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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgcccatgcc...

Basic information

species Oryza sativa
transcript LOC_Os09g29470.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29470.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G115304_T01 (Zea mays), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgcccatgcc
|||||||||||||||||||||| ||||| ||||| ||||||||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||||||||||||| ||||| |||| ||||| ||||| |||  | | | | ||  |||||  |   ||  |   ||||   | |||||||||| 
GTCCAAACAATCTTTATCCAGATGATCTAATTCCATTTACAAGATATCCACTGTTCCTTGTAATTGATAGTGAAAATAGCCATGCATTCAAGgcaggtttgtcagaacttaatcttggcttg-tagaagaaaaccattaccatcggcactctattgcttttctaaagtaacatgtttacc--aggttgcccatgc-

upper sequence: LOC_Os09g29470.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA05G30980.1 (Glycine max), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgcccatgcc
|| |||| ||||| || || |  ||||| || ||||| || ||  | || || |||||  |||| || ||||| || || |||||||||||||||||||||||| |||| |    | |  |   || ||    | |   |  | ||      | | ||    | |   |  | |   | |     || |   |   
GTTCAAATAATCTCTACCCTGGTGATCTTATCCCCTTCACTAGGAAACCTCTTTTCCTGATTATTGACAGTGATAACAGCCATGCATTCAAGgcaggtttgtcaaaactcagaacttgtgtataagttgcctgtgaactttgttag-gcggagctgttcaggatatttattccttgaatctaattttacttgt---

upper sequence: LOC_Os09g29470.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G14190.1 (Glycine max), 5'ss of exon 7
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttagcttggtagatgaaaatcattatcatgagtattttgttatttttcagagccaaacttactaccctggattgcccatgcc
||  ||| ||||| || || |  ||||| || |||||||| ||  | || || ||| |  |||| || ||||| || || |||||||||||||||||||||||| |||| |    | |  |   || ||    | |   |  | || ||   | | ||                                      
GTTTAAATAATCTCTACCCTGGCGATCTTATCCCCTTTACTAGGAAACCTCTTTTCTTAATTATTGACAGTGATAACAGCCATGCATTCAAGGCAGgtttgtcaaaactcagaacttgtgtataagttgcctgtgaactttgttag-atagagctgttcag-----------------------------------

upper sequence: LOC_Os09g29470.3 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G40050.1 (Arabidopsis thaliana), 5'ss of exon 6
GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttag----cttggtagatgaaaatcattatcatgagtattt-tgttatttttcagagccaaacttactaccctggattgcccatgcc
|| ||||||| ||||| || |  || || || || |||||| |  | ||||| ||| |  | || ||||| || | ||| | |||||||||||||||||||||| |||||| | ||      ||  | |||     ||  ||    | ||||  | ||  || |||        |   || ||   |  |    |      
GTTCAAACAACCTTTACCCTGGTGACCTAATCCCTTTTACACGGAAACCACTTTTCTTGATCATTGATAGCGACACTAGCCGTGCATTCAAGgcaggtttgtcataacttagtgtttcatttctctggagagtctgatagtttctctcagtaactatgcgatatttgctgatggattgtaataaaataaacaaactccag-

upper sequence: LOC_Os09g29470.3 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv07s0191g00140.t01 (Vitis vinifera), 5'ss of exon 6
GTCCAAACAAT---CTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcagaacttaatcttagcttggtaga-tgaaaatcattatcatg-agtattttgttatttttcagagccaaacttactaccctggattgcccatgcc
|| |||| |||   ||||| || |  ||| | ||||| ||||| |||   ||||| ||| |  |||| |||||||| || || |||||||||||||||||||||||| |||||     || |||| || | ||      |||||  |  || | | | | |  ||  | |       ||||| |  |  |  |        
GTTCAAATAATAACCTTTACCCTGGTGATATAATTCCTTTTACCAGAAGACCACTTTTCTTGATTATTGATAGTGACAACAGCCATGCATTCAAGgcaggtttgtcaaaacttgtatataacttgctacactgcttcaaattattctacagcagtgtat-agcttctaaactaggtgttacttctttcaaaagatg-----

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|58689151|gb|CK077838.1|CK077838
EST:     TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTC-A---AG                         GCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcaga ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
EST: gi|218494056|gb|FG946879.1|FG946879
EST:     TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTC-A---AG                         GCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcaga ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
EST: gi|29637839|gb|CB642848.1|CB642848
EST:     TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGC--                         --TATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT
genomic: TCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcaga ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCT

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: 50 (upstream exon), 27 (downstream exon)
Score: 3

GTCCAAACAATCTTTATCCAGAAGATCTGATTCCCTTTACAAGATATCCACTATTCCTTGTTATCGATAGTGAAAATAGTCATGCATTCAAGGCAGgtttgtcaga ... ataattgcagGCTATACATAATGCAGAGAAGGGAGAGCCAGCTGCCTTGCTACTTTCACCTAGGATAGCATCAGCAATGCCTGGTGTGGAATCCACGAGTAATGGAAGCC




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