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

AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g36070.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G104449_T03 (Zea mays), 5'ss of exon 9
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggc--atactacctcg-atacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatag-atttcgtggtact-gctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag
|||||||||||||||||| |||||||| || |||||||||||| | ||||||||||| |||||||||||||| |||||||| ||||| || ||||| ||||| ||||||   ||  |  | | | | ||  ||   | | || | || | |   ||||   ||||   |    ||| ||   |  |  | | |  ||  || |   | ||  |   |   |  ||||      || ||||| |        | || || ||||||   | || | ||||
AATAGCTAATATGGATATCAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATGTCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAAAAGgttagtggctggtaacattttgcacatttcagttcagctgtgttctctaca---atagttttttttggaccatagtgtgtggtggaggtggtaaatcagggcatcagataaatactgcatgataattgatgagcatgagattc--------agcattt-ctattggaatgtcat-gcag

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G135314_T01 (Zea mays), 5'ss of exon 2
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttg----ctattgacttatctttgcag
| ||||||||||||||||||||||||| || |||||||||||| | |||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||| ||||||     |  |    || |||  | |   |||    |||||    |    ||| | |||| |  || ||||       || ||   |   | | | ||  | | |   ||  |||      || |||  |  ||  || |||||       ||| |||   || | |||||
AGTAGCTAATATGGATATTAAGCTAGATTTTGTTCCACCATGGTTGATCAACTTCATATCAAGGCAACTAATAGGCAGCGGGCATAAGCTGTATCAAAAGgttagtggctggtaatgttttcacatttcagctatattgtctacaata---gttttccttgtaccatagt-gtgtggtggggtggtaaatcagggcat-cagataaatcgtgcatgctgattaatgagcatgag--cttctaattgaacaccaataacctactgaagcatttctgcag

upper sequence: LOC_Os11g36070.1 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ31074 (Selaginella moellendorffii), 5'ss of exon 8
AATAGCTAATATGGATATTAAGCTAGACTTCGTTCCACCATGGCTTATCAACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggcatactacctcgatacttttgtgatgatttgatatcaatatgcatagcgcttttcccattgcagtatggtctttacatagatttcgtggtactgctatgtggggtgagcaaattctgacacaagagatcccctgtttaaacacttgctattgacttatctttgcag
  | |  ||||||||||| ||||| ||||| |||||||| ||| | |||||||||||  || |||| ||  ||||||| ||| | ||||| ||||| |||||      |    | |||  | |  |||||| |  | | |    |  |  ||  |   | ||||||                                                                                                            
GTTGGTCAATATGGATATAAAGCTCGACTTTGTTCCACCTTGGGTGATCAACTTCATCACACGGCAGCTCGTTGGCAGTGGCTACAAACTTTATCAAAAGgt-----acgcgttgcct--acaagtttgtgcttttctaa----accactcagcggtttgttcccag-----------------------------------------------------------------------------------------------------------

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|58606537|gb|CK034570.1|CK034570
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88273561|gb|CI393967.1|CI393967
EST:     ACTTCATATCAAGGCAACTAATTTGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|29688057|gb|CB684332.1|CB684332
EST:     ATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27576960|gb|CA999654.1|CA999654
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|88581594|gb|CI698792.1|CI698792
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|27578183|gb|CB000878.1|CB000878
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTACTGTGGCAAATTGTGATGAGGATTACAAGAAAGCTTTGAGA
EST: gi|25778077|gb|CA752829.1|CA752829
EST:     ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTGTATCAGAAG                         GCAGTCAGTAC
genomic: ACTTCATATCAAGGCAACTAATTGGCAGCGGCCATAAACTCTATCAGAAGgtcagtggca ... atctttgcagGCAGTCAGTAC