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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatcttatctaatacaagcgaacagttggtttctgaatctcgtgtgacagtttgaacttttccatatgcctatagtatggtctattgaatatcttt...

Basic information

species Oryza sativa
transcript LOC_Os03g20420.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G30150.1 (Glycine max), 5'ss of exon 4
------CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatcttatctaatacaagcgaacagttggtttctgaa-tctcgtgtgacagtttgaacttttccatatgcctatagtatggtctattgaatatcttt
         | | ||| | || ||| |  | || |||      |  | | ||||| |||||||  | || |||||||||||||  |||||||||| ||||||||||||  |   | ||||    |||  |     |   ||| | || | |  | ||| ||    || | ||   | ||    |  | |  | | |  |||      
GCGAAATAAAGTCGCATTGCGTATGAACATTCTTTGT------AATGAATCTAATCCTTGCCCAGCTGGTGGTGTTGGTATCTCAAATCCTGGTTTCTGGGGCATGgtgag---taatct----caaatgttttttctttttataaaattttatttga-agagcaaaatattatttctgatcgtt-tctaatttttgtaatcag---

upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G00630.1 (Glycine max), 5'ss of exon 3
------CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatcttatctaatacaagcgaacagttggtttctgaatctcgtgtgacagtttgaacttttccatatgcctatagtatggtctattgaatatcttt
         | ||||| |  | ||| |||| || |||      |  | | ||||| ||||||| || || |||||||| ||||  |||||||||||||||||||||||| |        ||||   ||  | || |    || | ||| |    | |      ||| | ||   | ||   ||       | |  | || |     
GCGAAATAAAGTTGCATTAAGTATGAAAGTTCTTTGT------AATGAATCTAATCCTTGCCCATCGGGTGGTGTTGGCATCTCAAATCCTGGTTACTGGGGCATGgtaagtataatagtaatcttagtta-caatc---ttttaaatttttaataatgagc-gaaatattatttctgatcatttctaattttcgtaaacag----

upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G30450.1 (Glycine max), 5'ss of exon 4
CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatcttatctaatacaagcgaa-cagttggtttctgaatctcgtgtgacagtttgaacttttccatatgcctatagtatggtctattgaatatcttt--
     ||||||||||  |||| |||   ||||        ||    ||    |||||  | |  ||||||||| | ||||||||||||| ||||||||||||  ||   ||  | ||||    | | || ||   |  | |||||  |||| ||  |    | |   || |     | |  |    ||    || ||  ||  
TAAGGTTGCACTTCGATTGGAGGTATCATGTGACAGCGAAGGTGACAACATCTGCCCAGCTGATGGTGTTGGTGTTTATAATCCTGGTTTCTGGGGCATGgtgagac--taattgatacccttgcatcaattatatcataaatcttatgtg-catatatttcctgaacaaaaaaaaagacaaaaaactgaataacataattta

upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G27460.3 (Glycine max), 5'ss of exon 4
CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatcttatctaatacaagcgaa-cagttggtttctgaatctcgtgtg-acagtttgaacttttccatatgcctatagtatggtctattgaatatcttt-
|    ||||||| ||  |||| ||  | ||||     |  ||    ||    |||||  | |  ||||||||| ||||||| ||||||| ||||||||||||  ||   ||  | ||||    |   || ||   |  | ||||   |||| | || ||   ||   | | |     | |  |    ||  |||| | | |  
CAAGGTTGCACTCCGATTGGAGGTGTTATGTGACAGCAAAGGTGACAACATCTGCCCCGCTGATGGTGTTGGTGTCTATAACCCTGGTTTCTGGGGCATGgtgagac--taattgataccgttgcctcaattacatcataaatcctatgtgcatagatttc-ctgaacaagaaaaaaagacaaaaacctgatgaaaaacataa

upper sequence: LOC_Os03g20420.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA19G30460.1 (Glycine max), 5'ss of exon 3
---------CCCAATTGCACTTCGCATGGAAGTACTCTGTGGAGCTACCGGAACTAATGCTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatg--atcttatctaatacaagcgaacagttggtttctgaatctcgtgtgacagtttgaacttttccatatgcctatagtatggtctattgaatatcttt
            |  |||| | |  ||||| ||    ||||| |||  |  |       ||||||| |     ||||||||||||| ||| |||||||| |||||||||||| |  |  | || ||     |                || || |  | |  |    |    |||    |||   | | || |    | |  || |  |  
TGAGCGCAATAAAGCTGCATTGCAAATGGAGGTGTATTGTGGTGCTCACAAAC------CTTGCCCAT---ATGGTGTTGGTATCTCTAACCCTGGTTATTGGGGCATGgtaaggaaattaatatatcttgaaattcacacacacacatggattttttctttcttcatattttttcttgtattattgttgtgtatgttttaaaaaaaat--

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|29622779|gb|CB627790.1|CB627790
EST:     CTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATG                         AACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA
genomic: CTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatctt ... tctgctgcagAACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA
EST: gi|29680537|gb|CB676812.1|CB676812
EST:     CTTGCCCTTCAAGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATG                         AACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA
genomic: CTTGCCCTTCAGGAGGTGTTGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatctt ... tctgctgcagAACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA
EST: gi|33658179|gb|CF280793.1|CF280793
EST:     TGGTATCTATAATCCTGGTTACTGGGGCATG                         AACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA
genomic: TGGTATCTATAATCCTGGTTACTGGGGCATGgtatgatctt ... tctgctgcagAACATTGAAAAAACAAAGGTCTACAAAGTTAGCATGTACATTAGGTCATCA