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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatctataattaaagatttttatgtattttttcattcatgcagattttagagcctttttataatcaattttgatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 9
gtttgcatctataattaaagatttttatgtattttttcattcatgcagattttagagcctttttataatcaattttgatct--tatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG
||||||     || | |     | |||| ||||  |  || |  |   | | |||| ||| |   | |||| ||||| |||  || |||||||||||||||||| || ||||| ||||||||||| ||| |||| ||||  |||||||| |||
gtttgcgctcttagtaa-----tcttatatattcctgtatgctggtgcaatgtagaacctctac-tcatcagttttgttctcttacagGATCAAGATTTGGAGATGCGTTTCAAGAACCTGCTTCGTTTCTTGCTATAAAACCTTTGTTCGAG
















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|38475296|gb|CF959429.1|CF959429
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|33381296|gb|CF196639.1|CF196639
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|33666778|gb|CF297745.1|CF297745
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|86910785|gb|CI294785.1|CI294785
EST:     CAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: CAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|58666538|gb|CK055224.1|CK055224
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCT
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCT
EST: gi|58684548|gb|CK073235.1|CK073235
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTG
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTG
EST: gi|58593357|gb|CF991665.1|CF991665
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|29645586|gb|CB650593.1|CB650593
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         -ATCAAGATTTGGAGAGGCATTTCANGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
EST: gi|58675486|gb|CK064173.1|CK064173
EST:     ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAG                         GATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA
genomic: ACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAA

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), 52 (downstream exon)
Score: 59

GACATGTTCCCTCATTGAAGGAAGGAAACTCACAGGAGACTATATTTAATCCACCATGGCGGCATCAGCCAGTTGCAATAGgtttgcatct ... gatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcattcatgcagattttagagcctttttataatcaattttgatcttatagGATCAAGATTTGGAGAGGCATTTCAGGAACCTGCTTCTTTTGTTGCCATAAGGCCTTTGTTTGAG
                                         ttttgat  putative branch site (score: 59)
                            tttttataatcaattt  TA-rich tract