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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatctttgatattgtttgacacactttcattgtttaaatgggttgtattaacaaggagtatctgttgctcttgtgttttccttttcagCTCTTTGCCATCCTTCCTCTAGCTGTGGTCCATACTATGGGCAATCTTTTCACTAACATGAGCCTGGGGAAGGTTGCTGTGTCATTCACACATACCATCA

Basic information

species Oryza sativa
transcript LOC_Os08g25624.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25624.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G174107_T01 (Zea mays), 3'ss of exon 2
gtagatctttgatattgtttgacacacttt-cattgtttaaatgggt-tgtattaacaaggagtatctgttgctcttgtgttttccttttcagCTCTTTGCCATCCTTCCTCTAGCTGTGGTCCATACTATGGGCAATCTTTTCACTAACATGAGCCTGGGGAAGGTTGCTGTGTCATTCACACATACCATCA
||| | |||| | ||| | | |||   ||| |  | ||||  ||| | | |||||| |        ||  || || | | |     |||||||||  | |||||||| ||||| ||| | || ||||||||||||||||| ||||| ||||||||||| ||||| ||||| |||||||| || || |||||||
gta-acctttaacattttcttacaacttttacgctatttacttggatatatattaata--------ctcatgttcattt-taacaattttcagCTTGTAGCCATCCTACCTCTGGCTATTGTTCATACTATGGGCAATCTCTTCACCAACATGAGCCTTGGGAAAGTTGCAGTGTCATTTACGCACACCATCA
















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|88575372|gb|CI669517.1|CI669517
EST:     TCATGTGGATCACTGGTATCCTTAGGAGACCAAAGATTTCTGGTGCACAG                         CTCTTTGCCATCCTTCCTCTAGCTGTGGTCCATACTATGGGCAATCTTTTC
genomic: TCATGTGGATCACTGGTATCCTTAGGAGACCAAAGATTTCTGGTGCACAGgtagatcttt ... tccttttcagCTCTTTGCCATCCTTCCTCTAGCTGTGGTCCATACTATGGGCAATCTTTTC
EST: gi|58610772|gb|CK038484.1|CK038484
EST:     GTATCCTTAGGAGA-CAAAGATTTCTGGTGCACAG                         CTCTTTGCCATCCTTCCTCGTAGCTGTGGTCCATACTATGGGCAATCTTTT
genomic: GTATCCTTAGGAGACCAAAGATTTCTGGTGCACAGgtagatcttt ... tccttttcagCTCTTTGCCATCCTTCCTC-TAGCTGTGGTCCATACTATGGGCAATCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgggttgtattaacaaggagtatctgttgctcttgtgttttccttttcagCTCTTTGCCATCCTTCCTCTAGCTGTGGTCCATACTATGGGCAATCTTTTCACTAACATGAGCCTGGGGAAGGTTGCTGTGTCATTCACACATACCATCA
            tattaac  putative branch site (score: 1)
                               ttgctcttgtgttttc  putative PPT
         ttgtattaa  TA-rich tract