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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaccataataggtgaggttttatgaaatttactcaaataaaaaagatattcagcattgcaaatacttgaagctggcattttggtgaatgcaaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC

Basic information

species Oryza sativa
transcript LOC_Os04g52640.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G126858_T01 (Zea mays), 3'ss of exon 18
gaccataataggtgag-gttttatgaaatttactcaaataaaaaagatattcagcattgcaaatacttgaagctggcattttggtgaatgcaacctt--gcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC
 |  | | |   || |   | ||    |||||||| | || |   |||||| |   |      | |||  | ||    ||| |   ||| || | |   |||||||||  || | ||||| ||  | |||||| | || || |||||| |||||||||  |||||||| ||  |||||| | |||||||||||||||| ||||
-atgagattgattgggtactctagtgcatttactctattaca--tgatattgattttacttggtgcttataactcttttttagaaaaattcaccttctggcagGGTAAATTAGTTGATGGCAGTGTGGTGGCAATTAAACAACTATCTGAAACATCTCGCCAAGGGAAGAAGGAATTCGTAGCTGAAATAGAAACTATTTCCC

upper sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
gacca--taataggtgaggttttatg-aaatttactcaaataaaaaagatattcagcattgcaaatacttgaagctggcattttggtgaatgcaacct---tgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC
  | |  |  ||    || || ||   |  |||  | ||||   |  | || |     ||  |     || || ||  |||| | |  ||||  ||||   ||||||||||  ||   ||||||||| | ||||| || || ||| ||||| ||||||||||||| || ||| | ||||| ||| | |||||||||||||| || |
-tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttcta-----ttcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
















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|29632427|gb|CB637436.1|CB637436
EST:     TTAGTTCCAGCAACCGTCTTGGTGAAGGAGGATATGGGGCAGTTTATAAG                         GGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
genomic: TTAGTTCCAGCAACCGTCTTGGTGAAGGAGGATATGGGGCAGTTTATAAGgttagttcat ... aaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
EST: gi|87012044|gb|CI291499.1|CI291499
EST:     GATATGGGGCAGTTTATAAG                         GGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
genomic: GATATGGGGCAGTTTATAAGgttagttcat ... aaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
EST: gi|29634408|gb|CB639417.1|CB639417
EST:     TTAGTTCCAGCAACCGTCTTGGTGAAGGAGGATATGGGGCAGTTTATAAG                         GGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
genomic: TTAGTTCCAGCAACCGTCTTGGTGAAGGAGGATATGGGGCAGTTTATAAGgttagttcat ... aaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
EST: gi|29661115|gb|CB657390.1|CB657390
EST:     ATATGGGGCAGTTTATAAG                         GGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA
genomic: ATATGGGGCAGTTTATAAGgttagttcat ... aaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcagcattgcaaatacttgaagctggcattttggtgaatgcaaccttgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC
              aaatactt  TA-rich tract