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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttattgcttgtgctgttttcttctgtttgaactcaaaaggtgagcatatgggatttgacatgagctccttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g25370.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088653_T01 (Zea mays), 3'ss of exon 3
-------gtattttattgcttgtgctgttttcttctgt-ttgaactcaaaaggtg-agcatatggga-------tttgacatgagctcctt----gac-attttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
         |||||  ||||| ||    | | | | |  || |    | |   || |  ||||  |         |||  ||    | |||    ||| | |||||||  || |||||||||||||| || || ||||| |||||||| |||||||||  || ||| || ||||| || |||||||| |||||||||||||| |||
gtaattttcattttgctgcttctgaaactctttgcagagttaaggatacataatgtaatatatcagtataaattcttgctattcttttcttttccgactactttcagGCTATCAATTTGTATCTTGATCTTCTTAAAGAAAGGGAACTAAGAGAACCTTGCAGGTTCTTAAAATGTCATTTCTTCAACACCTTTTTCTACAAGAAG

upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G012601_T02 (Zea mays), 3'ss of exon 3
-------gtattttattgcttgtgctgttttcttctgtttg------------aactcaaaaggtgagcatatgggatttgacatgagctcctt---gac-attttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
         ||||| |||||| ||    | | | | |  |             ||  ||| | || || |||      ||   ||    |   |   ||| | |||||||| || |||||||||||||| ||||| |||||||||||||| |||||||||  |||||| || |||||||| |||||||| |||||||||||||| |||
gtatttttcattttgttgcttctgtaactctttgcggagtagtaagcatacataatgcaatatgtcagtataaaattctttctattttttttcttccgactactttcagGTTATCAATTTGTATCTTGATCTGCTTAAAGAGAGGGAACTAAGAGAACCTCGCAAGTTCTTAAAATGCCATTTCTTCAACACCTTTTTCTACAAGAAG

upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088653_T02 (Zea mays), 3'ss of exon 3
-------gtattttattgcttgtgctgttttcttctgt-ttgaactcaaaaggtg-agcatatggga-------tttgacatgagctcctt----gac-attttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG-
         |||||  ||||| ||    | | | | |  || |    | |   || |  ||||  |         |||  ||    | |||    ||| | |||||||  || |||||||||||||| || || ||||| |||||||| |||||||||  || ||| || ||||| || |||||||| |||||||||||||| ||| 
gtaattttcattttgctgcttctgaaactctttgcagagttaaggatacataatgtaatatatcagtataaattcttgctattcttttcttttccgactactttcagGCTATCAATTTGTATCTTGATCTTCTTAAAGAAAGGGAACTAAGAGAACCTTGCAGGTTCTTAAAATGTCATTTCTTCAACACCTTTTTCTACAAGAAGG

upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G15890.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------gtattttattgcttgtgctgttttcttctgtttgaactcaaaaggtgagcatatgggatttgacatgagctccttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
                                                    | | |||| | | |   |||| |  |  | |   |  |  | |  |    ||   |   | ||     |  |||| |  | | ||||| ||||||||||| || ||  |||| || |||||||| |  ||||||||    || ||| ||||||| || || ||||||||||||||||||||||||
gtaaacttgtttgctgattattagtttacccctttgttgttgagttgctgaagaaatttagtaccta-actgtatcatgatttgacatttttacaccttgaaattcagtgatggat-catgtacctttat-tgtgcagGTTATAAATTTGTACCTGGAATTGCTTAAGGAGAGGGAGCAAAGAGAACCACTGAAATTTCTGAAATGTCATTTTTTCAATACCTTTTTCTACAAAAAG

upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G03010.2 (Glycine max), 3'ss of exon 3
----------------------------------------gtattttattgcttgtgctgttttcttctgtttgaactcaaaaggtgagcatatgggatt-tgacat-----gagctc---cttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
                                         |  | |         |  |||     ||   |  | ||      |||   | | | | | ||| ||     || ||    | |  | ||| ||||| |||||| |||| |||||  ||||||||||||||||    ||||||||    |||||| |||| || || || ||||||||||||||||||||||||
gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG

upper sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G15880.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattttattgcttgtgctgttttcttctgtttgaactcaaaaggt----gagcatatgggatttgacatgagctcct-tgacatttt-cagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
      ||   ||||| |  |  | ||||     |  | || || |     | || ||    |||  | |||  || | |    ||||  |||| || ||| | || ||||| || || ||||| || |||   ||||| || || |||| |||||| || |||| |||||||||||||||||||||||||
-----gtacaacttgttccataatattctacacaa--ttaagagctcttaaatcacattttcttttgc-tgatttcttgttctgttttatagGTTATCAATGTCTACCTTGAACTACTCAAAGAAAGAGAAACTAGAGAGCCCAAAAAGTATTTGAAGTGTCACTACTTCAATACCTTTTTCTACAAAAAG

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|29613369|gb|CB618382.1|CB618382
EST:     CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAGCTGAGAGAACCT
genomic: CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
EST: gi|428598|gb|D24750.1|D24750
EST:     CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGNCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
genomic: CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT

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: 70 (upstream exon), 67 (downstream exon)
Score: 20

ACGTGAAAGGCTAGTGGTACATGAATCATCAAATATTGTCATAACAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaactcaaaaggtgagcatatgggatttgacatgagctccttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
                                        ccttgac  putative branch site (score: 20)
                                              cattttc  CT-rich tract
                                             acatttt  TA-rich tract