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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag

Basic information

species Oryza sativa
transcript LOC_Os05g11140.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G116151_T03 (Zea mays), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatat-attttag
||| || || |||||||||||||| || ||||| |||||||| |||||||| |||||||| |||||| | || |||||||||||||||||||||||||||||||| ||||||  ||      |  |||| |||  |  |  |               ||||| | |  |||      | || |||||||
TCATTTGGGGAGAACTGGAAGCAGGAGGGATGACCTTGAATCTCTTGCCTACACACTTGTATTTCTTCTGCGTGGTCGCCTTCCTTGGCAAGGATACCAGgtgaactttgtt-acaacctccaaattttcttaattactgatccc-----------cccttactcaaattttcagcaaaatgattttag

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 ||  | || ||||| || ||||| ||||||||  | ||||| ||||| || || ||||| |||||| | || ||||| || |||||||||||||||||||| |   ||  ||  | |   | || ||||    ||  | ||     ||  | |  | ||||      ||| ||||            
CCATCTTGGTAGAACAGGTAGCAGGAGAGATGACTTGGAATCTCTTGCTTACACTCTTGTCTTTCTTCTTCGTGGTCGGCTACCTTGGCAAGGATACCAGgttattattccttcaaat---agtcattttagtactaatggtaaatgaaaatatgattcttatgattttttttgttacag--------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G21570.1 (Glycine max), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 || ||||| ||||||| |||||| || |||||  | ||||| ||||| ||||||||  |||||||| | || ||||||||||| ||||| || | ||||||            || |   |    | ||||||   | ||||  | |   |  | ||     |||  ||| |               
ACATTTAGGGAGAACTGCAAGCAGGAGGGATGACTTGGAATCTCTTGCATATACACTGATTTTTCTTCTTCGAGGTCGCCTTCCATGGCAGGGGTTCCAGgttgga--------cattaaaataactcttttattcttacgttcagaaggttggtctctaacattatttttttag-------------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA07G01890.1 (Glycine max), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 || ||||| ||||||| |||||| || |||||  | ||||| ||||| ||||||||  |||||||| | || ||||||||||||||||| || | ||||||      | ||   |    || |    |||||| | ||   ||   ||   || |||  ||   |   || | |             
ACATTTAGGGAGAACTGCAAGCAGGAGGGATGACTTGGAATCTCTTGCATATACACTGATTTTTCTTCTTCGAGGTCGCCTTCCTTGGCAGGGTTTCCAGgttggacatatt---aaaatgattgaagttttat-tattatgttcagaattgttggtctctaac-attattttctcag----------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaa--gtttgtttgc--agtgcgaatctttttttatctgttcgttttgcaaccttttgtcct--tagttacctttgtgttgatatattttag
|||| | ||||| ||||||||||||||||||||| | ||||| ||||| || || ||  |||||||| | || || || || ||||||||||| ||||||||  |  ||||     |  |    | || || |||||| || |   | | || | || ||  |    || | | || |                
TCACCTTGGAAGGACTGGAAGCAGAAGAGATGATTTGGAATCTCTTGCTTACACCCTCATTTTTCTTCTCCGTGGACGGCTGCCTTGGCAAGGTTACCAGgttgacagtttccaaacttaaataggattttcttttatgtgatt-ctgtacatcattctgaaccaacagcttctttag----------------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ13521 (Selaginella moellendorffii), 5'ss of exon 9
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 ||| | || ||||| || || ||||| || ||||| ||||| |||||||| || ||  | ||  |  |||||||||| |||||||||||||| |||||||| |      || |   |   |     || ||  |||    |   ||  | |    |    ||                         
GCACCTGGGTAGAACCGGTAGTAGAAGGGACGATCTGGAATCTCTTGCCTACACGCTGATATTCTTACTACGGGGTCGTCTTCCTTGGCAAGGTTACCAGgttagaggctttggttttaaaa-----ttattgcctgcagctaaggctgcttgggttgtgcag-------------------------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ38433 (Selaginella moellendorffii), 5'ss of exon 7
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttt--tttatctgttcg-ttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 || || ||  | ||||| || ||| |||||||||| ||||| ||||  || || || || |||||  | || ||||| ||||||||||||||||||||||| | | |  |||    |   | | || |  ||||  ||  || ||||  |                                        
ACATTTGGGTCGTACTGGCAGTAGACGAGATGATCTGGAATCTCTTGGATACACGCTGGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgttttaatatattagttttatgttttacatgggcgcttttatag---------------------------------------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ19085 (Selaginella moellendorffii), 5'ss of exon 7
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 ||| | || ||||| || || ||||| || ||||| ||||| |||||||| || ||  | ||  |  |||||||||| |||||||||||||| |||||||| |      || |   |   |     || ||  |||    |   ||  | | |||| |                             
GCACCTGGGTAGAACCGGTAGTAGAAGGGACGATCTGGAATCTCTTGCCTACACGCTGATATTCTTACTACGGGGTCGTCTTCCTTGGCAAGGTTACCAGgttagaggctttggttttaaaa-----ttattgcctgcagctaaggctgcttgttgtgcag---------------------------

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ31718 (Selaginella moellendorffii), 5'ss of exon 7
TCACTTAGGAAGAACTGGAAGCAGAAGAGATGATCTTGAATCCCTTGCCTATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttgtttgcagtgcgaatctttttttatctgttcgttttgcaaccttttgtccttagttacctttgtgttgatatattttag
 || || ||  | ||||| || ||| |||||||||| ||||| ||||  || || || || |||||  | || ||||| ||||||||||||||||||||||| | | |  |||         || ||  |||   ||||     ||    ||||| |                               
ACATTTGGGTCGCACTGGCAGTAGACGAGATGATCTGGAATCGCTTGGATACACGCTAGTGTTTCTCCTTCGTGGTCGGCTTCCTTGGCAAGGATACCAGgtcaggctgtttta------atattttagttttattgttttacatgggcgcttttatag-----------------------------

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|29681938|gb|CB678213.1|CB678213
EST:     ATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAG                         GGAGAGAATAAAGGTTTCCTTGTTTGCAAG
genomic: ATACACTTGTTTTTCTTTTACGGGGTCGCCTTCCTTGGCAAGGATACCAGgtgaagtttg ... tatattttagGGAGAGAATAAAGGTTTCCTTGTTTGCAAG