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

gtgcccaatttgccccccatccctagggaatttatccaatttgctgaccaaattttatacgtgatcaaattcattcctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT

Basic information

species Oryza sativa
transcript LOC_Os08g08820.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 9
gtgcccaatttgccccccatccctagggaatttatccaatt--tgctgaccaaattttatacgtgatcaaattcattcctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT
|| |  |   |||    ||| | |     ||    |  |     |||  |    | |    |     | |   || | |   |  ||    ||    |||||||||||| || |||||||| ||||| ||||||||||||||||| ||||| |||||||| |||||||||||||  ||||| |||||||||||||||
gtacgta-cgtgcgtgtcatgcatgtccgatcctacgtaccaacgctctctctctctacctctctcccgatgacactgcatgcatgtcaatataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT

upper sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 8
gtgcccaatttgccccccatccctagggaatttatccaatttgctgaccaaattttatacgtgatcaaattcatt--cctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT
||   |  |||    || ||    |       |   | |   |   | |   | |  | || | |   |   |||  ||||||||  ||  | | | |||||||||||| || || ||||| || || |||||||||||||||||||||||||||||||| ||||||||||||| |||||| || ||||||||||||
gtagtcggtttcaaaccgatgatgatactgcgttctccaaacgtcaatcgtttgtgcttcgagctacgacctattttcctgacgaaatttaaat-ctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCCAACGGCCGGGACCATGGCAACTGTGTCTCCCTCCTTCGTGTCAAT
















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|29615070|gb|CB620083.1|CB620083
EST:     CTCCCGCCGCCGTCTTCGACTTCCTCCGTGACGAGACCTCTCGCAGCGAG                         TGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
genomic: CTCCCGCCGCCGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtgcccaatt ... atttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
EST: gi|88689663|gb|CI733239.1|CI733239
EST:     CTCCCGCCGCCGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
genomic: CTCCCGCCGCCGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtgcccaatt ... atttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
EST: gi|4716207|gb|AU057323.1|AU057323
EST:     CGACGAGACCNCTCGCAGCGAG                         TNGGACATTCTGTCCAACGGCGGCG-CGTCCAAGAAATGGCTCACATTGCC
genomic: CGACGAGACCTCTCGCAGCGAGgtgcccaatt ... atttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
EST: gi|29615392|gb|CB620404.1|CB620404
EST:     CTCCCGCCGCCGTCTTCGACTTCCTCCGTGACGAGACCTCTCGCAGCGAG                         TGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC
genomic: CTCCCGCCGCCGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtgcccaatt ... atttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaccaaattttatacgtgatcaaattcattcctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT
                              tcctgac  putative branch site (score: 2)
                                              tttccgc  putative PPT
     aaattttata  TA-rich tract