Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtcacctgttttgccctgtttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta...

Basic information

species Oryza sativa
transcript LOC_Os11g40510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 3
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtcacctgttttgccctg--tttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta
||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || |       | || | |||   |||| ||| ||| |||    || |      |  ||  |||      || ||   | | || |   |   | 
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttccaaatt-cttctttaagaacatctccataaaatatggcttttct-

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 2
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtcacctgttttgccctg--tttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta
||||||||||| || ||||| |||||||||||||| |||||||||||||||||||| || |||||||| || |       | || | |||   |||| ||| ||| |||    || |  |   |   |  |||      || |    | | || |   |     
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttctaaattcttcttttaagaacatctacataaaatatggcttttc--

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtc---acctgttttgccctgtttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta
|| || || |||   ||||| || ||||||||||| |||||| ||||||| ||||| ||||||| ||| ||||||   || | ||||   |  ||||  || |    | | |   | | || | |   |    || || |  ||     ||   |    |||   
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctatttta-tctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg--

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 5'ss of exon 2
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtcacctgttttgccctgttt--atgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta
|||||||| ||  | ||||| || ||||||||||| |||||||||||||||||||| ||||||| ||| |     |    ||||   || |||  || |     |    || |   |  | || | || ||||  |  |  |||    | ||    || | || 
ATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtcatatagacattttcttcttttttgattcttttcgtgtgttttggtttcttttgctcttattttatgtttattc-tttcgtttgtcaacactt-

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 2
ATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtatttgtca------cctgttttgccctgtttatgcccaaggaactttgttactgttgtttcactgatttggttctatttcgcaacattacgaaatagtta
|||||||| ||    ||||| || ||||||||||| |||||||||||||||||||| ||||||| ||| ||||||         | ||||    ||||| |      | |  |||||| ||  |  | ||   |  | |            |  || |  ||      
ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgtttgtctggacatttttttttcttttgttttttttgttgcatgtttgttgcttctcatgcatgcaactagaagagcacttttatttttcttaa------

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|58690866|gb|CK079553.1|CK079553
EST:     TGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT
genomic: TGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtattt ... ttctgaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT
EST: gi|25797088|gb|CA753049.1|CA753049
EST:     GGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT
genomic: GGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtattt ... ttctgaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT
EST: gi|58666336|gb|CK055022.1|CK055022
EST:     GTTAGTGGCAACCTGCCTCCTGGATTGGATTCAAGTACATGCCGGAGTGT                         GTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT
genomic: GTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGTgtaagtattt ... ttctgaatagGTATGTTGGCAATATCCATCTTCAAGTGACGGATTCACTGCTACATGAGGT