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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_Os01g25370.1
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|33692526|gb|CF320765.1|CF320765
EST:     AAACGGAGTGGCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
genomic: AAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
EST: gi|29662158|gb|CB658433.1|CB658433
EST:     CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
genomic: CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
EST: gi|428598|gb|D24750.1|D24750
EST:     CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGNCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
genomic: CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
EST: gi|218488315|gb|FG953540.1|FG953540
EST:     CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAG                         GTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT
genomic: CAAGAGAGACCTTGCAGTGCTTGAACGAAACGGAGTGGCTAAATGATGAGgtattttatt ... acattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaactcaaaaggtgagcatatgggatttgacatgagctccttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG
                                        ccttgac  putative branch site (score: 4)
                                              cattttc  CT-rich tract
                                             acatttt  TA-rich tract