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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcattatgacaaattttagcaaacagaaaggccccttggtttctcagtatgcattgccttcatatctccgtgtttatttatttttgtggt...

Basic information

species Oryza sativa
transcript LOC_Os01g55360.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G890512_T01 (Zea mays), 5'ss of exon 1
------ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcattatgacaaattttagcaaacagaaaggccccttggtttctcagtatgcattgccttcatatctccgtgtttatttatttttgtggt----------------------------------------------------------------
       |  | || ||| |||| |||||||||||||||||||  |||||||||||||||||||||| ||||  || |  || | || ||| ||| ||||  |  ||||| || |  |    ||| ||      |  | | | ||| | ||||  | | |     ||| | || || |    ||          ||||                                                                
TAACTTTTTGAGTACCAGTGATGTAAAGGGACACAAGCTCTAGCAATGTTTCTGCTTCTCATGTAGGCCGTGTAAGACGTCGCAAACATCCAACTAAGgttagtaatttc-ttgttcc----ttttgctcttttattg-cgctttgctctctctctct-ctccctctttagatttcagctaatacactgaaacatggttcaagctagagcagcagcctgttttaggtgttctttttcgtactaatcttggtcattttttcag

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G825110_T01 (Zea mays), 5'ss of exon 2
-----ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcattatga---caaattttagcaaacagaaaggccccttggtttc--tcagtat----gcattgcct---tcatatctccgtgtttatttatttttgtggt-------------------------------------------------------------------
      |  | || ||| |||| |||||||||| |||||||| ||||||||||||||||||||||| ||||  || |  || | || |||  |||||||  |  | ||| |  |          ||||     |          || | ||||   || |||    |||| |        | | |  |  | | || ||      ||||                                                                   
TAACTTTGGAGTACCAGTGATGCAAAGGGACACTAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGGCGTGTAAGACGTCGCAAACATCCATCTGAGgttagtaaattcttcttccatttgctctttattgcgctctgttctttctagatttcagccaatatataagcatggttcaaactagaacagcaagctaatatacaagcatggttcaaactagagcagcagcctgtttcaggtgctcttttttcgtaactaatcatgatcattttcttcag

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G452529_T02 (Zea mays), 5'ss of exon 2
------ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcat-----tatgacaaattttagcaaacagaaaggccccttggtttctcagtatgcattgcc-ttcatatctccgtgtttatttatttttgtggt----------------------------------------------------
       |  | || ||| |||| ||||||||||||||||||| ||||||||||||||||||||||||||||  || |  || | || ||| ||||||||  |  ||||| |     | |  |   || | ||   | |      | ||   | ||||  | |  ||| |   | |||       |  |  ||     |   |                                                     
TAACTTTTTGAGTACCAGTGATGCAAAGGGACACAAGCTCTAGCGATGTTTCTGCTTCTCATGTAGGACGTGTAAGACGTCGCAAACATCCAACTGAGgttagtaatttcttgttccttttgctctttattgcgctctgctctctctctctctctctctctctagatttcagctaatacactgaagcatggttcaagctagagcagcagcctgtttcaggtgctcttttacgtactaatcttggtcattttttcag

upper sequence: LOC_Os01g55360.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G031052_T01 (Zea mays), 5'ss of exon 1
--------ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcat---tatgacaaattttagcaaacagaaaggccccttggtttctcagtatgcattgccttcatatctccgtgtttatttatttttgtggt----------------------------------------------------
         |  | || ||| |||| |||||||||||||||||||  |||||||||||||||||||||| | ||  || |  || | || ||| ||||||||  |  ||||| |     |       ||||   | |        | ||   |  |||  ||    |   ||  |||          |  ||     |   |                                                     
AGTAACTTTTTGAGTACCAGTGATGTAAAGGGACACAAGCTCTAGCAATGTTTCTGCTTCTCATGTAGGCCATGTAAGACGTCGCAAACATCCAACTGAGgttagtaatttcttgttccttttgctctttattgagctttgctctctctctctccctctttagatttcagcta-atacactaaaacatggttcaagctagagcagcaacctgttttaggtgttctttttcgtactaatcttggtcattttttcag

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|29681974|gb|CB678249.1|CB678249
EST:     AGGACGTGCCACCCTGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: AGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|58661284|gb|CK049964.1|CK049964
EST:     TGTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|29673386|gb|CB669661.1|CB669661
EST:     TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
EST: gi|29679197|gb|CB675472.1|CB675472
EST:     TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAG                         GCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT
genomic: TTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatt ... ttttgttcagGCTACTGCAGATGGGAATAGAACCAATGGACCAGCTTTGCTTGTCAATGAT

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAATAGCAGCGATGGAAAGGGACACAAGCTCTAGTGATGTTTCTGCTTCTCATGTAGGACGTGCCAGGCAGCGAAGACGTCCTACTGAGgtaggctatttcattatgacaaattttagcaaacagaaaggccccttggtttctcagtatgcattgccttcatatctccgtgtttatttatttttgtggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA