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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaacttttcacatatttgtggggggtcattatttagaataggatatttcattattaacgaagatcaatcataatgtccatctattcgctatccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGGGAACTGTGACTTTCAGGAATATGTTCTGGTTCGAACAGACCTGGATACT

Basic information

species Oryza sativa
transcript LOC_Os01g56630.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G079389_T01 (Zea mays), 3'ss of exon 7
ttaacttttca-catatttgtggggggtca--ttatttagaataggatatttcattattaacgaagatcaatcataatgtccatctattcgctatccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGGGAACTGTGACTTTCAGGAATATGTTCTGGTTCGAACAGACCTGGATACT
 |   |||| | ||||||         |||  |||| |   |   || |  || || |||   |  ||   |||| |  | |   ||| |    ||| | ||| |||||||| |||||||||||||||||  ||||||||||||||||| |||||||||| ||||||||||||||||| |||||| |||||||| |||| |||
atgtttttttatcatattccattatactcaatttatcttctactagaaaaatc-ttctta--cagtattcttcattagtttctattatccttattccttacagGTGCTTAAATGATGAGAGCTCGGTTCTGTTGCTCTATTCTTTGGTCTATGGGAACTGCGACTTTCAGGAATATGTCCTGGTTAGAACAGACTTGGACACT

upper sequence: LOC_Os01g56630.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G078576_T01 (Zea mays), 3'ss of exon 7
-ttaacttttcacatatttgtggggggtca--ttatttagaataggatatttcattattaacgaagatcaatcataatgtccatctattcgctatccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGGGAACTGTGACTTTCAGGAATATGTTCTGGTTCGAACAGACCTGGATACT
  |   ||||  ||||||    |    |||   ||| |   | | || |  | ||| |||   |  ||   |||| |  |     |||      ||| | ||||| |||||| ||||||| | | |||||  ||||||||||||||||||||||||||||||||||||||||||| ||  |||||||||||||| ||||||||
tgttttttttatcatattccatgatactcaatctatcttctacaagaaaaat-attctta--cagtattcttcattagtttatattatctttgttccttacagATTCTTAAATGATGAGATCCCAGTTCTGTTGCTCTATTCTTTGGTCCATGGGAACTGTGACTTTCAGGAATACGTCTTGGTTCGAACAGACTTGGATACT
















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|29628456|gb|CB633467.1|CB633467
EST:     GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC                         ATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG
genomic: GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCACgtaagtaaca ... atccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG
EST: gi|58693104|gb|CK081791.1|CK081791
EST:     GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC                         ATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG
genomic: GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCACgtaagtaaca ... atccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG
EST: gi|58659682|gb|CK048362.1|CK048362
EST:     GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCAC                         ATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG
genomic: GGGCTAGTTGTCAGGTTGTCTTTTGCATCGCTATTTGACGCTCTTGGCACgtaagtaaca ... atccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcattattaacgaagatcaatcataatgtccatctattcgctatccatgcagATGCTTAAAAGATGAGAGCTCGGTTCTACTGCTCTATTCTTTGGTCCATGGGAACTGTGACTTTCAGGAATATGTTCTGGTTCGAACAGACCTGGATACT
       tattaac  putative branch site (score: 1)
     attattaa  TA-rich tract