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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttaggaccagactatttatactgcagaagccatcccactatatgttgatgcatgttcctgacttgtcacgttgttatgaaaatgcctag

Basic information

species Oryza sativa
transcript LOC_Os10g32730.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G30970.1 (Glycine max), 5'ss of exon 9
GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttaggaccagactatttatactgcagaagccatcccactat-atgttgatgcatgttcctg---acttgtcacgttgttatgaaaatgcctag------------
||||||||||| || || || |||  |||||| || || || || || ||||| |||||||| |||||||||||||| |||||||||     | |   || ||||| |  |  | ||    || | || | ||  |  | |     ||     |||| ||| |||    | ||| ||   |             
GAACCATGGTTACTCCATGACTTTAATGAAGATTTCTATGGGGAAGAACTGCGGCTTGTTATAGTTGGTTACATACGTCCCGAGgtacagctgaat--gagtattttttttctataatttttctccctgtcatccttgtactgtcccccatatacttttcaagtttcactaaaattgggcattgtgcacaacag

upper sequence: LOC_Os10g32730.2 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA08G06330.1 (Glycine max), 5'ss of exon 4
GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttaggac---cagactatttatactgcagaagccatcccactatatgttgatgcatgttcctg-----acttgtcacgttgttatgaaaatgcctag------------
||||||||||| ||||| || ||    ||||| || || ||||| || ||||| |||||||| |||||||||||||| |||||||||   | | |     | | ||| |   || |        | |  ||     |   || |   ||||      |||| ||| |||    | ||| ||   |             
GAACCATGGTTACTTCATGACTTCAACGAAGATTTCTATGGAGAAGAACTGCGGCTTGTTATAGTTGGTTACATACGTCCCGAGgtatagttgaatgtgtatattatattcgcttctactatttttctcctcgtcatccttgtactgtccttcatatacttttcaagtttcactaaaattgggcattgtgcataacag

upper sequence: LOC_Os10g32730.2 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ19251 (Selaginella moellendorffii), 5'ss of exon 9
GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttaggaccagactatttatactgcagaagccatcccactatatgttgatgcatgttcctgacttgtcacgttgttatgaaaatgcctag
||||| |||||  | ||||| ||    ||||| ||||||||||||||||| || || ||| |||| || ||||| || ||||||||||   |   |    | ||||    | ||||| | ||     | | |||  |                                         
GAACCCTGGTTATTGCACGAATTCCCAGAAGATTTTTACGGAGAGGAGCTCCGGCTCGTTGTTGTCGGCTACATTCGGCCCGAGgtaaac-aatccttatccattt-cgtttcagaaacaatggttgtctctgtccag----------------------------------------

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|27576586|gb|CA999280.1|CA999280
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29623339|gb|CB628350.1|CB628350
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCTCTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|58613263|gb|CK040975.1|CK040975
EST:     TGTTATTGTGGGTAACATACGACCCGAG                         GCCAACTTTCCTTCTCTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|89172764|gb|CI022643.1|CI022643
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|33689645|gb|CF317884.1|CF317884
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCTTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|86488009|gb|CI130642.1|CI130642
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|109713021|gb|CI105629.1|CI105629
EST:     TTATTGTGGGTTACATACGACCCGAG                         GCCAACTGTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29613709|gb|CB618722.1|CB618722
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCTCTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29631921|gb|CB636930.1|CB636930
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|86500552|gb|CI143185.1|CI143185
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29658983|gb|CB655258.1|CB655258
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29679505|gb|CB675780.1|CB675780
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29671820|gb|CB668095.1|CB668095
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29684882|gb|CB681157.1|CB681157
EST:     TTTACGGAGAGGAACTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|88907995|gb|CI090591.1|CI090591
EST:     ATACGACCCGAG                         GCCAACTGTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: ATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|86861088|gb|CI326597.1|CI326597
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29625607|gb|CB630618.1|CB630618
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCTCTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|33680484|gb|CF308723.1|CF308723
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
EST: gi|29629325|gb|CB634336.1|CB634336
EST:     TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAG                         GCCAACTTTCCTTCTCTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA
genomic: TTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttagg ... aaatgcctagGCCAACTTTCCTTCACTTGAGAGCTTGATAGAGAGGATTCACGAGGATGCA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACCATGGTTGCTTCACGATTTTGGTGAAGACTTTTACGGAGAGGAGCTGCGCCTTGTTATTGTTGGTTACATACGACCCGAGgtaatttaggaccagactatttatactgcagaagccatcccactatatgttgatgcatgttcctgacttgtcacgttgttatgaaaatgcctag

- - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - AGCTGC