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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag

Basic information

species Oryza sativa
transcript LOC_Os04g51610.3
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactg-----tgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag
|||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||| ||  ||||     | || | || || |||||     |||| |  |||| || ||  ||| |   |  || ||
GCAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactg-----tgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag
 ||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||| ||  ||||     | || | || || |||||     |||| |  |||| || ||  ||| |   |  || ||
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgt---acactgtgttctgttattggccttcc---atgactgcaactt----atagtattcttttctctcgcttttag-----------------------------------------------------------------------------------------------------------------
|||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||||| ||     |||   ||  |         ||||   | || |  || ||    |  | | |   |||  |  |  || |                                                                                                                 
GCAGATATTGGTCTATCAATGGGCATTCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTCGCATCAGTCGTGAGGgtacgttaaggactagtttgggaacaccattttcccaaaggattttaattttccaagggaaattagttcattttcccttgggaaaaatagaaatctcttgggaaaattgagttcccaaactagccctaaatgtgtttatatttttttgttagccttctgctactgtagttcatggtgtttgtttctggcttcag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 26
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac-tgtgttctgttattggccttccatgactgcaacttatagtattctttt--ctctcgcttttag--------------------------
|| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |||  |  | | | | || | | |  |   ||  |    |   |   ||  |   | |||  |     ||||| |                          
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagccctcatttcttatttgagagattttgaactgttcttataaatgatgcacgtttgacatctactttttgaaggttagtactcatttctggcatta

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 28
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggcctt----ccatgactgcaacttatagtattcttttctctcgcttttag--------------------------
|| ||||| |||||  | ||||| ||||| || || |||||||| || ||||| |||||||| || || ||||||||||||||||| || || |||| |||  || | |  |  |   ||    |  ||    |  |   |  || | || | ||  ||  |     | ||| |                          
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagtcctcatttcttatttggaagattttgaactgttcttataaatgat-gcatgtttaacatctaccttttgaaggactatttctggcattacttgaa

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgt--tctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttag-------------------------
|| ||||| ||||| || ||||||||||| |||||||||||||| || || || || |||||||| ||| | || || || |||||||| || || | |||| ||   || | |  |   || |  | |||    ||||      |||    |     | |||    ||  ||                          
GCTGATATTGGTCTTTCTATGGGCATCCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGATAACTTTGCATCAGTGGTAAAGgtaggtgttctatttaatacattctcaggcttggatatgatattgtcttccgtttcctgtatcttctcctagtaaattgttgggtaatcaacgctcccac

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtac-actgtgttctgttattg--------gccttccatgactgcaacttatagtattcttttctctcgcttttag--------------------------------------------------------------------------------------
|| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| |||||||| || || ||||||||||||||||| || || |||| ||| ||||| ||| ||   | || ||         |  ||     | |   | |   | |   |||||    | ||  | |                                                                                      
GCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgtactactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgt--gttctgtta--ttggccttccatgactg-caacttatagtattcttttctctcgc--ttttag----------------------
|||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |||| |     | |   |||  |||     |  ||  |||  || |   || | || |   |   |    |  ||| |                       
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttatttattcacttaagcatgtattatatggttgtctttttttggtgtctgtcattggtacaatttcacatgctcaacttagaagttataa

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag-----------------------------
|||||||| ||||| || ||||||||||| ||||| |||||||| || || ||||| |||||||| ||||||||||| || |||||||| || || | |||| |     ||| || | ||    | ||  |||   | ||   | |   || ||   ||   |   |||                              
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttgtcttttttttggtgtctgtcattggtacatgatttcacatgctcaacttaagaacttatatacatttctttggcaatgatttgcctag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 28
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgt--tctgttattggccttc--catgactgcaacttatagtattcttttctctcgcttttag-------------------------
|||||||| ||||| || |||||||||   |||||||||||||| || || || || |||||||| ||| | || ||||| |||||||| || || | |||| ||   || | |  | | || |  |||||    ||||      |||    |     | |||    ||  ||                          
GCAGATATTGGTCTTTCTATGGGCATCTCCGGAACTGAAGTTGCAAAAGAAAGCTCAGATATTATAATCCTAGACGACAACTTTGCATCAGTAGTAAAGgtaggtgttctatttaatatattctcagccttgggtatgatattgtcttccgtttcctgtatcttctcctagtaaaaagttattacttcattttccattg

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtac-----------actgtgttctgttattggcctt-ccatgactgcaacttatagtattcttttctctcgcttttag---------------------------------------------------------------------------------------
|| |||||||||||  | ||||| ||||| || || ||||||||||| ||||| || ||||| || || ||||||||||||||||| || || |||| |||  ||||           | | |  | |||| |     ||  ||| | |  || |   | |   |||||      ||  | |                                                                                       
GCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagtactactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtaca------ctgtgttctgttattggccttccatgactgca-----acttatagtattcttttctctcgcttttag----------------------------------------------------------------------------------------------------------------------
|||||||| |||||  | ||||| ||    ||||| ||||| || ||||||||||| || || ||||||||||||||||| ||||| || || || | ||| | | ||      || | ||||  | |     |||  |   || |        |  |  |  | |   || |   || |                                                                                                                       
GCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAGgtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacact--gtgttctgttatt--ggccttccatgactgcaact----tatagtattcttttctctcg-----cttttag-----------------------------------------------------------------------------------------------------------
||||||||||||||| | ||||| ||||| || || |||||||| ||||| |  || || || || |||||||||||||| |||| ||| || |||| ||| ||||  ||  |    |    |||      |   || |  | | ||    | |  || |||| | |  ||     ||||| |                                                                                                           
GCAGATATAGGTCTCGCAATGGGTATCCAAGGCACCGAAGTTGCAAAGGAAAAGTCAGACATCATTATCTTGGATGACAACTTTGAATCCGTTGTGAAGgtttgtatccttagaaaccaaggattcaaatttcttataaaagaagctcctttttgatactcttctgttgcgtgatacttttggaatttcttttcctcgtaaatgtcctcctttgggctttggggctatttgtgatctttttaattatcctgaattagatatccattttaataatcgtctcattcctatag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 25
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgactgcaacttatagtattcttttctct-cgcttttag--------------------------
||||||||||||||||| ||||| ||    |||||||||||||| || ||||||||||| || || || ||||||||||||||||| || || || | |||  ||  |||   | |   ||| |           || | || | ||   ||| | | | | |  || ||                           
GCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAGgttagtctactacat-caaatatagaaacatgtgatcttctacat-tatccttcatctttatgcttttctaatcaataaactctgtttactcttccag

upper sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 27
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactgtgttctgttattggccttccatgact--gcaacttatagt----attcttttctctcgcttttag-----------------------
||||||||||||||||| |||||||| || |||||||||||||| || || || || || || || ||||||||||| || ||||| || || || | |||  ||  |       |  ||||  |  |    || ||  | || || ||||    |||||    | |    ||||                        
GCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAGgttagtgtaagcaaaccatttatgtgagtaaattgtcttgggaatttgtagttatgattctaccttgttatatttaaaacaaaaatactgtcaatccttt

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|88351169|gb|CI623391.1|CI623391
EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
EST: gi|58594188|gb|CF992496.1|CF992496
EST:     AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCAGTTTATGCAAACATTCAGAAATTTATACAG
genomic: AGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
EST: gi|218500877|gb|FG965670.1|FG965670
EST:     CAATTTTGCATCGGTCGTGAGG                         GTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG
genomic: CAATTTTGCATCGGTCGTGAGGgtatgtacac ... tcgcttttagGTTGTCAGATGGGGTCGCTCGGTTTATGCAAACATTCAGAAATTTATACAG