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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaggttctactcttttaggtctctctgcttatgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaataagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGGTAAGAGTAAAATAATGCTTCTGCATTAGTCTTCTCAGTT

Basic information

species Oryza sativa
transcript LOC_Os07g14150.6
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G008216_T03 (Zea mays), 3'ss of exon 1
gttgaaggttctactcttttaggtctctctgcttatgaa--gttgccaatg-atcatgtcctcaatatgtaaaataagctaaaataagttacttttc--ctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGGTAAGAGTAAAATAATGCTTCTGCATTAGTCTTCTCAGTT
  |||||    |  ||  |||    |   ||  ||  ||        || | |||   | ||    ||  |  || | || ||   |    |||| |  ||| |||||||||||||||||||||||||||||| ||||||||||||||||||||| | || ||||                                        
--tgaag---ttggtcgcttaaaattggttgtataataacgaacattaacgtatcggtttcttctgataaatcatgaccttaatgtatgcgctttcctactgcagTTGTGGAGTCAAAGGATGGAACCATCTCGGTTGCTTCTGCATTTGCTGGTTATCAGGAAG----------------------------------------

upper sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 1
gttgaaggttctactcttttaggtctctctgctt-atgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaataagt-tacttttc--ctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGGTAAGAGTAAAATAATGCTTCTGCATTAGTCTTCTCAGTT
    ||  |  |      |||| | | | |  |  ||        ||  | |  |      ||    | |  | |     ||    | | |||||   ||| ||||||||||||||||||||||||||||||||||||||||||||||| || ||| || ||||                                        
----aatttaatcgctgattagctgtatataatcgatattagcagcacggtttcttctgataaaccatgacctcaatctcaacgtatgtgcttttgtactgcagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAG----------------------------------------

upper sequence: LOC_Os07g14150.6 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 1
gttgaaggttctactcttttaggtctctct-gcttatgaagttgccaatgatcatgtcctcaatatgtaaaataagctaaaa-taagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGGTAAGAGTAAAATAATGCTTCTGCATTAGTCTTCTCAGTT
  ||||      |     |  ||| | | | |   |  | |||  || | ||    |  |   ||| | |  |   ||     |   ||| | ||  |  ||| |||||  | |||||||||||  ||||||| ||| |||| |||||||||||||| ||||                                        
-ctgaacaacagagcaaatatggtgtatttagaacacaatgtt-tcatttatttcattgtgtttattttatgttttctttgtcttttttaatattatttcagTCGTGGAAACTAAGGATGGAACTGTCTCAGTAGCTGCTGCGTTTGCTGGTCACCAGGAAG----------------------------------------

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|33684611|gb|CF312850.1|CF312850
EST:     GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGT                         TTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC
genomic: GTTTGCTGGATTTGCTCCTCTCCCTCTCTCCGCCATGGAGGAGGCCCAGTgtacgtctct ... tttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgatcatgtcctcaatatgtaaaataagctaaaataagttacttttcctgtagTTGTGGAGTCAAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGGTCACCATGAAGGTAAGAGTAAAATAATGCTTCTGCATTAGTCTTCTCAGTT
                            agctaaa  putative branch site (score: 3)
                                        ttacttttcct  putative PPT
               aatatgtaaaataagc  TA-rich tract