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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacatacagcatttagctctcagtctctactttctcattgttgcttgttgtaacaagcaattaaaggctcagagatctgttagtttgatagaatag...

Basic information

species Oryza sativa
transcript LOC_Os01g60440.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G098078_T01 (Zea mays), 5'ss of exon 16
GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacatacagcatttagctctcagtctctactttctcattgttgcttgttgtaacaagcaattaaaggctcagagatctgttagtttgatagaatag
| |||||||| || ||||||||| |||||||||| ||||||||||||||||||||||| || ||||||||| ||||||||||||||||||| |||||||||||                   |||| |||||| |||||| |||||  |||  |||||||    |   |  |    | |  |  |||             
GAATCATGGCACTGAGTGTCACTGGTTCATACTACGAAATGACAGAGATTGCAACTCGCATCCTGCCTAACATTGTTGTCCTCACATTTGACCCAGATAGgtaag-----------------ctcaatctctaatttctccttgttagttg--gtaacaacaggtctcatccctgtaaaatttctag-------------

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 16
lower sequence: AC218972.3_FGT001 (Zea mays), 5'ss of exon 16
GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacatacagcatttagctctcagtctctactttctcattgttg--cttgttgtaacaagcaattaaaggctcagagatctgttagtttgatagaatag-
| |||||||| || |||||||||||||||||||||||||||||||||||||||||||| || ||||||||| ||||||| ||||||||||| ||| ||||||| | | ||  |  ||||  |     |  |||  |  | ||    |   |  |      ||   |||   || || || ||   |   | | |     |   
GAATCATGGCACTGAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGCATCCTGCCTAACATTGTTGTGCTCACATTTGACCCAAATAGgta-agctta--gtctttatgttctccttgctagctggtaataacaggcttcatccctgtaaaacatttggggatctgaaatagatgcatgtaagctttttat

upper sequence: LOC_Os01g60440.1 (Oryza sativa), 5'ss of exon 16
lower sequence: Vv13s0067g03110.t01 (Vitis vinifera), 5'ss of exon 16
GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacatacagcatttagctctcagtctctactttctcattgttgct-tgttgtaacaagcaattaaaggctcagagatctgttagtttgatagaatag--
|  | |||||  || |||  || ||||| || ||||| || ||||||||||||||||| |||||||| || |||||||| || ||  ||||||| || |||| || | |        | |  | |  || ||  | | |   |||| || | |||  | |   ||  || |   |     |||  |  | |   |   | |  
GAGTTATGGCTTTATGTGCGACCAGTTCTTATTATGACATCACAGAGATTGCAACTCGGATTCTGCCAAATGTTGTTGTACTTACCATTGATCCTGACAGgt-tatcttttctttcattgtcccctttcactgttgtttggatgtttctctcttgatatacataaacaaggatgctc--ctcttcttctatagcaatcttgat

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|29656612|gb|CB652887.1|CB652887
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|701421|gb|D47712.1|D47712
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGG
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAG-
EST: gi|109974420|gb|DT806899.1|DT806899
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAAATAG                         TGATGTGAGGACCAAGGCTTTCCAAGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|701323|gb|D47614.1|D47614
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|300215776|gb|HO088402.1|HO088402
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|426538|gb|D22359.1|D22359
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|29640582|gb|CB645591.1|CB645591
EST:     GCAACTCCTATTCAGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCGATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
EST: gi|58607870|gb|CK035903.1|CK035903
EST:     GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAG                         TGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC
genomic: GCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGC

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: 67 (upstream exon), 71 (downstream exon)
Score: 45

GCATCATGGCGCTAAGTGTCACTAGTTCATACTATGAAATGACAGAGATTGCAACTCGTATTCTGCCTAACGTTGTTGTCCTCACATTTGATCCAGATAGgtataacata ... ggttttgtagTGATGTGAGGACCAAGGCTTTCCAGGCTACTGATCAATTCTTGCAAATAGCAAAACAACATCATGAAAAG




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