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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG

Basic information

species Oryza sativa
transcript LOC_Os01g59340.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcaca--tggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                    | | ||    |     |  |   || |   ||||    || |   | || |         || | |   |||| |  |  || |  | |||||||  |||  |     ||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||||||||  | |||||||| |||||||| ||||
--------------------------------------------------------------------ttaattgctgagaggcaatgttacattacctgct-atggagaaggaaactt-------atgttgcatttttcatagttacataaacacctaactgtactttgt-----tgcagCTTGTAGGTACTGATCACTGCACATTCAACTCCACACAGAAAGCTTTTGGTTCTGATGATTTTCGGAAGATTCCCAATGGTGTAAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                          | |||    |     ||  |  | |||      | |||| ||||  ||   | || |   || |||||     ||  | || ||   |   ||  | || |  |  ||||          ||| |||||||||||||||||  |||| || ||||| ||||||||| | ||   |||||| ||| | || |||||||||||||| ||||
----------------------------------------------------------tgtttctgagctctgtattatctaata------ccctgtgtgct--caattaattcttttttactaag--actgattatttgaccaagggtaccgttta-caacctttca----------gCTGGTAGGAACTGATCATTGTGCCTTTAATTCCACCCAGAAAGCTCTTGGAATTGATGACTTCCGGAAAATTCCTAATGGTGTCAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                   ||   ||  |    | |  |     |||      |||||  | | | || | | | ||  | ||  |   |  | |    |   | ||    |  |       ||| |||||||||||||||||||||| ||||| ||||| || ||||| |||||| | ||   |||||||||| | |  || ||||||||||||||||
-------------------------------------------------------------------gtttctttcctcgctgt--gcataaactagagaattgcatga-cctgtagcat-caaaatgttaagatcttctaaacacctttttctccttttattgggataatctctgcagCTTGTAGGAACTGATCACTGCACTTTCAATTCTACACAAAAAGCTCTAGGACTTGATGATTTCCGCAGAATACCTAATGGTGTTAATG

upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 8
gtgatacttttcataccctcagtttgacatcacggagttactttttcatcttagctaatatttggaggtcagttagcaaattataggggcgcactgtttgcttgcagaaacttataccttgctaaggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                                                                             | |||  |||       || |          ||  |  |  ||| ||      ||  | |||   ||   |  || ||  |     | |      | ||||||||||||| |||||||||||  ||||||| ||||||||||||||||| ||   |||||||||| |||| |||||||||||||| ||||
--------------------------------------------------------------------------tctacattg-aggataatgttgatcctaaagcataatcttgatattgttacttaa-agtgatctttgaat---tttctttcccatgatgcgtttccattttgcagCTTGTAGGGACTGATCATTGTGCCTTCAATTCCACACAGAAAGCTTTTGGAATTGATGATTTCCGAAAAATTCCTAATGGTGTCAATG

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), 63 (downstream exon)
Score: 25

GTATGTAATGAGTCCTCCTATCCGAGAAGCAGGACATAATAAAGCACTTCAAGTTGCTCTTTCATCAGGAATTTTACAGgtgatacttt ... ttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggggtagaaaacttcacatggatgactatctaactgctcttcatttctatgcagCTTGTAGGAACTGATCATTGCACCTTCAACTCCACACAGAAAGCTTTCGGCTCTGATGATTTCAGAAAGATTCCTAATGGTGTTAATG
                            atctaac  putative branch site (score: 25)
                                  ctgctcttcatttct  CT-rich tract
                                           atttctat  TA-rich tract