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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagccaagatctccgcctcacccacacgcctttctaaccaagcttattgcgcaaaaatgcttcgtcatccagatttcgctcttgattccggtacatctgtctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCACTTCAGGGACAACAACTTCGTCCTCGACGAAGGGCGGGGGATCATCAGGC

Basic information

species Oryza sativa
transcript LOC_Os11g29380.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 17
gtatgagccaagatctccgcctcacccacacgcctttctaaccaagcttattgcgcaaaaatgcttcgtcatccagatttcgctcttgattccgg--tacatctgt-ctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCACTTCAGGGACAACAACTTCGTCCTCGACGAAGGGCGGGGGATCATCAGGC
                             | |||||  | |    ||||    | |||||   |  |       ||    | ||||    || ||  | || ||||  |||  |||||||| || ||||| ||||| || ||||  |||||||||||||||||   |||||||||||||  |||| | || || |||||||| |||||||||||||
---------------------------gtaagccttcatgagt--gctt-ccacacaaaag-acaaccgagctgagtgacctctctaacatctggactgcacctgtgttgacccagGCCCAAGAATACGAGATCTACGATCTGAAGCCGTTCTTCTCCAGCGCGTGCTTCAGGGACAACGGCTTCCTTCTGGATGAAGGGCGTGGGATCATCAGGC
















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|86597612|gb|CI274603.1|CI274603
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87016236|gb|CI271647.1|CI271647
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86429086|gb|CI075767.1|CI075767
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86437499|gb|CI119221.1|CI119221
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCGGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87030869|gb|CI362083.1|CI362083
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAAC-AG                         GCCCAGGAGTACGAAATGTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|89183587|gb|CI046152.1|CI046152
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86482314|gb|CI124947.1|CI124947
EST:     CGACGCGCCTGACTCACATCGGGGTTAGAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88845092|gb|CI084017.1|CI084017
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GTCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86480334|gb|CI122967.1|CI122967
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86437458|gb|CI119180.1|CI119180
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87023311|gb|CI272139.1|CI272139
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87032692|gb|CI270327.1|CI270327
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86436900|gb|CI118622.1|CI118622
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|58661287|gb|CK049967.1|CK049967
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|15008468|gb|AU222856.1|AU222856
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88244982|gb|CI244831.1|CI244831
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86493580|gb|CI136213.1|CI136213
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86437708|gb|CI119628.1|CI119628
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86597015|gb|CI272610.1|CI272610
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88251574|gb|CI350002.1|CI350002
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAATACGAAATCTATGACCTGAAACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86481049|gb|CI123682.1|CI123682
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87017949|gb|CI273971.1|CI273971
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88831233|gb|CI082043.1|CI082043
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87031839|gb|CI272540.1|CI272540
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|29630148|gb|CB635157.1|CB635157
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88254890|gb|CI351518.1|CI351518
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         TCCCAGGATTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|87021134|gb|CI271941.1|CI271941
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86518590|gb|CI158796.1|CI158796
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|86429095|gb|CI075776.1|CI075776
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
EST: gi|88267036|gb|CI378971.1|CI378971
EST:     CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAG                         GCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC
genomic: CGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCAC

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), 50 (downstream exon)
Score: 15

CACCCTGGTCAAGGATGTGCTGCACTTCGAAGAAATCGTTTCAGGACCAACGACGCGCCTGACTCACATCGAGGTTAAAGTAGAGGACCTGAAGAACAAGgtatgagcca ... tctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCACTTCAGGGACAACAACTTCGTCCTCGACGAAGGGCGGGGGATCATCAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgcttcgtcatccagatttcgctcttgattccggtacatctgtctgatgcagGCCCAGGAGTACGAAATCTATGACCTGAGACCGTTCTTCTCCAGCGCCCACTTCAGGGACAACAACTTCGTCCTCGACGAAGGGCGGGGGATCATCAGGC
                                            gtctgat  putative branch site (score: 15)
                                         tctgtct  CT-rich tract