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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttctcgcatgattctgacttcctgctttaaatatgactagcacaaccatttgatgacaaattccttcatggaaatttag

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G146472_T02 (Zea mays), 5'ss of exon 7
GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttctcgcatgattctgacttcctgctttaaatatgactagcacaaccatttgatgacaaattccttcatggaa-atttag
 |||||||||||||||||||||||||| |||| ||| |||||||||||||| || ||||||    |||||   ||||  |  ||||||        | ||   || |  | |   | |  || | |   ||||| |   ||||||
ATACCAGCCACCTATCCCAGCTGAAGAGGTGAAACCTGCTTTTGACTATGATCATGAAGgtgacattctcagttgatcttctcttcctaac---gctgtggtcaggatcatcgcataaccaccattatgttcattgtttatttag

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G050982_T01 (Zea mays), 5'ss of exon 6
GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttctcgcatgattctgacttcctgctttaaatatgactagcacaaccatttgatgacaaattccttcatggaaatttag
 ||||| ||||||||||||||||||||||||| ||| |||||||||||||| || ||||||| | |||||   ||||  |  || |||| |     | |   ||| |  |     | |  || | ||  ||||||   ||||||
ATACCAACCACCTATCCCAGCTGAAGAAGTGAAACCTGCTTTTGACTATGACCATGAAGgtaatattctcagttgatcttctctacctgat---gctgtagttaggatcattggataacaaccattttgttcatgattatttag
















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|38474629|gb|CF958762.1|CF958762
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCGCTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCGCTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|66916064|gb|CX102912.1|CX102912
EST:     ACCCATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCGCTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|29677610|gb|CB673885.1|CB673885
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|86897912|gb|CI289086.1|CI289086
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAG
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAG
EST: gi|38474027|gb|CF958159.1|CF958159
EST:     ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATAAACACGAAG                         AATCTTTCCCCGCTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: ACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
EST: gi|8527776|gb|AU092591.1|AU092591
EST:     CCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAG                         AATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA
genomic: CCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttct ... ggaaatttagAATCTTTCCCCACTAATCGTGGAAGAGGCCGTGGTGGTGGCAGAAGAGGCA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCAGCCACCTATCCCAGCTGAAGAAGTGAGACCCGCTTTTGACTATGAACACGAAGgtattgttctcgcatgattctgacttcctgctttaaatatgactagcacaaccatttgatgacaaattccttcatggaaatttag

- - - - - - - -  CAGCTG
- - - - - - - - - AGCTGA
- - - - - - - - - - CTGAAG
- - - - - - - - - -  TGAAGA
- - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - AGAAGT