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

AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaactgatgagtgcacgtgcaaaagatcatttgtgatgaaaggtcgtggttg...

Basic information

species Oryza sativa
transcript LOC_Os04g41100.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G179097_T01 (Zea mays), 5'ss of exon 9
AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
  ||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
--AAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G179097_T02 (Zea mays), 5'ss of exon 8
----------------------------AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
                            ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | || |  
TCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGGTAA-Tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-catgatat

upper sequence: LOC_Os04g41100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G179097_T03 (Zea mays), 5'ss of exon 7
---------------------------------AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgactaaaa-ctgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
                                 ||||||| ||||||||||||||||||||||| || |||||||||||||| || |||||||||||  ||||||| | |||  |||| ||| || |  |||||||||| ||||| ||||||| ||  ||||||   | |          ||||||||  ||  | |||| | | |     
TTTGATCTTTGCGTTTTGTTTGCAAGAGACAAAAGAAGCGCAGGGGAAGGATGCCTTTTGCTTT-CATCAGGAAATCAATGG-CATTAATACAACTTAGAAGgtaa-tgtatg-aaaagccaattgctgcaagtgatgtgttgctaactaaaaactagtgagtgtgggagttcttcactgaaagatcagctgc-acgaaatg-cat-----

upper sequence: LOC_Os04g41100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G139038_T01 (Zea mays), 5'ss of exon 8
---------------------------------AGAAGCGAAGGGGAAGGATGCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatattcaaaaaccatttacctcaagtgatgtattgctgacta-aaactgatgagtgcacgtgc--------aaaagatcatttgtgatgaaaggtcgtggttg
                                 ||||||| |||||||||| ||||||||||||| | ||||||||||||| ||| |||||||||||  ||||||| ||||| ||||| ||| || |  ||||||| || ||||| |||| ||||| ||||  |   | |          ||| ||||  ||     || ||         
TTTGATCTTTGCATTTTGTTTGCAAGAGACGAAAGAAGCGCAGGGGAAGGAAGCCTTTTGCTTTT-ATCAGGAAATCAATG-ACATTAATACAACTTAGAAGgtaa-tatat-caaaagccaattgctgcaagtgacgtgttgctaactagaaactaatgaacgagggagttctttactgaaaaatcaggtgcatgaaatggat-------

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|29623101|gb|CB628112.1|CB628112
EST:     GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAG                         CTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGG
genomic: GCCTTTTGCTTTTCACCAGGAAATCAATGGACAGTAATACAACTTGAAAGgtaaatatat ... ctcactacagCTGTTGTCTGTGACACGTCTGCAGCTTAAGCTGTGGCTGCTTCAAGATAGG