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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttctctagaagattgcatactcctcacatgtcaaaagttttacccacattatatagaactgctacctgttgtctaaaaaaactatgacttgtttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGAGTGCTTCTTAAAATATCTTTGCAGTCTTCAATTTTTGGCAATCTAGATC

Basic information

species Oryza sativa
transcript LOC_Os05g09500.1
intron # 6
splice site 3'
intron type U2

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|66947280|gb|AU312124.1|AU312124
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAG                         ATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
EST: gi|33681408|gb|CF309647.1|CF309647
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAG                         ATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
EST: gi|29672516|gb|CB668791.1|CB668791
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAC                         ATCTTCGATAAATTGATTTCAGGAATGTATCTAAGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
EST: gi|29672557|gb|CB668832.1|CB668832
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTACACCCTGGAGAGCAG                         ATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
EST: gi|29669106|gb|CB665381.1|CB665381
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAG                         ATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
EST: gi|29672558|gb|CB668833.1|CB668833
EST:     CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAG                         ATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA
genomic: CAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGA

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: 62 (upstream exon), 61 (downstream exon)
Score: 18

GTTATTAATACAGAATGGGGTAACTTCTCCTCATCCTGTCTTCCAATAACAGAATATGATGAAGCACTAGATAAAGAGAGCTTAAACCCTGGAGAGCAGgcaagtttct ... tttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGAGTGCTTCTTAAAATATCTTTGCAGTCTTCAATTTTTGGCAATCTAGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattatatagaactgctacctgttgtctaaaaaaactatgacttgtttttttcagATCTTCGAGAAATTGATTTCAGGAATGTATCTAGGTGAAATCGTAAGGAGAGTGCTTCTTAAAATATCTTTGCAGTCTTCAATTTTTGGCAATCTAGATC
                        gtctaaa  putative branch site (score: 18)
                                         cttgtttttttc  putative PPT
                         tctaaaaaaactat  TA-rich tract