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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactcaaatcctgcttcctaatatttgcttcattaagaggattttgttctaagtggcttatatttctctgaag

Basic information

species Oryza sativa
transcript LOC_Os01g05800.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G839422_T01 (Zea mays), 5'ss of exon 5
GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactcaaatcctgcttcctaatatttgcttcattaagaggatttt-gttctaagtggcttatatttctctgaag
||||||||||||| || |||||||| ||||| |||||||| || ||||| |||||||||||||||||||| |||||||   |  | |||  || | | |   |||||| ||| || |  |||| |  || |||| ||| |||  |  |||||
GATGTTTTCCAACGTTAGCAACAATTCCTGTATGGATTGGTCTTTACCAGGCCCTTTCAAATGTAGCAAATGAGgtaag--ttcagtccaactgctttaagcttgcttgattgagtgtttttttgggctgagtgtcttttatgaca-tgaag

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G110063_T01 (Zea mays), 5'ss of exon 6
GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactcaaatcctgcttcctaatatttgcttcattaagaggattttgtt--ctaagtggcttatatttctctgaag
||||||||||||| ||||||||||||||||| |||||||| || ||||| || ||||||||||||||||| |||||||   |  | |||  || | | |   |||||| |||||| |  |||| |   || ||||  || |||   | |||||
GATGTTTTCCAACATTGGCAACAATACCTGTATGGATTGGTCTTTACCAGGCACTTTCAAATGTAGCAAATGAGgtaag--tttagtccaactactttaagcttgcttgattaagtgttttttttgggctgagtgtgttctatga-tgtgaag

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G14960.1 (Glycine max), 5'ss of exon 5
GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaa-----aactcaaatcctgcttcct--aatatttgcttcattaagaggattttgttctaagtggcttatatttctc-tgaag-------------------
| ||||| |||||| |||| ||||| || ||||||||||| |||||||||||  | |||||||| ||||| |||||||      |   |||   |  ||  |  |  |     |||  |      |||     |  |     | || || ||  | | |                   
GTTGTTTACCAACTCTGGCTACAATTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaattaatgatataaacttttattatttgagcagagatttcgatggacaaattacacacagaaaatatgattttgctaattatgttaaatctttaatttgaag

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA12G06920.1 (Glycine max), 5'ss of exon 5
GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactcaa--atcctgcttcctaatatttg--------cttcattaagaggattttgttctaagtggcttatatttctctgaag----------------------
| ||||| ||||||||||| ||||| || ||||||||||| |||||||||||  | |||||||| ||||| ||||||| | | ||  ||      |  ||  |||||         ||   |      |||     |  |     | || |||   | |                        
GTTGTTTACCAACTTTGGCTACAATTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataattaattatataaacttttatcatttgagcggagattttgatggacaaattacacacagaaaatatgattttttgttaattatggaaaatctttaatttgaag

upper sequence: LOC_Os01g05800.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 5'ss of exon 5
GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactcaaatcctgcttcctaatatttgct-tcattaagaggattttgtt-----ctaagtggcttatatt---tctctgaag--------------
||||||| ||||||||||| |||||||| |||||||| ||  | || ||||| ||||||||||| ||||| ||||| ||  | ||   ||  |  ||  ||| || | |        ||||| |  |      ||| | | ||||  |   | ||| ||               
GATGTTTCCCAACTTTGGCCACAATACCAGTCTGGATAGGTTTGTATCAAGCTCTTTCAAATGTGGCAAATGAGgtgaa--taaatatctcatctctcttatgtgatgttgacggttggattctaatgcagattaaattgtttatgctaactatctcaacctttttactcaaag

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|29615536|gb|CB620548.1|CB620548
EST:     TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG                         GGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
genomic: TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactca ... ttctctgaagGGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
EST: gi|13896049|gb|AU182385.1|AU182385
EST:     TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG                         GGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
genomic: TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactca ... ttctctgaagGGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
EST: gi|29620327|gb|CB625339.1|CB625339
EST:     TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG                         GGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
genomic: TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactca ... ttctctgaagGGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
EST: gi|58694651|gb|CK083338.1|CK083338
EST:     TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAG                         GGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA
genomic: TACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactca ... ttctctgaagGGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACA

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: 73 (upstream exon), 75 (downstream exon)
Score: 67

GATGTTTTCCAACTTTGGCAACAATACCTGTCTGGATTGGCCTCTACCAAGCCCTTTCAAATGTAGCAAACGAGgtaaaactca ... ttctctgaagGGATTACTGACAGAAGGATTTTTCTGGATTCCATCTTTGGGAGGCCCTACAACAATTGCTGCTCGGCAAAGTGGTGCTGGCATTTCTTGGCTCTTGCCTT




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