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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcattggagcatcttctctttttttctgttgttctactgttctgttatattgatggttgatggattttgtttgatgtgtttgcttccag

Basic information

species Oryza sativa
transcript LOC_Os02g17500.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17500.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G412899_T05 (Zea mays), 5'ss of exon 10
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcattggagcatcttctctttttttctgttgttctact-gttctgttatattgatggttgatggattttgtttgatgtgtttgcttccag
||||||||||||||||||||||||||||||||||| |||||||||||||| |||||| |||||||||| |||||||||||||||||  | ||| |||||||||  ||||    |||    | |||  |    || | || |  |  || ||| | ||   |  ||  ||  |  ||| | |               
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactca---aagc----tgtctcatacagtggtattatgttcattttgtcacatgacttatttttgtgtgctgtcttacag------------

upper sequence: LOC_Os02g17500.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G79820.2 (Arabidopsis thaliana), 5'ss of exon 10
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcattggagcatcttctctttttttctgttgt--tctactgttctgttatattgatggttgatggattttgtttg-atgtgtttgcttccag---
|| |||||| ||||||||||||||||||||||||| ||||  |  |  ||||| ||  |   |  ||| ||||||||  | ||  |    ||  | | ||||      | ||   | | ||||  |   ||||  | |    |      |  | ||||| ||| |        |  |   | | |||  |||   |     
GGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACCTTCAGCCTCTGCAAACATATGTGTAGGAGTTTGCAACCTCTTAGgtat-tgaaatgtgactttttcttgtacattctactatggcttgaaaggccatcatattcatgataagctagataagcaagtaggtgaatgcagtcttcct

upper sequence: LOC_Os02g17500.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g04380.t01 (Vitis vinifera), 5'ss of exon 9
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgg-gctcattggagcatcttctctttttttctgttgttctactgttctgttat-attgatggttgatggattttgtttgatgtgtttgcttccag
||||||||| |||||||||||||||| |||||||| |||| | | |  || || || ||  ||||||| || || ||  | || || |||||||||||||||   | ||| ||       ||     | | || ||| ||  | |      |||| |||     ||  |  | | |      |    ||  ||    
GGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACCTCCAGACCTTGCAAATATGTGTGTTGGAATTGCAAATTTATCAGgtaaagatcactgacttcagttgcaaatatctcagtt-ttgcattccaaaattatgattagccatttctttactgtaccctttaaacttctttag--

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|29643521|gb|CB648528.1|CB648528
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|218501803|gb|FG948060.1|FG948060
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|218493904|gb|FG949299.1|FG949299
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|218498875|gb|FG949815.1|FG949815
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|88827907|gb|CI778472.1|CI778472
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|218496023|gb|FG951379.1|FG951379
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|88732502|gb|CI755679.1|CI755679
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
EST: gi|66922886|gb|CX109734.1|CX109734
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTAC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTAC
EST: gi|218498315|gb|FG958350.1|FG958350
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGA
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGA
EST: gi|88827571|gb|CI778136.1|CI778136
EST:     TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAG                         GCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC
genomic: TGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTC

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: 66 (upstream exon), 69 (downstream exon)
Score: 82

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcat ... ttgcttccagGCTCAATTGTAGCTATGCTTCTAATGGACAAACTAGGAAGGAAAGTACTTCTTTCAGGGAGCTTCCTTGGCATG




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