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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATCCTTTTTATCTTGCTATCCGTGAAGGTGAGACTTTAGCAGAAGTAAAGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatctgttgaagtttcttatgaaagcgtggaattataacatgttttggcttgctctttatccttgtccaccttgggattatgctgatatataag...

Basic information

species Oryza sativa
transcript LOC_Os11g36470.1
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G418232_T01 (Zea mays), 5'ss of exon 8
AGATCCTTTTTATCTTGCTATCCGTGAAGGTGAGACTTTAGCAGAAGTAAAGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatctgttgaagtttcttatgaaagcgtggaattataacatgttttggcttgctctt--tatccttgtccaccttgggattatgctgatatataag
||| |||||   | | |   | | |||||||||||||||||||||||| ||| ||||||||||||  ||||| |||||| ||| ||| ||||| | ||||||||||||||| |||||||||||| | || |  |||| | |  |||| ||     |      |  || |  | |      |  | || | |||  |      
AGACCCTTTCGTTTTGGTCGTTCATGAAGGTGAGACTTTAGCAGAAGTCAAGAAGCGCATACAGAGTAAACTGCAAGTCTCTGCTGATGAATTTTCCAAGgtgatccatcttttgaagtttctt-ttaatggatggagtgacgacatattggtattcataaatagtaccgctatttctgatctggttcttctgtaacgggc-

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 25
lower sequence: GLYMA20G11330.1 (Glycine max), 5'ss of exon 21
AGATCCTTTTTATCTTGCTATCCGTGAAGGTGAGACTTTAGCAGAAGTAAAGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatctgttgaagtttcttatgaaagcgtggaattataacatgttttggcttgctctttatccttgtccaccttgggattatgctgatatataag--------------------------------------------------
 || ||||||| ||| | ||| | ||||||||| ||| | |  ||| | || | ||| ||||| || ||||| ||||| |||||||| |||||||||||||||||   |||  ||   ||| ||  |  | | |    || |    |  ||| | |||||   | |  |  |  |      | | ||    | || | |                                                   
GGAACCTTTTTTTCTGGTTATACATGAAGGTGAAACTCTTGACGAAATTAAAGTGCGAATACAAAAGAAACTTCAAGTTCCTGATGATGAATTCTGCAAGgtgatt--tctcgtgttatttttttggtgaccat---ctttttgattaattttgtttgcttgatgttttaattgagaaaaagttcatatgtacatttgatttcagttcacctaactgtttttttttttttactatttcttgtttggccag

upper sequence: LOC_Os11g36470.1 (Oryza sativa), 5'ss of exon 25
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 5'ss of exon 29
AGATCCTTTTTATCTTGCTATCCGTGAAGGTGAGACTTTAGCAGAAGTAAAGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatctgttgaagtttcttatgaaagcgtggaattataacatgttttggcttgctct-ttatccttgtccaccttgggattatgctgatatataag
||| || ||||   | |  |||| ||| |||||||||||||| ||||| || | |||||||||||| ||| | || || ||||||||||| ||||  ||||| ||   | | |      | |   || |    ||   |  |  ||  |       ||   | | ||   |  | || |    ||  ||||  |    | |
AGAACCCTTTTTCTTGGTCATCCATGAGGGTGAGACTTTAGCTGAAGTTAAAGTGCGCATACAGAAGAAATTACAGGTTCCTGATGAGGAGTTCTCAAAGgt-atttttttttccttcctgcccttgcagctatgttctactgccacctaaaactatgggttatcatatgttacaacatcataatcctgctttttaccatg

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|86901522|gb|CI308503.1|CI308503
EST:     AGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAG                         TGGAAATTCGCTTTCATATCCATGAACCGGCTAGATTACCTCCAAGTTTCA
genomic: AGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatc ... atatgatcagTGGAAATTCGCTTTCATATCCATGAACCGGCCAGATTACCTCCAAGATTCA
EST: gi|58675540|gb|CK064227.1|CK064227
EST:     AGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAG                         TGGAAATTCGCTTTCATATCCATGAACCGGCCAGATTACCTCCAAGATTCA
genomic: AGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatc ... atatgatcagTGGAAATTCGCTTTCATATCCATGAACCGGCCAGATTACCTCCAAGATTCA

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: 70 (upstream exon), 50 (downstream exon)
Score: 13

AGATCCTTTTTATCTTGCTATCCGTGAAGGTGAGACTTTAGCAGAAGTAAAGGAGCGCATACAGAAAAAACTCCAAGTCCCTGATGAGGAATTCTGCAAGgtgatccatc ... atatgatcagTGGAAATTCGCTTTCATATCCATGAACCGGCCAGATTACCTCCAAGATTCAGATGTTGTATCTGCCCGTTTCCAG




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