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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCCACCGCGGCACCTCGTTCCCCGTGGCCCGGCGCCACCATGGGTTCCACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgtgtatatacactataatgatattgtcaagtgcaatgcttagataccagagagcatatacgttagttttcaattggttcttaggatgtatatttgtttgatgtttctgtag

Basic information

species Oryza sativa
transcript LOC_Os06g24070.1
intron # 3
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|33669836|gb|CF298075.1|CF298075
EST:     CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
genomic: CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
EST: gi|86851181|gb|CI312582.1|CI312582
EST:     CGCCGCCGCCGTGGGNACCCCCGCTTTTTTGGCACCACCNTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAAAGGGGACACCTTGCATGGCGATGCCCC
genomic: CGCCGCCGCCGTCGG-A-CCCTGC-TTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTC-AA-GGGACACCTTGCATGGCGATG-CCC
EST: gi|29646518|gb|CB651525.1|CB651525
EST:     CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
genomic: CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
EST: gi|29677764|gb|CB674039.1|CB674039
EST:     CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
genomic: CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
EST: gi|87015668|gb|CI277626.1|CI277626
EST:     CACCGCCGCCGCCGTCGGANCCTGCTTTCTGGCACCACCCTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
genomic: CACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
EST: gi|38474383|gb|CF958515.1|CF958515
EST:     CTGGCACCACCCTTACATGAGG                         GGGCCAGCACATGTGCCAACTCAATGGACACCTTGCATGGCGATGCCCATG
genomic: CTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG
EST: gi|22306077|gb|BQ907299.1|BQ907299
EST:     CTGCTTTCTGGCACCACCCTTACATGA-G                         GGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCAT-GCGATGCCCATG
genomic: CTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATG

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: 51 (upstream exon), 41 (downstream exon)
Score: 4

GTGGCCACCGCGGCACCTCGTTCCCCGTGGCCCGGCGCCACCATGGGTTCCACCGCCGCCGCCGTCGGACCCTGCTTTCTGGCACCACCCTTACATGAGGgtaagtatgt ... gtttctgtagGGGCCAGCACATGTGCCAACTCAAGGGACACCTTGCATGGCGATGCCCATGCCAGCTGCG




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