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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttacctccatagttctgttctcttgagaatcatggagttatatgcatttgttttctcctgcaattaatttatatctttgcccttatttatgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g17320.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g17320.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 9
atttacctccatagttctgttct--cttgagaatc--atggagttatatgcatttgttttctcctgcaattaat---ttatatct-----ttgcccttatttatgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG
           | | ||| || |  ||| || ||    |||| ||| |||  ||||| ||||| ||  || | |   | |||| |     |  | |||  |||||  |||||| || ||||||||||| || |||||||||||||| |||||||||||||||||||| || ||
-----------ttgctctcttgtaacttaagtatgtggtggaattacatgtgtttgtattctc-tgtgatcagtacttcatatttccctgtcacactttattatgtatgcagGGTCTGTTTACACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTATCTCAGTGATCAGGAG

upper sequence: LOC_Os02g17320.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 11
atttacctccatagttctgttctcttgagaatc--atggagttatatgcatttgttttctcct--gcaattaatttatatcttt-----gcccttatttatgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG
             ||  |||   ||| || ||   ||||| ||| ||   ||||| |||||    |  | || ||||||| ||      || |||  || ||  ||||||||| ||||||||||| || |||||||||||||| ||||||||| |||||||||| || ||
--------ttgctgtcttgtag-cttaagtatttgatggaattacatctgtttgtattctctgtggttagtactttatattttctcggcgcactttattgtgtatgcagGATCTGTTTACACTGGTGTGGAGTTCTCCAAAAGGTTGTGTGGTGTCTCAGTGATCAGGAG
















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|86902718|gb|CI306521.1|CI306521
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|33675270|gb|CF303509.1|CF303509
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACA
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACA
EST: gi|29643325|gb|CB648332.1|CB648332
EST:     GGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCNCA-CTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCT
genomic: GGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTC-CAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCT
EST: gi|12623049|gb|AU173262.1|AU173262
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGGGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|66922909|gb|CX109757.1|CX109757
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GCTCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
EST: gi|58687647|gb|CK076334.1|CK076334
EST:     TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTG                         GATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG
genomic: TGGTCTTGGTCATCTTCCATTCAAGGAAAAGCAGGTCATAACTCCAACTGgtaggtagta ... atgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatttgttttctcctgcaattaatttatatctttgcccttatttatgcgtgcagGATCGGTTTACACTGGGGTAGAGTTCTCCAAAAGATTGTGTGGTATCTCAGTGATTAGAAG
                  aattaat  putative branch site (score: 3)
                  aattaatttatatctt  TA-rich tract