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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC

Basic information

species Oryza sativa
transcript LOC_Os01g64780.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G046098_T04 (Zea mays), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttacca-aacaaaaagtaaaaaat---catgcattgt-tcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC-----
||||  | || |||  |||  || ||| |||||| ||| | | | |  ||     |    ||||||  | | ||  |    |||| | | ||||| || || || || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||| |||     
gtacgcccttcacaataactgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtagTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATCAACAT

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149662_T01 (Zea mays), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcat---tgttcttcttcccttttttttttt--gcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
||||| | || ||| |||   || ||| | |||| ||| |   |     |    | ||  ||   || |||  |||   | |||| | |  |||| || || || ||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || |||||||||||| |||| |||
gtacacccttcacaagaattgagctaaacctgttgccatatctatgtataccttttatttatgcctgatctatttcttgtgttttatgtatgcagTGTAGTCCTTTTTCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAAATTGGAATC

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttacca-aacaaaaagtaaaaaat---catgcattgt-tcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
||||  | || |||  |||  || ||| |||||| ||| | | | |  ||     |    ||||||  | | ||  |    |||| | | ||||| || || || || |||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||| |||
gtacgcccttcacaataactgagctaaacatgttgccatagctatatataccttttatgtatgcatgatatatttcttgtgttttatgtctgcagTGTAGTCCTTTTCCCTGTTGCAGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGGTTTTTCAGTCCCCTATATGCAAAACTTGGAATC

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttt---tttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
          |  | |||| ||  ||   ||       |  |||   ||  |          ||| ||| |||  ||  ||||   | |||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||| ||||  | |  || ||||| 
----------gtaatgaacaaaactacttattgagatgattaaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGGATA

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
     |  | ||||  |  | | |||   |  | |  ||    |   | |    |  ||   |  | ||| |    ||||   | |||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || ||| ||||  | |  || || || 
----gtaatggacaaaa--ctacttattgagatgattaattttatcatcattgttggtgtgct--tattcatttagttttgaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTATTCAGTTTGTTGATGGTTTCTTTAGTCCAATATACTCCAGGCTCGGCATA

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcat-gcattgttcttcttccctt---tttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
||| ||   |   || | ||   |||      ||  || ||  |   |   ||||| | | ||  ||    |    ||   | || | | | || ||||| || |||||||| ||||| || ||| ||||||| ||||||||||| || || |||||||| || ||||| ||  |||| |  || |||||  | 
gtaaataactcgtagcacccttttta------ttttcatactcatgatttgaaatctttgtatcattggggtctaattgggtgttgtgtggtagTGTCGTACTCTTTCCTGTAGCTGTTACATTCCTCATCACTTGGTGGTTTATCCAGTTCGTTGATGGTTTCTTCAGTCCGATATACGAGAACCTTGGTGTT

upper sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 2
-------gtacatctttgacaggaaccaagttaagcatgttaccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
       |   | || || |   |   |   ||    | ||||    ||     ||  |  |       |    ||       ||||    |||||| || ||||| ||||| ||||| || || || ||  | ||||||||||||||||| || |||||||| || ||||| ||| |||||| |   ||||| |||
gtaatatgcttacctatgccttaatatattctagatgt-ttact---cattttttattattttccagcctaacattgagttgattttgaaattgcagTGTTGTTCTTTTTCCAGTTGCAGTTACATTTTTTGTTACATGGTGGTTTATTCAGTTCGTTGATGGTTTCTTCAGTCCATTATATGAACGGCTTGGCATC

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|29683440|gb|CB679715.1|CB679715
EST:     CATGCTGCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATG                         CGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: C-TGC-GCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATGgtacatcttt ... ttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTAT
EST: gi|29688878|gb|CB685153.1|CB685153
EST:     TGCTGCGCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATG                         CGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTAT
genomic: TGCTGCGCTGTTCTTCAAAGTTGGGTGTCAAGAAAATTTATGACTGGATGgtacatcttt ... ttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaacaaaaagtaaaaaatcatgcattgttcttcttccctttttttttttgcagCGTCGTTCTGTTTCCTGTTGCTGTCACGTTCTTCATCACATGGTGGTTTATTCAATTTGTTGATGGCTTTTTCAGCCCACTATATGCAAAACTTGGGATC
                   tcatgcattgttcttc  CT-rich tract
      aaaaagtaaaaaatca  TA-rich tract