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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacagtgctagtgtccttaacttttctaagaacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g43930.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 3
gtaattacagtgctagtgtccttaacttttctaagaacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttct--tacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
           |  |||  | |||  |    ||| | | |   | |   |    || |||| |    | ||     |||   |      | | ||  ||| |  | |||||| ||||| ||||||||||||||| ||||||||||||| || || || || || ||||||||||| ||||| || ||| |||||||||||
-----------gtaagtaacattacataacataaca-cgtacttctttattatttttcatttcaatgttttcatggtaataataccatcattgttcatttttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 3
gtaattacagtgctagtgtccttaacttttctaag-aacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
                               |||| |||     |||||  ||       ||     |   | |||| |  ||     | | ||||| || ||  |||||| || || || ||| |||||||| |||| | |||||| || ||||| || || ||||||||| | ||||| |||||| |||||||||||
------------------------------gtaagtaactccattatgcaaacaaaattgtttaattaatatatgctca--ttc---accattctttatt-ctgccagTCTTCTTGCAATTGCTCAGGAGACCCTGGCGGCGTTCCTTTCAAAAGCTACTGGAACTGCTGTCAACTGGGTCCAAATGATTGGGATGAAG

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 3
gtaattacagt--gctagtgtccttaacttttctaagaacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
 |||  | |     | | |  | ||      || || || ||   |||    | |  |  || |    |       | ||||  |  ||  | | ||||||| || |||||| ||||| ||||||||||||||| ||||||||||||| || || || || || ||||||||||| ||||| || ||| |||||||||||
-taacaaaaactaacaattaacatttgtagatccaaaaa-ataaatattttcatcagtaaatagtaata------acataaggattgtg-gattatttgtttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattacagtgctagtgtccttaacttttctaagaacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
               ||        || || |       ||||| ||   |    | ||||| |  ||  |  |   |   |  ||| |    |||   | |   ||||| ||| | || || |||||||||||||| |||||||| |  || || || || ||||||||||| ||||| || ||| |||||||||||
---------------gtaaggaaggctctttt-------tttgtttgtgaatttct-cattgtgacattatgagaagagactaaatggagtgtttt---tttggtagTCTTCTCTCGATTGCGGAGGAGACCTTGGCGGAGTTCCTTTGCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 3
gtaattacagtgctagtgtccttaacttttctaagaacatttgtatgcctacccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
           |  | |  | || |  | | |||    || |  | |   |  | |   || |  | |  ||| | |   |  || ||     ||||| | | | ||||||||||| ||||||||||||||| |||||||||||||||| || || || || ||||||||||| ||||| || ||| |||||||||||
-----------gtaacttactttcaactatttaatctgatataaa-gaaaatacctaatttcctggttgatttacatgcttacga-gccttcttttgtgtgtcatagTCTACTCGCAATAGCTGAGGAGACCCTGGCAGAGTTCCTGTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

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|58665470|gb|CK054156.1|CK054156
EST:     CAAAACCCAGCAGCCACGCGTCCGCAAAGGGACGCGAACAACCCAGCTGG                         TCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGAC
genomic: CAAAACCCAGCAGCCACGCGTCCGCAAAGGGACGCGAACAACCCAGCTGGgtaattacag ... tttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGAC
EST: gi|29625769|gb|CB630780.1|CB630780
EST:     CAAAACCCAGCAGCCACGCGTCCGCAAAGGGACGCGAACAACCCAGCTGG                         TCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGAC
genomic: CAAAACCCAGCAGCCACGCGTCCGCAAAGGGACGCGAACAACCCAGCTGGgtaattacag ... tttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgcattgcgcgatcttttgcttaagtttgatgcaactctttgtttcttacagTCTACTCGCTATAGCTGAGGAGACCTTGGCAGAGTTCCTGTCGAAAGCGACGGGTACTGCTGTCGATTGGGTGCAAATGGTTGGGATGAAG
                           gtttgat  putative branch site (score: 5)
                                      ctctttgtttcttac  putative PPT
                       ttaagttt  TA-rich tract