttgtgtattcaatattcttcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcag
|||||  | ||||| ||||||||||| ||||||||| |||| || |  ||||| |||||||| |||||||| || || || ||  |  | ||||| || ||| |||  | |            ||||||   ||||   |  | | |||  | || |      |    ||   ||    | |   || |    |||   ||||||
AATGTCTTAAAGCTTTGTGATTTTGGTAATGCAATGTTTGCAGGCAAAAACGAAGTTACACCGTATCTTGTTAGTCGCTTTTACAGATCCCCTGAAATTAgtaagtatcat------------attttgggttgtaaagaggacttttc--attggtgaagaat----atgtgactgaagcttctattc----tttccattgcag

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 5'ss of exon 9
AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttccttttctcgcacttcattttgttgtgtat-------tcaatattct-tcctactgttattctgtctccatactacatgtggtctgatgcacaatttttcttgcag------------------------------
||||| ||||| |||||||||||||| ||||| ||| || |||| |  || ||  ||||||| |||||||||||||| || |||||||| |||||||||||| ||| || ||       | ||   ||| | ||| |       | |||||  | | ||   ||||    || | |  | ||  | |  | ||  | |   | | ||||  |                               
AATGTCCTGAAACTCTGTGATTTTGGTAATGCCATGTTTTCTGGTAAAAATGAAATTACACCATATCTTGTGAGCCGCTTTTATCGTGCCCCTGAGATAAgtaagtcccattctcgaaccatcccgttgatttgtttgaaatgattaatataatcttctttagttaggtagtttgccaaataattatt-tttggagaatgctgtctcttaaatcatttagtctctaattctttccttctgcag

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: 69 (upstream exon), 62 (downstream exon)
Score: 18

AATGTGCTGAAGCTCTGTGATTTTGGCAATGCAATGCTTGCTGGAATGAACGAGGTTACACCTTATCTTGTGAGCCGTTTCTATCGTGCACCTGAGATAAgtgagttcct ... tttcttgcagTTCTTGGGTTACCCTACGACCACCCATTAGACATGTGGTCAGTTGGCTGCTGTCTATATGAACTTTACACCGGAAAAGTCCTATTTCCAGGTCCATCAAA




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