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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgctagtactgtacctgatgataaaggtttttgcgagcacacttcaaattgttgtcacatttgatatttgcttcctttaccatagtttctctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACA

Basic information

species Oryza sativa
transcript LOC_Os01g67220.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 11
acgctag-tactgtacctgatgataaaggtttttgcgagcacacttcaaattgttgtcacatttgatatttgcttcctttaccatagtttctct-catgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACA
  | ||| |  |    |   ||  |   | | || |   | || |   |||       | |          |     | |    |   ||   | |||| |||||||||||| || || |||||||| |||||||||||||| ||| | || || ||||||||||| |||||||||||||| ||||||   |||||||| ||
-tgatagcttttactgccattggcatgcgctgtttctgaccca-tctgaataaaaaaaagacagagcgcgcgtggattatgatgtttctttcgtgcatgcagGCATGGATGAAGAGGACGATCAATCCGCAACGCTTGACCAGGTCCTAAACGACACGACGAGGGTCGGTTACTTCAAAGGGTACCTCAATTCAGTTGCGCA

upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 11
lower sequence: AC155376.2_FGT005 (Zea mays), 3'ss of exon 11
--acgctagtactgtacctgatgataaaggtttttgcgagcacacttcaaattgttgtcacatttgatatttgcttcctttaccatagtttctctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACA
     |   || ||||  |||  | |||   || | | |  |      | | |||       | ||  || || |  | ||||| |||||||| |  || |||||||||||| ||||| ||||| || || ||| ||||||| ||| | || || |||| ||| || || ||||||||||||||||||   || ||||||||
ttctacagatattgtag-tgactaaaaactcttatacaacgaatagaaatagtgtgtgtgtgtgtggaatgtgatgtccttacc-tagtttctttgctgcagGCATGGATGATGAAGACGATCAGTCCGCGACGATTGACCAGGTCCTAAACGACACGAAGAGAGTCGGCTACTTCAAAGGATACCTCAATTCGGTTGCACA
















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|88844089|gb|CI001146.1|CI001146
EST:     TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATG                         GCATGGATGAGGAAGATGATCAATCGCCAACGCTTGACCAAGTCTTGAATG
genomic: TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATGgtaaggtttc ... tctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
EST: gi|3761659|gb|C98907.1|C98907
EST:     GGAAATCCTGTGATATATGTAACTGAGAATG                         GCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
genomic: GGAAATCCTGTGATATATGTAACTGAGAATGgtaaggtttc ... tctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
EST: gi|58672934|gb|CK061620.1|CK061620
EST:     TGGAAATCCTGTGATATATGTAACTGAGAATG                         GCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
genomic: TGGAAATCCTGTGATATATGTAACTGAGAATGgtaaggtttc ... tctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
EST: gi|29625132|gb|CB630143.1|CB630143
EST:     TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATG                         GCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
genomic: TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATGgtaaggtttc ... tctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
EST: gi|25806962|gb|CA762923.1|CA762923
EST:     TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATG                         GCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG
genomic: TTATGCAGCAAAGAGATATGGAAATCCTGTGATATATGTAACTGAGAATGgtaaggtttc ... tctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaattgttgtcacatttgatatttgcttcctttaccatagtttctctcatgtagGCATGGATGAGGAAGATGATCAATCGGCAACGCTTGACCAAGTCTTGAATGATACGACGAGGGTTGGTTACTTCAAAGGATACCTCGCGTCAGTTGCACA
              atttgat  putative branch site (score: 5)
                                         tttctctcat  putative PPT
              atttgatattt  TA-rich tract