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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTCTCTTACTCAGAAGGGAAAAGGTTCTGACCATGGTCCGGTTTCTAGTGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagactttttttcaaattgctctaatcatgagtattaagctcagttttcatcactagatagggatcacgggctataaatgaaagaggaaaaatgtaaatatcttaaaagaggattaacaaagtatatgacgtgttacagttgaatgtgagctcttatcatttgtcaattctactgtcacag

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 19
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|38480058|gb|CF964147.1|CF964147
EST:     TGCAAATGCTAGCAACTCTCAAATTTGAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|29656612|gb|CB652887.1|CB652887
EST:     TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|58603390|gb|CK013918.1|CK013918
EST:     TGGAAATGCTAGCAACTCTCAAATTTCAGCAAGCGCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|300215776|gb|HO088402.1|HO088402
EST:     TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|29640582|gb|CB645591.1|CB645591
EST:     TGCAAATGCTACCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|218482575|gb|FG966889.1|FG966889
EST:     TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|218497307|gb|FG954387.1|FG954387
EST:     CTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: CTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
EST: gi|38477603|gb|CF961736.1|CF961736
EST:     TCAAATTTCAG--ACCTCCAGTGTCACATCCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTGTGGCTCTCTT
genomic: TCAAATTTCAGCAACCTCCAGTGTCACAT-CAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTT
EST: gi|33675788|gb|CF304027.1|CF304027
EST:     TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAG                         ATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG
genomic: TGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTG

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: 71 (upstream exon), 71 (downstream exon)
Score: 30

AGTTCTCTTACTCAGAAGGGAAAAGGTTCTGACCATGGTCCGGTTTCTAGTGCAAATGCTAGCAACTCTCAAATTTCAGCAACCTCCAGTGTCACATCAGgtattagact ... actgtcacagATAATAGATCTTCCACCGTAGCATATGCACCATCCACTTCTAGCTCTCTTGATCAAACTGCACCAGCATCAGCAAGGTCCTCGGTGGATGGGTGGGGTGA




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