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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcccctagccaactatttagtgtactgtccttcattttgctcagtgaaactgtgtaacctgatcttgcactactttaccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 13
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|89168225|gb|CI109429.1|CI109429
EST:     GTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: GTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29673249|gb|CB669524.1|CB669524
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29680675|gb|CB676950.1|CB676950
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|88956524|gb|CI092758.1|CI092758
EST:     TCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|89184026|gb|CI046591.1|CI046591
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29616239|gb|CB621251.1|CB621251
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|88904274|gb|CI002007.1|CI002007
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29641724|gb|CB646731.1|CB646731
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29641418|gb|CB646425.1|CB646425
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|58695050|gb|CK083737.1|CK083737
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|58596057|gb|CK006585.1|CK006585
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         AGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|29676039|gb|CB672314.1|CB672314
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|86892851|gb|CI312140.1|CI312140
EST:     CAATGGATTGTTTCATCCAAGCTTG-GCCATCAACTTGGAAACCAG                         GGCAACGCCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: CAATGGATTG-TTCAT-CAAGC-TGTGCCATC-ACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACG-CAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|86869962|gb|CI316690.1|CI316690
EST:     ATCACATGGAAACCAG                         GGCAACGCAGAGAACGGAAAAGCACCATGGGAAGGG
genomic: ATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|38475807|gb|CF959940.1|CF959940
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         NGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|38478883|gb|CF963016.1|CF963016
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGNGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATG-GGAAGGG
EST: gi|86892855|gb|CI312142.1|CI312142
EST:     CGATGCTCAATGGATTGTTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: CGATGCTCAATGGATTG-TTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|58685144|gb|CK073831.1|CK073831
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         TGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|27577797|gb|CB000492.1|CB000492
EST:     TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAA--G
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
EST: gi|58603030|gb|CK013558.1|CK013558
EST:     TTGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG                         GGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
genomic: TCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG

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: 70 (upstream exon), 36 (downstream exon)
Score: 32

CCTGCTCATGAGAAGATTGGAGTCGTCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAGgttagcccct ... taccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattttgctcagtgaaactgtgtaacctgatcttgcactactttaccttgcagGGCAACGCAGAGAATGGAAAAGCACCATGGGAAGGG
                                          ctttacctt  CT-rich tract
                                        tacttta  TA-rich tract