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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttag

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 13
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa--tattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttag
|| ||||||  |||| ||||| |||||||| ||||| ||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||| || ||||||||||  |||||| | |   |   |  | |||  |  | |  | || ||| ||| | |  |   |   ||| ||| ||| ||| |||
TTATGGTGGGGTATTGTTGGCAATGTGTTCTAGTGACTTCATCTGCTTTTATGACTGGGCTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgagtcaaaagtattatttttccttgggtggaaatt--ttgtatgtatgagtttaatattaacct---tttgtttatca-tgtgtttatag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 12
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattg-atacttttaacgaattt-catactgaaataactagttttgtcactgtatttttag
|||||||||  |||| ||||| |||||||| ||||||||||| |||||||||||||||| ||| ||||||||||||||||| || ||||||||||| || |||| |||| |||||| | ||  |   |  | |||   ||  |  || | ||     ||||   |    |   ||| ||| || |||| |||
TTTTGGTGGGGTATTGTTGGCAATGTGTTCTAGTGATTTCATCTGCTTTTATGACTGGGTTGATTGTAGACTAATACGCCGAATCGATGTGAATGTTAAGgtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatca-tgcatttatag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 2
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaa-taactagttttgtcactgtatttttag-----
 |||||||| |   ||||||| ||||| || | ||||||||| ||||||||||| |||||||| || ||  | || || || |||||||| ||||| ||||| |||    |   ||    ||| ||    || ||  | ||||||      ||| |||||    |   || |||||| |   | || ||       
ATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGGCTGAATGCAGGTTGATTCGTCGTATTGATGTTAATGTTAAAgtaagt--gcttgcatgaggtgacatc---agctttctgcttttattt--cttcttactgtttcttgttaattttgttaaaattttcttgtgtcag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 13
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattgatacttttaacgaat-ttcatactgaaataactagttttgtcactgtatttttag---
 |||||||| |   || |||||||||| ||||  |||||||| |||||||||||||||||||| || ||  | ||    ||||||||||| ||||| ||||| |||  | | | ||    ||| |||||   ||     |||||      | |||||  |  ||||  || |||||| | |    || |     
ATTTGGTGGCACTCTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagt--actttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaata--taattttgttattaatcttgtgtcag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 13
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttag----
 || ||||| |  ||| |||||||||| ||||  |||||||| |||||||||||||||||||| || ||  | ||    ||||||||||| ||||| ||||| |||  | | | ||    ||| || ||   ||     |||||  |   ||      ||    |  || |||||| | | ||| ||  |    
ATTCGGTGGCACTTTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGGCTGAATGCAGGTTGATCTATCGCATTGATGTCAATGTGAAAgtaagt--actttgattaggtgacatctagttatctgctcttttc-cttcttattcgttgtttaatttaattttgttatt-tatcttgtgtcag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 13
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaata--ttatctattgatatttatagattgatactttta-acgaatttcatactgaaataactagttttgtcactgt-atttttag-------------------------------------------------------
 ||||| ||||  || || || |||||||| ||||||||||| ||||||||||| |||||||| ||||| || || |  || ||||| || | ||| || ||    ||  ||  ||  ||     ||||   |||    |||||  | ||  ||||   |  |    ||||| | |  |  |  | | ||| ||                                                       
CTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGGCTGAATGTAGGCTGATTCAACGTATTGACGTCACTGTAAAGgtatcccagttaacttggctcagtttattgtaagaagtttacttcaagacatatttggaatagtggaaactaatatcattgccttcagtttgaggttttcctcgtttgtttcttctctaatttgtagtgttgctacataacgtttgcag

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 13
TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagt-caaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttt--tgtcactgtatttttag---------------------
|||||| ||||  |||||||| ||||| || | |||||| ||||| || |||||||||||||| || || || || || || |||||||| ||||||||||| ||  | || || ||    || |   ||  |  || || | ||  |  ||  || |||| |  || |  ||   |||  || | || ||                       
TTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGGCTGAATGCAGGCTGATTCGACGAATTGATGTTAATGTCAAAgtaagcactaacatgatggcctgttggctaccg--tggtattgttttc--atgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcag

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|58660118|gb|CK048798.1|CK048798
EST:     ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA                         AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
EST: gi|29630380|gb|CB635389.1|CB635389
EST:     ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA                         AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA