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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttacatagtttgagctccaaatagggtgttgcttttctgctttcgtgttaca...

Basic information

species Oryza sativa
transcript LOC_Os06g39520.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G406603_T02 (Zea mays), 5'ss of exon 3
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttctta-catagtttgagctccaaatagggtgttgcttttctgctttcgtgttaca----------
||||||| ||||| |||||||| || |||||||||||||||||| ||||||||||||| || |||||||||||||| ||| | ||||||||||| ||||||||| ||       || ||   ||| ||||| ||||| ||  ||||||||| | |  ||||||||  ||||| | |    |   | || || | |||              
TGCTAGGTGATGGATTTGGCTCCACACCAGAGATGAGTAAACGAAACTTGTTCTGGGTGGTTAGCCAAATGCAGGCCATCATCGAGCGTTATCCATGCTGgtatgat-------ttccat-catc-gcatgatcttg-ttcagttttcttatcgtgatttgagcttgaaataag-taacacccatgtggttacttgtggagacatggaatt

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G025211_T01 (Zea mays), 5'ss of exon 7
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttac-atagtttgagctccaaatagggtgttgcttttctgct-ttcgtgtt-aca------
| ||||| ||||| || ||||| || | ||||||||||||| |  ||||||||| ||| || ||||| |||||||| ||||| ||||||||||| |||||||||  |  |  |   ||        ||||| ||||| ||  |||||||||   |  ||||||||  ||||| | ||   |  |   ||| || |||   |||      
TACTAGGTGATGGATTCGGCTCCACACTAGAGATGAGTAAATGGAACTTGTTCTAGGTGGTTAGCCAGATGCAGGCTATCGTCGAGCGTTATCCATGCTGgtatggt-ttgcagcatc--------gcatgatcttgtttcagttttcttattgtgatttgagcttgaaataagttgcacccatgtggctatttgtggagacatagaat

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G079308_T01 (Zea mays), 5'ss of exon 10
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttctta-catagtttgagctccaaatagggtgttgcttttctgct-ttcgtgtt-aca------
||||||| ||||| || ||||| || |||||||||||||||||  |||| |||||||| || ||||| |||||||| ||||| ||||||||||| |||||||||  |  |  |   ||        ||||| ||||| ||  ||||||||| | |  ||||||||  ||||| | ||   |  |  |||| || |||   |||      
TGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTATTCTGGGTGGTTAGCCAGATGCAGGCTATCGTCGAGCGTTATCCATGCTGgtatggt-ttgcagcatc--------gcatgatcttgtttcagttttcttatcgtgatttgagcttgaaataagttgcacccatgttgctatttgtggagacatagaat

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G140298_T01 (Zea mays), 5'ss of exon 6
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttac-atagtttgagctccaaatagggtgttgcttttctgct-ttcgtgtt-aca------
||||||| ||||| || ||||| || |||||||||||||||||  ||||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||||||  |  |  |   ||        ||||| ||||| ||  |||||||||   |  ||||||||  ||||| | ||   |  |   ||| || |||   |||      
TGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTGTTCTGGGTGGTTAGCCAGATGCAGGCTATCGTCGAGCGTTATCCATGCTGgtatggt-ttgcagcatc--------gcatgatcttgtttcagttttcttattgtgatttgagcttgaaataagttgcacccatgtggctatttgtggagacatagaat

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G700221_T01 (Zea mays), 5'ss of exon 5
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttac-atagtttgagctccaaatagggtgttgcttttctgct-ttcgtgtt-aca------
||||||| ||||| || || || || ||| |||||||||||||  ||||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||||||  |  |  ||  ||||||        | ||||| ||  |||||||||   |  ||| ||||  ||||| | ||   |  |   ||| || |||   |||      
TGCTAGGTGATGGATTCGGGTCCACACCAAAGATGAGTAAACGGAACTTGTTCTGGGTGGTTAGCCAGATGCAGGCTATCGTCGAGCGTTATCCATGCTGgtatggt-ttgcaacatcacat--------gatcttgtttcagttttcttattgtgatttcagcttgaaataagttgcacccatgtggctatttgtggagacatagaat

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G330521_T01 (Zea mays), 5'ss of exon 6
----------------------------------TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttacatagtttgagctccaaatagggtgttgcttt-tctgctttcg---tgttaca-----------------------------------------------
                                  ||||||| ||||| || ||||| || |||||||||||||||||  ||||||||||||| || ||||| |||||||| ||||| ||||||||||| |||||||||  |  |  |   ||        ||||| ||||| ||  |||||||||    |  |          | | | ||||||   || ||||      || ||||                                               
GAAACGACACTTAATCATGTGAAGACCGCTGGGCTGCTAGGTGATGGATTCGGCTCCACACCAGAGATGAGTAAACGGAACTTGTTCTGGGTGgttagccagatgcaggctatcgtcgagcgttatccatgctggtatggt-ttgcagcatc--------gcatgatcttgtttcagttttcttattgtgactagtagggtgctcgtgcgttgctacgtcagcttaaaaattgatacaaaatagtgatgcaatataattacaatctttgattgatgattttgtag

upper sequence: LOC_Os06g39520.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0016g04480.t01 (Vitis vinifera), 5'ss of exon 3
TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatactataatttcacatatcagcatgttcttggttttgttttcttacatagtttgagctccaaatagggtgttgcttttctgctttcgtgttaca-
| || || ||||||||||| ||||||||||||||||| | | |  || |  | ||||| ||||  | ||||||||   | || || || || ||    |||||    |    ||    |  || ||     |||    ||      | | |  |  |||    |     |  |||  || |  |      || |    || 
TTCTGGGTGATGGTTTTGGTTCAACGCCAGAGATGAGCATAAGGAACCTAATATGGGTGGTCACTCGAATGCAGGTTGTGGTAGATCGGTACCCTACTTGgtaagccatccaaagcctagctagcaaagctttcccaatta-accatatgatttttttttttttttttttgtggtcatggtggttccacatcataagccag

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), 73 (downstream exon)
Score: 11

TGCTAGGAGATGGTTTTGGCTCAACGCCAGAGATGAGTAAACGAGACTTGTTCTGGGTTGTCAGCCAAATGCAGGCAATCGTTGAGCGTTATCCGTGCTGgtataatact ... ctgtgtgcagGGGTGATACTGTCGAAGTAGATACATGGGTTGGTGCTCATGGTAAAAATGGAATGCGCAGAGACTGGCATATACGTGATTCTGTAACAGGCCATACAATA




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