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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaatgccggttcctacgatcttgtttcgcattagctttggatgaatacagcatctcccttatgcgctttgaacggttgcag

Basic information

species Oryza sativa
transcript LOC_Os04g45970.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA01G41310.1 (Glycine max), 5'ss of exon 8
ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaatgccggttcctacgatcttgtttcgcattagctttggatgaatacagcatctcccttatgcgctttgaacggttgcag
||  |  | ||||| ||||| | ||||||||| ||||| || || ||  ||||||| ||||  || ||||| |||||||||||||||||||| | |            ||  ||    ||| ||   |||     ||||  ||   | | | || ||   | |    | ||||||
ATATTGTCTAAGAAAGGAGTCATCATATTACCCGACATATATGCTAATGCCGGTGGAGTGACTGTGAGCTACTTTGAGTGGGTTCAGgtaatgggatcaataaa----acactcaaaattctcaaaggctc-acttgaaagcaaagttttcattttgaaatctctgtg-ttgcag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA05G05460.1 (Glycine max), 5'ss of exon 8
ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaat----gccggttccta----cgatcttg-----tttcgcattagctttggatgaatacagcatctcccttatgcgctttgaacggttgcag
||  |  | ||||| ||||| |  ||||||||||| ||||| |||||  | ||||| ||||  || ||||| ||||| ||||||||||||| ||||||           |  |    | ||||||      |||    |  || |   | |||     |||||  ||  || || ||   |  | |||
ATCTTGTCTAAGAAAGGAGTCATTATATTACCTGATATTTATGCCAATGCTGGTGGAGTGACTGTGAGCTACTTTGAATGGGTTCAGgtaaatgaaatcaacataaacactcaaagccaatcttgaaaatcttcctgctgtctctttcttaatgttaaatctcatttg-gctctatgc-tgccttcag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0039g02720.t01 (Vitis vinifera), 5'ss of exon 8
ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaatgccggttcctacg-atcttg--tttcgcattagctttggatgaatacagcatctcccttatgcgctttgaacggttgcag-------------------------------
|||||  ||||||| |||||    ||  | |||||||| || || ||  | || ||||||| ||| |||||||||||||||||||||||||||          ||| ||   ||| ||  |||      |  ||     |  |  | ||       |    |     |   || | |                                
ATTCTATCCAAGAAAGGAGTCGTAATCCTGCCTGACATCTATGCTAATGCTGGAGGTGTGACCGTGAGCTATTTTGAGTGGGTTCAGgtaattccctctatatttcttatatatcatgggttttatgaaaaattatatcgtttgaaacacagataattgatggggaaagtagtagtaacatcttaggattaatggttttatgttggcag

upper sequence: LOC_Os04g45970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0039g02750.t01 (Vitis vinifera), 5'ss of exon 8
ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaatgccggttcctacg-atcttg--tttcgcattagctttggatgaatacagcatctcccttatgcgctttgaacggttgcag-------------------------------
|||||  |||||||||||||    ||  | || ||||| || || ||  | || |||||||  || |||||||||||||||||||||||||||          ||| ||   ||  ||  |||  || |   ||     |  |  | |||      |          |   || | |                                
ATTCTATCCAAGAAGGGAGTTGTAATCCTTCCCGACATCTATGCTAATGCTGGAGGTGTGACTGTGAGCTATTTTGAGTGGGTTCAGgtaattccctctatatttcttatatatgatggattttacaatgaattatatcgtttgaaacatagataattgataggaaaagtagtagtaacatcttaggattaatggttttatgttggcag

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|29632163|gb|CB637172.1|CB637172
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86432770|gb|CI086381.1|CI086381
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTAAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|89188766|gb|CI048502.1|CI048502
EST:     GTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: GTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|38473890|gb|CF958022.1|CF958022
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86415342|gb|CI069745.1|CI069745
EST:     TTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88902577|gb|CI088115.1|CI088115
EST:     TATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88833849|gb|CI077330.1|CI077330
EST:     TATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86260536|gb|CI066409.1|CI066409
EST:     TGTACGCCAACTCCGTTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86428842|gb|CI075523.1|CI075523
EST:     TATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|29639773|gb|CB644782.1|CB644782
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88829462|gb|CI074332.1|CI074332
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTAAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86499922|gb|CI142555.1|CI142555
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88967853|gb|CI098095.1|CI098095
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTNAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86431647|gb|CI085258.1|CI085258
EST:     TATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88955631|gb|CI091920.1|CI091920
EST:     ATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: ATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88907604|gb|CI090398.1|CI090398
EST:     TATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88845496|gb|CI084421.1|CI084421
EST:     ATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: ATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86260911|gb|CI066586.1|CI066586
EST:     TGTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|29643302|gb|CB648309.1|CB648309
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|38470565|gb|CF954696.1|CF954696
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86412880|gb|CI067285.1|CI067285
EST:     TNTACGCCAACTCCGGTGGTGTGATCGTNAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86436720|gb|CI118442.1|CI118442
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86429658|gb|CI076339.1|CI076339
EST:     TGTACGCCAACTCCGGTGGTGTGATCGTGAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88828694|gb|CI073564.1|CI073564
EST:     GCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: GCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|25804045|gb|CA760006.1|CA760006
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTNTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|86422962|gb|CI060535.1|CI060535
EST:     ACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: ACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88906052|gb|CI089638.1|CI089638
EST:     ATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: ATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88278297|gb|CI399297.1|CI399297
EST:     GTTAGCTATTTTNAGTTGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGNAGCTCCAC
genomic: GTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|29669247|gb|CB665522.1|CB665522
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|29678533|gb|CB674808.1|CB674808
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88829134|gb|CI074004.1|CI074004
EST:     TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: TTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
EST: gi|88841606|gb|CI080862.1|CI080862
EST:     ATTTTGAGTGGGTTCAG                         AACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC
genomic: ATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCAC

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: 75 (upstream exon), 74 (downstream exon)
Score: 90

ATTCTTGCCAAGAAGGGAGTGACCATATTACCTGACATTTACGCCAACTCCGGTGGTGTGATCGTTAGCTATTTTGAGTGGGTTCAGgtaattgaaa ... acggttgcagAACATTCAAGGGTTCATGTGGGATGAGGAGAAGGTGAACATGGAGCTCCACAAGTACATGAACAATTCTTTCCAGCACATCAAGGCCATGTGTAAATCTC




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