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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatacattatttgtcattgttgttttgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGAGGAACATCATCTGGGATAGCCCCCCTCTTGGATGTCCTTGATTCCTAGT

Basic information

species Oryza sativa
transcript LOC_Os01g23610.1
intron # 14
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|88851216|gb|CI373974.1|CI373974
EST:     CACACCCAACTTTGTCTGAGGGTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAAGGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88284358|gb|CI405804.1|CI405804
EST:     CACACCCAACTTTGTGTGAGTTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTNTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|29637258|gb|CB642267.1|CB642267
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88477276|gb|CI414547.1|CI414547
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCNTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88556074|gb|CI486380.1|CI486380
EST:     GTCTGAGTTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCCCAGCCTAGAGA
genomic: GTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|86887058|gb|CI325873.1|CI325873
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|22304992|gb|BQ906214.1|BQ906214
EST:     CACACCC-ACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
EST: gi|88518587|gb|CI446241.1|CI446241
EST:     CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTGTTCAAAGCTGCCAAG                         GTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA
genomic: CACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGA

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: 72 (upstream exon), 70 (downstream exon)
Score: 32

GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAGgtatatacat ... ctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGAGGAACATCATCTGGGATAGCCCCCCTCTTGGATGTCCTTGATTCCTAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaattatttgcaccaataatatagtcaactgtacgtgatatgcctcttttcagGTTAATGCAGGTGTTCCTCATTCCGTAAATGAGCCCGTCGCAGCCTAGAGAGGAACATCATCTGGGATAGCCCCCCTCTTGGATGTCCTTGATTCCTAGT
                                          tgcctcttttc  CT-rich tract
                aataatatagtcaa  TA-rich tract