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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcaaaagtatatgtatattttaccatatgttctctctttctggttgtattaacgtggggcattacaactcctaattcttcaacaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA

Basic information

species Oryza sativa
transcript LOC_Os05g49970.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G007038_T01 (Zea mays), 3'ss of exon 3
----------gtatagcaaaagtatatgtatattttaccatatgttctctctttctggt-tgtatt--aacgtggggcattacaactcctaattcttcaacaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA
           |||| |    ||   | | || |  ||  |     |  | | | |  | |  | |  | | |  | |||||| | || ||||||||  | | |   |||| |||||||||||||||||||| || ||||| ||||| |||||||||||  |||||||  ||||||||||||||||||| |||||||||| ||||||||
gtgtatatatatataacttctgttgttatgtagtccacagttcacccgttttattttatgtacacttaagcatatgccattactattcttaattctttgagatct-cagGCGTTTGGTGCAATGAGAGCTCGAGGAGCTAGAGTAACCGATATCTGTATTGTTGTTGTTGCTGCGGATGATGGTGTTCGGCCACAAACAAGTGAGGCAA

upper sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G40370.1 (Glycine max), 3'ss of exon 3
------gtatagcaaaagtatatgtatattttaccatatgttctctctttctggttgtattaacgtggggcatt-acaactcctaattcttcaacaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA
       | || |  || |||   ||  | | || ||| ||  ||| ||     |  | |      |  |  |  |  |    || |   |  |   |  ||||||||||| |||||||||||||| || || || ||||| || ||   ||| ||||||||  |||| ||||||||  ||||||| ||||||||||| || |
tgtagtttttaactgaattat---taactataactataagtaatcttttcactttcatttcctttagaagtctagatgatatatattatatgcattcctgtagGCATTTGGAGCAATGAGAGCTCGTGGAGCAAGCGTAACAGACATTGCTATTATTGTTGTGGCTGCTGATGATGGGATTCGTCCTCAAACAAATGAAGCTA

upper sequence: LOC_Os05g49970.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G17220.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------gtatagcaaaagtatatgtatattttaccatatgttctctctttctggt-tgtattaacgtggg-------gcattacaactcctaattcttcaacaacaa-tagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA
                                                                  ||   ||  ||  |   || || | | ||| | |  |  || |||    | ||||     |         |  ||||   || || || |    |  ||  |||||||||||||||||||||||||| || ||  | || ||||| ||    |||||||| ||  |||| ||||||||  ||||||| ||||||||||| ||||
gtagattctttttcttgcaattgaatcttcgcatgttcatttctgatgctgaagtatcattaattatacttcatgagctttcttacatgt-agcatgtttattgactatctcacatctattgctaggcataccatagttttactcatcttacttttatgtcctcatctagGCATTTGGTGCAATGAGAGCTCGCGGAGCACGAGTCACTGACATTGCAATCATTGTGGTTGCTGCTGATGATGGAATTCGTCCTCAAACAAATGAAGCAA

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|29687527|gb|CB683802.1|CB683802
EST:     TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAG                         GCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC
genomic: TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAGgtatagcaaa ... acaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC
EST: gi|58664948|gb|CK053634.1|CK053634
EST:     TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAG                         GCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC
genomic: TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAGgtatagcaaa ... acaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC
EST: gi|29622812|gb|CB627823.1|CB627823
EST:     TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAG                         GCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC
genomic: TTGATGGAAACCCTCATGCTTGTGTTTTTCTTGATACTCCAGGGCACGAGgtatagcaaa ... acaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctggttgtattaacgtggggcattacaactcctaattcttcaacaacaatagGCATTTGGTGCAATGAGAGCTCGGGGTGCTAGGGTAACTGATATCTGTATCATTGTTGTCTCTGCGGATGATGGTGTTCGTCCACAAACAAATGAGGCAA
       ttgtattaa  TA-rich tract