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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgaattcaaatgccatcgttttattctgctaaatttactttccacaagatgaaatgtgaaaaccgcaagcattgtcagcattttgttttccttgattcatgaatatcacttgtttggtttgctttctcgtatattgcaaaatcattaaatgaatggtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTGGACGAGTCTCTTGCCCAAGTTTGTTCAGAAAGTGGTGCATTGGATCCCC

Basic information

species Oryza sativa
transcript LOC_Os02g51430.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 8
gtatatgaattcaaatgccatcgttttattctgctaaatttactttccacaagatgaaat-gtgaaaaccgcaagcattgtcagcattttgttttccttgattcatgaatatcacttgtttggtttgctttctcgtatattgcaaaatcattaaatgaatggtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTGGACGAGTCTCTTGCCCAAGTTTGTTCAGAAAGTGGTGCATTGGATCCCC
                                    |  |||  |   | |  || |  |  |    || |||  | || |||| ||| || |  | | | |||| || ||     |   |  |||    |   ||   | ||||  |||||||  || |  ||||||||||| || |||||||| ||| |||| ||||||||  | || |||||||||||||| || || ||||||||||||||||| ||||||||||||||||||||||
----------------------------------gtaccttatctcaaatatcataattttattctcactgca--ccttttcag-attgtgctc-cttcggttcaggagtaatgagtaaatattttttacttctgttcttagcaagctcattaatagactaatcactgtagGTGACTGGTTGGGTCGTGCAATATCAAGAAAACTTGATTGGTCTTGGTGTGGATGAATCACTTGCCCAAGTTTGTTCTGAAAGTGGTGCATTGGATCCCC

upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv12s0034g02360.t01 (Vitis vinifera), 3'ss of exon 13
gtatatgaattcaaatgccatcgttttattctgctaaatttactttccacaagatgaaatgtgaaaaccgcaagcattgtcagcattttgttttccttgattcatgaatatcacttgtttggtt-tgctttctcgtatattgcaaaatcattaaatgaatggtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTGGACGAGTCTCTTGCCCAAGTTTGTTCAGAAAGTGGTGCATTGGATCCCC
                                                          ||   | |||    | || |||  |    |||||||  | | ||      | || ||| | |  |  |  ||| | || |||     |||  ||   |   | |  |||  ||||||| |||||||||||  |||||||||| ||||| || || |||||||| || || ||| | || ||||| ||||| || ||||||||  ||||||| |
--------------------------------------------------------ttatcatagaacttttatcactgtttgt-ccttgtttttttagtttt-----tttcccttttatcatcataattttttgtttat-----aatttttgttt--cttgcaact--agGTAACTGGTTGGGTTGTTGAATACCAAGACAATCTAATTGGGCTTGGTGTTGATGATTCTTTAGCTCAAGTGTGTTCTGAGAGTGGTGCTATGGATCCTC

upper sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv03s0097g00670.t01 (Vitis vinifera), 3'ss of exon 13
gtatatgaattcaaatgccatcgttttattctgctaaatttactttccacaagatgaaatgtgaaaaccgcaagcattgtcagcattttgttttccttgattcatgaatatcacttgtttggtttgctttctcgtatattgcaaaatcattaaatgaatggtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTGGACGAGTCTCTTGCCCAAGTTTGTTCAGAAAGTGGTGCATTGGATCCCC
                                                                  | | || | | | | | || | | || | |||| ||  |   | |      |||  |   | |  |  | | ||  | |||  ||   |   | |  |||  ||||||| |||||||||||  |||||||||| ||||| || || |||||||| || || ||| | || ||||||||||| || ||||||||  ||||||| |
---------------------------------------------------------------cttatcaca-gaacttttatcactgt-ttgttcttgttttttagcttttttcccttttatcatcataattttttgtt-tataat--ttgtgtttcttgcaact--agGTAACTGGTTGGGTTGTTGAATACCAAGATAATCTAATTGGGCTTGGTGTTGATGATTCTTTAGCTCAAGTTTGTTCTGAGAGTGGTGCTATGGATCCTC

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|58665364|gb|CK054050.1|CK054050
EST:     GACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAATATTCTTAAG                         GTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTG
genomic: GACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAATATTCTTAAGgtatatgaat ... gtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTG
EST: gi|29666539|gb|CB662814.1|CB662814
EST:     GACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAATATTCTTAAG                         GTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTG
genomic: GACTTCTCAGTGATAGAGCAAATGATATTCCAAATATAAATATTCTTAAGgtatatgaat ... gtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttggtttgctttctcgtatattgcaaaatcattaaatgaatggtcactgtagGTAACAGGTTGGGTTGTGAAATACCAAGAAAATCTTATCGGTCTTGGTGTGGACGAGTCTCTTGCCCAAGTTTGTTCAGAAAGTGGTGCATTGGATCCCC
                   tatattgcaaaatcat  TA-rich tract