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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtacctttcttgtgttatccatatcttcctctgcataattgcaattgttattgagtgatgccatattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGATCATCGCCGAATACGGTCAGGAGTATGGCAAGGACAATCCAATCTGCGTG

Basic information

species Oryza sativa
transcript LOC_Os01g67490.2
intron # 4
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|87031599|gb|CI263972.1|CI263972
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|88992413|gb|CI035551.1|CI035551
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|89168675|gb|CI038527.1|CI038527
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|66923799|gb|CX110647.1|CX110647
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAA                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|86833096|gb|CI333695.1|CI333695
EST:     CATGTTTGGGGAGGAGAACCTGAACGGCTCATTTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTTATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|88991813|gb|CI034951.1|CI034951
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
EST: gi|88987206|gb|CI034219.1|CI034219
EST:     CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAG                         GATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT
genomic: CATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGAT

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: 41 (upstream exon), 75 (downstream exon)
Score: 22

GTTTCTTGAAGGAGATTTCGAGAGCTATGTGAGACAGATAAGAAAGCCTCATGTTTGGGGAGGAGAACCTGAACTGCTCATGTGCTCCCATGTTCTTAGgtaggtacct ... catattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGATCATCGCCGAATACGGTCAGGAGTATGGCAAGGACAATCCAATCTGCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccatatcttcctctgcataattgcaattgttattgagtgatgccatattgcagGATGCCTATCACTGTTTACATGTATACCAAGGGCTCTGATAGCCCCAGGATCATCGCCGAATACGGTCAGGAGTATGGCAAGGACAATCCAATCTGCGTG
                          aattgttatt  TA-rich tract