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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacacttcttcttttcttgtttttaatttgtagcatatcactcccctgaaataaaaacatactctgttgccatttatttgaaagcatatttaattct...

Basic information

species Oryza sativa
transcript LOC_Os11g33240.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 9
GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacacttcttcttttcttgtttttaatttgtagcatatcactcccctgaaataaaaacatactctgttgcc--atttatttgaaagcatatttaattct
  ||||| ||||||||||| ||||||||||| |||||||| ||||| ||||||||||||||||| || || ||||| ||||| || |   ||||  |||     |   || | |  | | | ||||   |  |||  |        | ||   | ||  |  |||||     |     ||  | |
CTCATGTCTATAAGGCAATAGATGCTCTCCCAGTAACTGCACATCCTATGACACAGTTTACCACGGGAGTAATGGCTCTTCAGgtgagtccttccacttcctaagagatttagtatttgaacatca--gctttgatgttttgctggagtcaaatacctaagatatttaggtcccatcctaggtgt

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G063909_T02 (Zea mays), 5'ss of exon 8
GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacacttcttctttt--cttgtttttaatttgtagcata--tcactcccctgaaataaaaacatactctgttgcca-tttatttgaaagcatatttaattct
              | ||| ||||||||||| |||||||| ||||| |||||||| |||||| ||||  | ||||| ||||| || | | ||||  ||| |  |    | |  |||   || |||  ||||     |||||||||  || | |   |||| | |||||||| |    | ||||   | 
--------------GTAATAGATGCTCTCCCAGTAACTGCACATCCTATGACACAATTTACCGCAGGAATAATGGCTCTTCAGgtgagcccttccacttctggcacactgtctattctaagtataaatcacagttgtgaaataaat-cacatttccttgcgaatttatttgca---ttttttagaac-

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G063851_T02 (Zea mays), 5'ss of exon 8
-----------------GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaa--acacttcttcttttcttgtttttaatttgtagcatatcactcccctgaaataaaaacatactctg-ttgccatttatttgaaagcatatttaattct--
                   ||||| |||||| |||| ||||||||||| |||  ||| ||||| |||||||||||||||||||| || ||||| ||||| || |  ||| ||||    | ||  ||| |||    ||  ||||||      ||||||||||    | | |  |||  ||||||||| |  | | ||  | |    
AATTAATATGGTTGCAGCTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacatttctgtcatgctcttttctaa---atataatatcataattgtgaaataaaatagcattttccttgtgatttatttgca--ctttttagaattgga

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 9
GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaa--acacttcttcttttcttgtttttaatttgtagcatatcactcccctgaaataaaaacatactctg-ttgccatttatttgaaagcatatttaattct--
  ||||| |||||| |||| ||||||||||| |||  ||| ||||| |||||||||||||||||||| || ||||| ||||| || |  ||| ||||    | ||  ||| |||    ||  ||||||      ||||||||||    | | |  |||  ||||||||| |  | | ||  | |    
CTCATGTCTATAAGACAATAGATGCTCTCCCAGTAGATGCACATCCTATGACACAGTTTACCACAGGAGTAATGGCTCTTCAGgtgattacatttctgtcatgctcttttctaa---atataatatcataattgtgaaataaaatagcattttccttgtgatttatttgca--ctttttagaattgga

upper sequence: LOC_Os11g33240.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 8
GCCATGTGTATAAGGCAATTGATGCTCTCCCTGTAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacacttcttctttt--cttgtttttaatttgtagcata--tcactcccctgaaataaaaacatactctgttgcca-tttatttgaaagcatatttaattct
  ||||| ||||||| ||| ||||||||||| |||||||| ||||| |||||||| |||||| ||||  | ||||| ||||| || | | ||||  ||| |  |    | |  |||   || |||  ||||     |||||||||  || | |   |||| | |||||||| |    | ||||   | 
CTCATGTCTATAAGGTAATAGATGCTCTCCCAGTAACTGCACATCCTATGACACAATTTACCGCAGGAATAATGGCTCTTCAGgtgagcccttccacttctggcacactgtctattctaagtataaatcacagttgtgaaataaat-cacatttccttgcgaatttatttgca---ttttttagaac-

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|38470398|gb|CF954529.1|CF954529
EST:     TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAA                         GTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
genomic: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacactt ... ttattttcagGTTGAGAGTGAGTTTCAAAAAGCTTACGACAAAGGAATGCCAAAATCAAA
EST: gi|86904765|gb|CI310558.1|CI310558
EST:     TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAA                         GTTGAGAGTGAGTTTCAAAAAGCT
genomic: TAACTGCTCATCCAATGACACAGTTTACCACAGGGGTGATGGCACTTCAAgtaaacactt ... ttattttcagGTTGAGAGTGAGTTTCAAAAAGCT