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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtactcgtgatcattagcacatcggataattttttttgagcttttgtttcatcggtgtaattaagtgttaattgtccattgattgattttgcttgtgcagGACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGTTGCTTGCTCAGGCTCCAAGTTGTGCTTCATCTCCAGTTGCCGTGGTAGCTA

Basic information

species Oryza sativa
transcript LOC_Os08g42420.5
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42420.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G138425_T02 (Zea mays), 3'ss of exon 1
-------gtactcgtgatcattagcacatcggataattttttttgagcttttgtttcatcggtgtaattaagtgttaattgtccattgattgattttgcttgtgcagGACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGTTGCTTGCTCAGGCTCCAAGTTGTGCTTCATCTCCAGTTGCCGTGGTAGCTA-------------
       | |           |||| ||| | |     |    | | ||       || | | ||  | |||| |  | || || | ||     ||||||| ||||||||| |||||             |||||| | ||||||||||| |||||||||||||| || |||||| |||||||||||||||||||||| ||||||               
atgaactgaatgaagtgatgctagctcatggcaagcaatagcattaactg--agcccagctgagtggtgaagtatgtaatgcccgtcga-----tttgcttctgcagGACTCTGATG-------------GGCATGGTTCATCCTAGGTTTCTGGTTGCTTGCTCGGGGTCCAAGCTGTGCTTCATCTCCAGTTGCCGCGGTAGCAGCGCAAAGATGATG
















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|88391229|gb|CI595483.1|CI595483
EST:     TAGGGGAGAAGCCGGGTACTCGTAGTAGGTTCTGGCGTGACGTTTTGAAG                         GACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGTTG
genomic: TAGGGGAGAAGCCGGGTACTCGTAGTAGGTTCTGGCGTGACGTTTTGAAGgtgagaaatc ... gcttgtgcagGACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGTTG
EST: gi|88397284|gb|CI580794.1|CI580794
EST:     TAGGGGAGAAGCCGGGTAATCGTAGTAGGTTCTGGCGTGACTTTTTGAAG                         GACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGCTT
genomic: TAGGGGAGAAGCCGGGTACTCGTAGTAGGTTCTGGCGTGACGTTTTGAAGgtgagaaatc ... gcttgtgcagGACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGG-TT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcatcggtgtaattaagtgttaattgtccattgattgattttgcttgtgcagGACTGTGATGTGTGATCCCCACTGGCATGTTGCATCCTAGGTTCCTGGTTGCTTGCTCAGGCTCCAAGTTGTGCTTCATCTCCAGTTGCCGTGGTAGCTA
                                         ttttgctt  CT-rich tract
            taattaagtgttaatt  TA-rich tract