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

ACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaacctaattaatcacccaaatagttgttgattctgctcatcattttcacctttctttcacctgtgttcgtagcagtacaattcttttttttag...

Basic information

species Oryza sativa
transcript LOC_Os04g53540.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53540.3 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ34024 (Selaginella moellendorffii), 5'ss of exon 2
ACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaacctaattaatcacccaaatagttgttgattctgctcatcattttcacctttctttcacctgtgttcgtagcagtacaattcttttttttag
 || || || |||||||||||| ||||||||||||||||||| || ||||||||||  ||||| |||||||||||||||||    ||||| ||  | |||||   | |        || |  |||||   || |   |   | |  | || |  |  | |   |   ||||                             
TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtaggatag-------aagc-tccaaaagcttttctttggcgtttctgatgtaaagatcttccttgtctgtccag-------------------------

upper sequence: LOC_Os04g53540.3 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ10492 (Selaginella moellendorffii), 5'ss of exon 3
ACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaacctaattaatcacccaaatagttgttgattctgctcatcattttcacctttctttcacctgtgttcgtagcagtacaattcttttttttag
 || || ||||| ||||||||  ||||||| ||||||||||||||  ||||||| |  ||||| ||||| |||||||||||     | |||||  | |||||      |                | |  ||| || || | || ||| |||   | || | ||   | ||   |  ||                     
GCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAATCGAAGGACCCAGCTCAAGgtaggggga---------------gagttcttgctggtttt-cttatcgttt---ctttgccttgttccgtcgcc-cag---------------------

upper sequence: LOC_Os04g53540.3 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ37532 (Selaginella moellendorffii), 5'ss of exon 2
ACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaacctaattaatcacccaaatagttgttgattctgctcatcattttcacctttctttcacctgtgttcgtagcagtacaattcttttttttag
 || || || |||||||||||| ||||||||||||||||||| || ||||||||||  ||||| |||||||||||||||||    ||||| ||  | |||||   | |        || |  |||||   || |   |   | |  | |  |  |  | |   |  |||||                             
TCATCCCGACGATAAGCAGCGCCAGGAGCTGAGCCGGGAGCTAGGACTGGAGCCTCGGCAAGTCAAGTTCTGGTTCCAGAATCGCCGCACGCAGCTCAAGgtaggatag-------aagc-tccaaaagcttttctttggcgtttctgacgtaaagatcttccttgcctgtccag-------------------------

upper sequence: LOC_Os04g53540.3 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ19972 (Selaginella moellendorffii), 5'ss of exon 3
ACACCCAGATGATAAGCAGCGCAAGGAGCTGAGCCGGGAGCTCGGCCTGGAGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaacctaattaatcacccaaatagttgttgattctgctcatcattttcacctttctttcacctgtgttcgtagcagtacaattcttttttttag
 || || ||||| ||||||||  ||||||| ||||||||||||||  ||||||| |  ||||| ||||| |||||||||||     | |||||  | |||||   |  |                | |  ||| || || | || |||||||     |  |||   ||   |  |                         
GCATCCGGATGACAAGCAGCGGCAGGAGCTCAGCCGGGAGCTCGGATTGGAGCCGCGGCAAGTCAAGTTTTGGTTCCAGAATCGAAGGACCCAGCTCAAGgtaggagga---------------gagttcttgctggtttt-cttatcatttct--ttgccttgttccatcgcccag-----------------------

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|58670786|gb|CK059472.1|CK059472
EST:     AGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAG                         AACCAGCATGAGAGGCACGAGAACTCGCAGCTGCGGTCGGATAACGAGAAG
genomic: AGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaac ... gagagtgcagAACCAGCATGAGAGGCACGAGAACTCGCAGCTGCGGTCGGATAACGAGAAG
EST: gi|58671274|gb|CK059960.1|CK059960
EST:     AGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAG                         AACCAGCATGAGAGGCACGAGAACTCGCAGCTGCGGTCGGATAACGAGAAG
genomic: AGCCTCTCCAAGTGAAGTTCTGGTTCCAGAACAAGCGCACCCAAATGAAGgtgaaaaaac ... gagagtgcagAACCAGCATGAGAGGCACGAGAACTCGCAGCTGCGGTCGGATAACGAGAAG