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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatacataatttgaaatgtttctgtcagatcataatacgctttttggtatttgaactacatatttttcactaacttaatatagcagttccattttgcagTTCTCCTGGCCACCATTTGTAATGGGATCAAGTTTTTTTGTTATTCTTCTCATAATGAAAAATCTA

Basic information

species Oryza sativa
transcript LOC_Os09g06499.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 4
-----------gcatacataatttgaaatg---tttctgtcagatcataatacgctttttggtatttgaactacatatttttcactaacttaatatagcagttccattttgcagTTCTCCTGGCCACCATTTGTAATGGGATCAAGTTTTTTTGTTATTCTTCTCATAATGAAAAATCTA
           |||   ||  |||  |||    | ||  ||| || |  |||    || |  |||||||  |||| | ||| ||||||||||| | ||||||||             |||||||| || ||||| |||||||||| |||| |||  |||||||| || |||||||||  |
tacagtgaactgcacttatgctttacaatccattgtcgttcaaattagtatatcaattctcatatttgatttacacacttt-cactaacttaacaaagcagTTC-------------TCCTGGCCTCCGTTTGTGATGGGATCAATTTTTCTTGCGATTCTTCTAATTATGAAAAATACA
















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|29643060|gb|CB648067.1|CB648067
EST:     GCAGCAAAATTATACCACTTATTGAGAGTATAATTGGAGGAATAGATCAG                         TTCTCCTGGCCACCATTTGTAATGGGATCAAGNNNNNNNGTTATTCTTCTC
genomic: GCAGCAAAATTATACCACTTATTGAGAGTATAATTGGAGGAATAGATCAGgtgggctttg ... cattttgcagTTCTCCTGGCCACCATTTGTAATGGGATCAAGTTTTTTTGTTATTCTTCTC
EST: gi|29613614|gb|CB618627.1|CB618627
EST:     GCAGCAAAATTATACCACTTATTGAGAGTATAATTGGAGGAATAGATCAG                         TTCTCCTGGCCACCATTTGTAATGGGATCAAGNNNNNNNGTTATTCTTCTC
genomic: GCAGCAAAATTATACCACTTATTGAGAGTATAATTGGAGGAATAGATCAGgtgggctttg ... cattttgcagTTCTCCTGGCCACCATTTGTAATGGGATCAAGTTTTTTTGTTATTCTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatttgaactacatatttttcactaacttaatatagcagttccattttgcagTTCTCCTGGCCACCATTTGTAATGGGATCAAGTTTTTTTGTTATTCTTCTCATAATGAAAAATCTA
                                          ttccatttt  CT-rich tract
               atatttttcactaact  TA-rich tract