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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTCAAACAAGCATCAGgtaccatctctatgtcatcacaatcaaagttttttctgtcaagtcattcatgcctttatatagtagccatttaatttttatcatcctcgaaaaggatcac...

Basic information

species Oryza sativa
transcript LOC_Os08g15040.1
intron # 4
splice site 5'
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|86478438|gb|CI121071.1|CI121071
EST:     ATCTCGGTGGTCAAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
EST: gi|8956150|gb|BE229954.1|BE229954
EST:     ATCTCGGTGGTCAAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
EST: gi|27554607|gb|CA998507.1|CA998507
EST:     ATCTCGGTGGTCAAACAAGCATCAA                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
EST: gi|88383993|gb|CI631883.1|CI631883
EST:     ATCTCGGTGGTCAAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAACATACC-AGGCTATCATTTATGTTG
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAA-ATACCCAGGCTATCATTTATGTTG
EST: gi|218486133|gb|FG956315.1|FG956315
EST:     ATCTCGGTGGTCAAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
EST: gi|87011925|gb|CI283812.1|CI283812
EST:     AAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: AAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
EST: gi|27554323|gb|CA998223.1|CA998223
EST:     ATCTCGGTGGTCAAACAAGCATCAG                         GCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT
genomic: ATCTCGGTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGT

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: 19 (upstream exon), 70 (downstream exon)
Score: 33

GTGGTCAAACAAGCATCAGgtaccatctc ... acctttttagGCCATACTGGAGATGCTACTTTCCAAATACCCAGGCTATCATTTATGTTGTCGATTCAAGTGATACAGATAGGCTTGTAACGGCAAAAGAAGAGTTTCAT




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