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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacacacaattaccttacaagttcatgatccattaataatattagaacttttgtacttctctgcattactttgctgatttcccctttcaactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g14810.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G044819_T02 (Zea mays), 3'ss of exon 8
-------gttaacacacaattaccttacaagttcatgatccattaataatattagaacttttgtacttctctgcattactttgctgatttcccctttcaactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCAT
        ||||    | |      |     |  |||||| ||| |   || ||||||  |||| ||  | |||      | |||  ||||| |   |||   ||||||||||||||| ||||||||| ||||| || ||||||| ||| ||||| |||||||||||||||||||||||||||||||| |||||||||||| ||| ||
gtgttctcttaatcttctacatttatggtgctgtatgatcaattcagtgtaatagaaccattgtgctgatatgc------tggct--tttcctccaacaaactatcagGCTGGAAAAAAGTTGCTTCTCATTACTAATTCAGATTTCCATTATACAAACAAAATGATGAATCATGCATTCAATCGCTTTCTTCCTAATGATGTGGGAT

upper sequence: LOC_Os01g14810.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA15G21240.1 (Glycine max), 3'ss of exon 8
gttaacacacaattaccttacaagttcatgatccattaataatattagaacttttgtacttctctgcattactttgctgatttcccctttcaactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCAT
           ||| | ||| | ||   ||   |  |       |   |  |  ||| |||||   |||||||| | || ||||        |   | ||||| || ||||   |  | |||||||| ||||||||||| || |||||  ||||||||||| ||||| |||||||| | |||||||| ||||| ||||  |
---------gtattgc-ttata-gtatgtgtatctctg----cctcgcacataatgtgcttctgctcattacttggttgttttc--------atgaaacagGCAGGCAAAAAACTTGTACTTATTACCAACTCAGATTATCATTATACACACAAAATGATGCATCATTCATTCAATAGATTCCTTCCCAATGACATGGGTT
















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|29627736|gb|CB632747.1|CB632747
EST:     TTGTAGAGCCTGATCCTGAACTGCCTTTAGCTCTTCTGGATCAAAAGGAG                         GCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAAC
genomic: TTGTAGAGCCTGATCCTGAACTGCCTTTAGCTCTTCTGGATCAAAAGGAGgttaacacac ... aactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAAC
EST: gi|29673384|gb|CB669659.1|CB669659
EST:     TTGTAGAGCCTGATCCTGAACTGCCTTTAGCTCTTCTGGATCAAAAGGAG                         GCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAAC
genomic: TTGTAGAGCCTGATCCTGAACTGCCTTTAGCTCTTCTGGATCAAAAGGAGgttaacacac ... aactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacttttgtacttctctgcattactttgctgatttcccctttcaactcatcagGCTGGAAAAAGGTTGCTTCTTATTACAAACTCAGATTACCACTATACGAACAAAATGATGAATCATGCATTCAATCGCTTCCTTCCTAATGATATGGCAT
                            tgctgat  putative branch site (score: 3)
                                  tttcccctttcaactc  CT-rich tract
                     attacttt  TA-rich tract