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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATAAAGGAACACCAAAAAAATGGGTAAGAAAGGAAATTGGTTCAGTGCTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaaacttatctgcttcctcaataaatcgctatacttgtcataaaaattctccttgcttcaatatatatcttttgattaccatgaag

Basic information

species Oryza sativa
transcript LOC_Os01g61720.10
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g61720.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155954_T04 (Zea mays), 5'ss of exon 2
ACAATAAAGGAACACCAAAAAAATGGGTAAGAAAGGAAATTGGTTCAGTGCTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaaacttatctgcttcctcaataaatcgctatacttgtcataaaaattctccttgcttcaatatatatcttttgattaccatgaag
   |    | |  ||| ||| ||||||||||| |||||| ||||| ||||| || ||||||||||||||||| |||||||||||||| | |||||| |||||| | | ||| |  |     | | ||| |||              | ||||| ||  |||| |   || |   |  | |||   ||  ||||
TTGAAGGCGCAGAACCCAAAGAATGGGTAAGAGAGGAAAGTGGTTTAGTGCGGTGAAGAAAGTCTTCAGCTCCTCCGATCCAGATGGAAAGGAAGCCAAGgtacgtcgaaattcct---tattcacaacaaa--------------aaaaaaagtccacttggtgacatgtggctactatgaaggcccagaag

upper sequence: LOC_Os01g61720.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155954_T05 (Zea mays), 5'ss of exon 2
ACAATAAAGGAACACCAAAAAAATGGGTAAGAAAGGAAATTGGTTCAGTGCTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaaacttatctgcttcctcaataaatcgctatacttgtcataaaaattctccttgcttcaatatatatcttttgattaccatgaag
   |    | |  ||| ||| ||||||||||| |||||| ||||| ||||| || ||||||||||||||||| |||||||||||||| | |||||| |||||| | | ||| |  |     | | ||| |||              | ||||| ||  ||||          |  | | ||  ||| ||||||
TTGAAGGCGCAGAACCCAAAGAATGGGTAAGAGAGGAAAGTGGTTTAGTGCGGTGAAGAAAGTCTTCAGCTCCTCCGATCCAGATGGAAAGGAAGCCAAGgtacgtcgaaattcct---tattcacaacaaa--------------aaaaaaagtccacttg---------gtgacatgtggctactatgaag
















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|29633865|gb|CB638874.1|CB638874
EST:     CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|88398384|gb|CI595785.1|CI595785
EST:     CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58692460|gb|CK081147.1|CK081147
EST:     CTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58667874|gb|CK056560.1|CK056560
EST:     CTGTCAAGAAAGTCTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58683061|gb|CK071748.1|CK071748
EST:     CTGTCAAGAAAGTCTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|88360261|gb|CI611980.1|CI611980
EST:     CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|29638610|gb|CB643619.1|CB643619
EST:     CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58683289|gb|CK071976.1|CK071976
EST:     CTGTCAAGAAAGTCTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58670378|gb|CK059064.1|CK059064
EST:     GGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGTGAAATGGCCATTTGGAAA
genomic: GGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAG-GAAATGGCCATTTGGAAA
EST: gi|58660985|gb|CK049665.1|CK049665
EST:     GAAAGTCTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGGAATGGCCATTTGGAAAG
genomic: GAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
EST: gi|58683800|gb|CK072487.1|CK072487
EST:     CTGTCAAGAAAGTCTTCAGCTCATCTGATCCAGATGGGAGGGAAGCTAAG                         ATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG
genomic: CTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaa ... taccatgaagATCGAGAAGGCGGACAAGTCGAGATCCAGGAGGAAATGGCCATTTGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAATAAAGGAACACCAAAAAAATGGGTAAGAAAGGAAATTGGTTCAGTGCTGTCAAGAAAGTCTTCAGCTCATCCGATCCAGATGGGAGGGAAGCTAAGgtatgccaaaacttatctgcttcctcaataaatcgctatacttgtcataaaaattctccttgcttcaatatatatcttttgattaccatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG