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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAACAAAGGAAGAGCTCCATAAACTAGAGAAGGATTGCAAGATGAAGGAAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcatagagcattaatcagctactctatgttctattttaatctccaaatgaacttcccaaacttagaagttattttgtcataaaattttcatccaaca...

Basic information

species Oryza sativa
transcript LOC_Os01g63060.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G004949_T01 (Zea mays), 5'ss of exon 9
CAGAACAAAGGAAGAGCTCCATAAACTAGAGAAGGATTGCAAGATGAAGGAAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcatagagcattaatcagctactctatgttctattttaatctccaaatgaacttcccaaacttagaagt-tattttgtcata---aaattttcatccaaca----------------------------------------------------------------------------------------------
 || |  |||||||| |||||||| || ||||||||  | | ||||| ||| |||||||||||||| ||||||||||||||||||||| |||| ||| |||||  ||||  ||||  | |   |||  |   | | | |       ||||||   ||   | || |   | |  |      |||    ||| |   | | |||                                                                                               
GAGGATGAAGGAAGAACTCCATAAGCTTGAGAAGGACGGGAGGATGATGGATGAGTTCCATAAATTATTAAATGGAAACACTGTCGATGCTACAGATTGGgtactataggacatttctta-tcacttcacaatttctgtattatcgcaaatgggtttgggatacctttcaatgcacggctgcatgcgcaaactcaaaccgaactattatatgtcactgttttttgcagttcattacatcattaccttgtgcttttggtactgagttttgctgatattatccttttctgattatttcag

upper sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G169293_T01 (Zea mays), 5'ss of exon 11
CAGAACAAAGGAAGAGCTCCATAAACTAGAGAAGGATTGCAAGATGAAGGAAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcatagagcattaatcagctactctatgttctattttaatctccaaatgaacttcc-caaacttagaa---gttattttgtcataa------aattttcatccaaca------------------------------------------------------
||| |  |||||||| ||||||||||| ||||||||  | | ||||| ||| ||||||||||||||||||||||||||| || ||||| |||| ||| ||||| |  | ||  |        |  |  | |  ||      | ||   |||| ||  |  ||  | || ||   | ||||   | |||         ||||  | ||  |                                                      
CAGGATGAAGGAAGAACTCCATAAACTTGAGAAGGACGGGAGGATGATGGATGAGTTCCATAAATTGTTAAATGGAAACTCTATCGATGCTACAGATTGGgtacctcacagtttctgaattatcgtaaacgggctgggcgtacctttcaatgcacggctgcatgcataaaatgagctattagattatatctcactgttttttgttcataacctcgtgcttttggtactgagttttgttgatatatccctttctgattattccag
















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|38475796|gb|CF959929.1|CF959929
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|89166101|gb|CI103191.1|CI103191
EST:     ACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: ACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|87004430|gb|CI298962.1|CI298962
EST:     GAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: GAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|300215948|gb|HO088574.1|HO088574
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGNCA-CGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACAC
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGG-CAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACAC
EST: gi|8528209|gb|AU093024.1|AU093024
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|33796561|gb|CF324148.1|CF324148
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAAACATGGCGAGGACATCAACCCCAC
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGG-AAAACATGGCGAGGACATCAA--CCAC
EST: gi|88219746|gb|CI219306.1|CI219306
EST:     TAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: TAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
EST: gi|29646377|gb|CB651384.1|CB651384
EST:     AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGG                         CGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA
genomic: AAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACA

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), 69 (downstream exon)
Score: 17

CAGAACAAAGGAAGAGCTCCATAAACTAGAGAAGGATTGCAAGATGAAGGAAGAGTTCCATAAATTGTTAAATGGAAACACTGTCGATTCTACTGATCGGgtatcataga ... gattatccagCGGCAACGTGTGCAGATGAACGGAAAACATGGCGAGGACATCAACCACACACTCTCAGATGCCACTCCCAATGGCACATGATCAGCTGCTTTTCATCAGG




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