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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g12670.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G058366_T01 (Zea mays), 3'ss of exon 7
--tttagta-cattgtgctctcgattg--tagtgctttaccatgtgaaa-cgaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG----
   | |||| || ||| |||   || |  ||||||  |    ||| ||| |||||   || ||  ||| ||     ||| |  | || |||  ||| |||  ||||||| |||||||||||||||||||  |||||||||||||||||||| || |||||||| ||||| ||||||| ||| |    || | ||      ||   |    
acctaagtatcagtgt-ctcaaaatggattagtgcagtggtgtgttaaagcgaatctcatataatattttc---cctaata--gtaagtgttgcacttgctcgcagCCGTATACCTGGGCACTGGGTTCCACCACCCCCTCCAGCTGATGAGGTTTGGGCATCTTATTTGGTGCAGCACAAGT----AAATCACCATGGGTATGAGAAAT

upper sequence: LOC_Os01g12670.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G05400.1 (Glycine max), 3'ss of exon 7
-tttagtacattgtgctctcgattgtagtgctttaccatgtgaaacgaattcta-tgtagcattct--cttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAA-GTAACTCCACTTAGCTG
    | |  ||||   | || | |||     ||||  | |||  |  |||   | |  |||||| |  ||||||| |   ||   |  |  || || | | |||||| ||||| ||||| ||||||||||| || ||||||||| ||||  |||||||||| || || |||   || || ||   |   | | |  ||  | |  
tgcaactgtattggtttttctaatgt---cttttatgaagtgtgaaaaatgaaaataaagcattttatcttatttgattttgtt-tccttgcaacttcatccagCCGCATACCAGGGCATTGGGTTCAGCCTCCTCCTCCAGCTAATGAGATATGGGCATCTTACTTGGTGAGACCTAAATGATTATTATTAGTTAACAAATCA-
















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|218496734|gb|FG958313.1|FG958313
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|29678140|gb|CB674415.1|CB674415
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
EST: gi|33793232|gb|CF322496.1|CF322496
EST:     GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAG                         CCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG
genomic: GTCCGCAGGATGTGGGATTCCTTTATTAGAGCTGGAGGAAGgtatgacttt ... ctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattctatgtagcattctcttatttaacaatgcaattgtctcacctgcctgcagCCGAATACCTGGGCACTGGGTTCAGCCACCCCCTCCAGCTGATGAAGTATGGGCATCCTATTTAGTGCAGCCCAACTGTCCAAGTAACTCCACTTAGCTG
                                      gtctcac  putative branch site (score: 3)
                                       tctcacct  CT-rich tract
              attctcttatttaa  TA-rich tract