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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os04g58880.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G074530_T01 (Zea mays), 3'ss of exon 2
gtatgttcttatgaagtaaggtataaacaaattcgcaata--gccaataggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
                    ||||   |  || |  | ||  || |  | |  ||||||   | | ||| |||     | || ||||||||||| ||   ||||||||||||||||||||| ||||| |||||||||||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||| | |||
--------------------gtatgttcttataccaagtaatgctaggaagaaagtaacaata-gtgtgtgtactaccttatactctcttttctgtcactcagATCAGAAGCCAAAGATTTGTTGGGTGATGACTGGATTCAAAGGCACCGAAGGATTGTACAACAAAATGCCAATCAGTATAGAAGGATTGCTTGGGCGAAG

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G52340.1 (Arabidopsis thaliana), 3'ss of exon 8
gtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactggatgag--tgggtatagtttaatgctctcttttctttcttc-cagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
           |   ||   || |   |   | |    |    ||   |     |||  ||  ||  |    ||| |     | |    || | || ||| ||| |||||||| ||||||||||| || ||||| ||| ||||||  ||||||||||||||||||||| |||||||||| || |  ||  || ||||| |||||
----------gtttggttctgtttcttcggctccatctttcttaaacag-----aaccagaaaagcctaaacataatcctgagttagagttacatttttcacagGTCAGAAGCAAAAGATTTATTAGGTGATGATTGGGTTCAAATACATCGAAGAATTGTACAACAACATGCAAATCAGTACAAGAGAGTTTCTTGGGCAAAG

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactgga--tgagtgggtatagtt--taatgctctcttt-tctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
|| ||||  ||   | |   |||    |||| |  |  |     | | ||||  |  | |   |   ||   ||   |  || |||| |   | | ||  || ||| || ||||||||||||||||| |||||||| ||| | ||||| |||||||| ||||| || ||  |||||||||| || |  |||| ||| ||| |||||
gtttgtttcta--gacttctgtacttccaaacttccttt---tgaaatgttataagtttgtcttccatgcagatcactgatagtgcttttgatgtgttgttttcagGTCTGAAGCCAAAGATTTATTAGGGGATGATTGGGTGCAAAGACATCGAAGGATTGTGCAGCAGCATGCAAATCAGTACAAGAGGAATGCCTGGGCAAAG

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ09561 (Selaginella moellendorffii), 3'ss of exon 8
gtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
                                                 | || ||       ||       || | || |   || |  || ||| | || || || || |||||  |  | ||||||||||||||||||||||||||  | || || || ||  ||||  |    |||    | |  || |||  ||||
----------------------------------------------gtataagcaagcaagcaagccttgggagctaaaag---tcatacctctctgc-agGTCGGAGGCTAAAGACCTTCTCGGGGATGACTGGATTCAAAGGCATCGCCGCATCGTCCAGCAGCATGCTCAGGCATATCAGCGCACAGCGTGGGGAAAG

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ18152 (Selaginella moellendorffii), 3'ss of exon 8
gtatgttcttatgaagtaaggtataaacaaattcgcaatagccaataggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
                                            ||| |  || ||       ||   |  | |     |        | | |   | ||| || || || |||||  |  | ||||||||||||||||||||||||||  | || || || ||  ||||  |    |||    | |  || |||  ||||
------------------------------------------gtataagcaagcaagcaagcaagcaagccttgggagctaaaagtcatacctctctgcagGTCGGAGGCTAAAGACCTTCTCGGGGATGACTGGATTCAAAGGCATCGCCGCATCGTCCAGCAGCATGCTCAGGCATATCAGCGCACAGCGTGGGGAAAG

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|218484890|gb|FG963139.1|FG963139
EST:     TTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: TTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29627850|gb|CB632861.1|CB632861
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29630824|gb|CB635833.1|CB635833
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29624958|gb|CB629969.1|CB629969
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29677754|gb|CB674029.1|CB674029
EST:     TAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: TAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29677753|gb|CB674028.1|CB674028
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29641429|gb|CB646436.1|CB646436
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
EST: gi|29665182|gb|CB661457.1|CB661457
EST:     CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAG                         ATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG
genomic: CACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAG

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: 69 (upstream exon), 73 (downstream exon)
Score: 25

AGAATAATCTGGATGCAAAAGCAAAACAATACAAGGATCCAGCTTTGATGCACATATTTTTGATGAATAACATTCATTATATCGTGAAATCTGTCCGCAGgtatgttctt ... tttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggttagtaactggatgagtgggtatagtttaatgctctcttttctttcttccagATCAGAAGCCAAAGATTTATTGGGGGATGACTGGATTCAAAGGCATCGAAGAATTGTACAACAAAATGCAAATCATTATAGAAGGATTGCTTGGTCAAAG
                            tttaatgctctctttt  CT-rich tract
                       tatagtttaat  TA-rich tract