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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taactgaataagtgaaaatggtggctgaaaaagtgtagtgattgtaaaatattactacaaattactcttttttctcaattgatgaataactggttttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGGGATGGTCTGCAAAATGAGAAGAGTACTGTACCAGCTTCTGTAAAGATTG

Basic information

species Oryza sativa
transcript LOC_Os11g04210.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G44610.1 (Glycine max), 3'ss of exon 3
taactgaataagtgaaaatggtggctgaaaaagtgtagtgattgtaaaatatta-ctacaaattactcttttttctcaattgat-gaataactggtt--ttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGGGATGGTCTGCAAAATGAGAAGAGTACTGTACCAGCTTCTGTAAAGATTG-----------
||| | ||| | | | || | | | || | | || || | ||||| | ||||| || || | |||| | | | ||| | || | |||| |||||| |||||||| ||||| || ||| ||||||| | ||||||||||||| | |||||| || ||||||||||||
--gtaatatattttaaactttttgttgtcgttttatt-ttatcgcatttccttttctgctaattaacatattttcaattttaattggataatggcatgatgcagtatctgaatagTATACCAAAGTTTGTAAAGATAGTAGAAGTTGGTCCAAGGGATGGATTACAAAATGAGAAGAACATTGTACCTACTGCTGTAAAGATTGAATTGATTCAC

upper sequence: LOC_Os11g04210.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 3'ss of exon 2
taactgaataagtgaaaat-----ggtggctgaaaaagtgtagtgattgtaaaatattactacaaattactcttttttctcaattgatgaataactggttttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGGGATGGTCTGCAAAATGAGAAGAGTACTGTACCAGCTTCTGTAAAGATTG
||| |||| | || | || | || ||| || | ||| | | || | |||| | | | | |||| | ||| |||| | | | |||| ||||||||||||||| ||||| || ||| ||||||| ||||||||||||||| || |||||| | ||||||| | |
taataatataattttgcattttacaatctttgtgttactggagttgtttcatctgatttattttattttatgttttatttttgtactttgataagag-----cagTTTTTAGGAGGTATACCAAAGTTTGTGAAGATAGTGGAAGTTGGTCCAAGGGATGGATTGCAAAATGAGAAGAATATTGTACCTACAGCTGTAAAAGTGG
















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|88311590|gb|CI574807.1|CI574807
EST:     ATTCCTCCTGCAATGGAGTGGATATGGAGTT-AGAGCTCTTCCAGGGAAG                         GTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGG
genomic: ATTCCTCCTGCAATGGAGTGGATATGGAGTTCAGAGCTCTTCCACGGAAGgtattttgat ... tggttttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGG
EST: gi|88314256|gb|CI602588.1|CI602588
EST:     ATTCCTCCTGCAATGGAGTGGATATGGAGTTCAGAGCTCTTCCACGGAAG                         GTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGG
genomic: ATTCCTCCTGCAATGGAGTGGATATGGAGTTCAGAGCTCTTCCACGGAAGgtattttgat ... tggttttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatattactacaaattactcttttttctcaattgatgaataactggttttcagGTTTTGTGGGAGCTTCCAAGGTTTGTGAAGATAGTTGAAGTCGGACCACGGGATGGTCTGCAAAATGAGAAGAGTACTGTACCAGCTTCTGTAAAGATTG
                                      gaataac  putative branch site (score: 2)
 ttttc  putative PPT
 aaattactctttttt  TA-rich tract