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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