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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattacttgccagcctttctctgtggaggttcatataaaaaagagtacttctggaggtttatcgctgattttctctgatattttatctatgggacattgcag

Basic information

species Oryza sativa
transcript LOC_Os06g09290.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G42370.2 (Glycine max), 5'ss of exon 4
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattact-------tgccagcctttctctgtggaggttcatataaaaaa---gagtactt---ctggaggt-ttatcgctgattttctctgat-attttatctatgggacattgcag-------------------------------------------------------------
|| ||||| |||||||||||||| | ||| ||| | || ||||| |||||||| ||||| || ||||| ||||| ||||| |   ||  ||| |  | |       |||||  || || |  ||    |    | |   |    | || |||    || || | |||    | | || || | || |  ||||| |||||       ||                                                             
GTAGCAAGGTGCACAAAGATCATAAACCCGAACTCAGAAGATGCCAAATATGTAATCAACGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagatgccaaactgtcccattgtttttcaccacatctatcccgtgttcttgttttgaagatgttagacttcacttactgttatgaaattatcaatgggttggcaaagctgttgattctttgattatgctgtcaggactagtaatccttctgcttttttttaatgacag

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 4
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattacttgccagcctttctctgtggaggttcatataaaaaagagtacttctggaggtttatcgctgattttctctgatattttatctatgggacattgcag
|| ||||||||||||||||| || ||||| ||  | || ||||| |||||||| || ||||| || |||||||| ||||| ||      |||||  |||   | |  | |  || | ||   |  || |  |  || |   | |    |||  |   || |||  ||  |      || | |            
GTGGCAAGATGCACAAAGATAATTAGCCCCAATTCTGAGGATGCCAAATATGTGATAAATGTTAAACAAATTGCAAAGgtaagcttcaattttaagact---ctgtttcttcctatagaaacttgtaaagcatggactttctttttctgttcctt-ttgttttgttcaaacgcaaaattttt------------

upper sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EDP03835 (Chlamydomonas reinhardtii), 5'ss of exon 5
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattacttgccagcctttctctgtggaggttcatataaaaaagagtacttctggaggtttatcgctgattttct-ctgatattttatctatgggacattgcag
|| ||  | ||||| |||||||||| ||| ||||||||||| || || || |||||||| ||||||||  |   |  |  ||| |        || ||     ||  | |  | | ||| | ||     |   |  | |        ||| |   |  | | |    | |  |                      
GTGGCTCGCTGCACCAAGATCATCAACCCCAACACGGACGACGCCAAGTACGTCATCAACGTCAAGCAGgtgcgggcgaggaggcgg------atgacagaggagtgtatggcggcggatgatcgggggagggaagggaaggggcacggtctggaggcggtatcgagcgggcaac--------------------

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|58586381|gb|CF984689.1|CF984689
EST:     CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCAAAG                         TTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
genomic: CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatg ... gacattgcagTTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
EST: gi|58653641|gb|CK042321.1|CK042321
EST:     CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAG                         TTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
genomic: CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatg ... gacattgcagTTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
EST: gi|29666226|gb|CB662501.1|CB662501
EST:     CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAG                         TTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
genomic: CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatg ... gacattgcagTTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
EST: gi|58592633|gb|CF990941.1|CF990941
EST:     CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAG                         TTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA
genomic: CTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatg ... gacattgcagTTTGTGGTTGGGTTGGGCGACAAGGTCTCCCCCACTGATATCGAGGAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCAAGATGCACAAAGATCATCAGCCCTAACACGGACGATGCTAAATATGTCATCAATGTCAAGCAAATTGCGAAGgtgagtcatgcttttattacttgccagcctttctctgtggaggttcatataaaaaagagtacttctggaggtttatcgctgattttctctgatattttatctatgggacattgcag

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