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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccatcagctttagattcgatctttggaattgaagcataaatgactcagctagtgttgctatctaataattcatttggctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAACAAAATTGGTCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAA

Basic information

species Oryza sativa
transcript LOC_Os01g06600.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06600.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G862219_T02 (Zea mays), 3'ss of exon 8
-----------------------------------------------------------------------gtaaaccatcagctttagattcgatctt----tggaattgaagcataaatgact--cagctagtgttgctatctaataattcatttggctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAACAAAATTGGTCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAA
                                                                         || |  |   ||  ||   | | | |    | |  ||  |   | | |  |      | |||  |||  |    |  ||  | | ||| |    || || |||||| |||| || ||||||||| |||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| |||||||| || || 
gtaaatcatcttgccttggaccaccattgtacttaagcatccaaccgattatgaacacgctatattttcttccaatctgttgtctcaagcgccaaccctatcttcgtgttataaagtcagtttccactgacgagttctgcgttgccttgttt--tctcgcttccaccagGTTCATTGTGCGGAAAGGAGCTCCTGGCCTGAAAGCTACAAAGATCGAGAACAAAATTGGCCTCAGGATGGTTCAGAACGGTGACATAGTTTTGAACAAG
















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|29666427|gb|CB662702.1|CB662702
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29666426|gb|CB662701.1|CB662701
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|14713699|gb|AU197670.1|AU197670
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29676104|gb|CB672379.1|CB672379
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTNGAA-GCTACAAAGATTGA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTT-GAAAGCTACAAAGATTGA
EST: gi|33683998|gb|CF312237.1|CF312237
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTG-GNAGGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAG
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTG-A-GGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAG
EST: gi|88344179|gb|CI654609.1|CI654609
EST:     TCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: TCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|13165132|gb|AU173929.1|AU173929
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|56157778|gb|C26441.2|C26441
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29666428|gb|CB662703.1|CB662703
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
EST: gi|29678764|gb|CB675039.1|CB675039
EST:     GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGG                         ATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA
genomic: GATGTGCTCGTGGTATTAGCTAGGAATGCCAATACAAAACAACTAAATGGgtaaaccatc ... ctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcataaatgactcagctagtgttgctatctaataattcatttggctccttgtagATTTATTGTGAGGAAGGGTGCTCCTGGCTTGAAAGCTACAAAGATTGAGAACAAAATTGGTCTCAGAATGGTTCAGAACGGTGATATAGTTTTTAATAAA
                           atctaat  putative branch site (score: 3)
                                             ctccttgt  putative PPT
                          tatctaataattcatt  TA-rich tract