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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagttgcaaaaaatagggtctggcaggtggtgtgctactttttgggctaattcttgaaaatgattcagttctcctaacctagcctttgtgtgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGACCGAGTGCATGCTAGAGGGGTAGGGCCTCTACCTATACCAGTTGATCAAT

Basic information

species Oryza sativa
transcript LOC_Os04g04254.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g04254.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G007721_T01 (Zea mays), 3'ss of exon 10
cagttgcaaaaaatagggtctggcaggtggtgtgc-----tactttttgggctaattcttgaaaatg-attcagttctcctaacctagcctttgtgtgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGACCGAGTGCATGCTAGAGGGGTAGGGCCTCTACCTATACCAGTTGATCAAT
    |  |||| |     ||| || | || ||  |     || | |  | | |   |  |  |  || | | | ||    |   |  |    | | ||||| | |||| || || ||||||||||| ||||||||||||||||| |||||||| ||||| |||||||| |||||| |||||||||  ||||| ||||||||||| |
----tctaaaatacctt-tcttgctgttgctgcacactagtattctcagaggtttcttgtacagttgtacttaatttagttgttcacgttagtctatgatt-gcagTGTCCCACGACTATTGTACCCTTCTTTGGTGACCAACCTTTCTGGGGTGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT

upper sequence: LOC_Os04g04254.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G021849_T02 (Zea mays), 3'ss of exon 7
cagttgcaaaa-aatagggtctggcaggtgg-tgtgctactttttgggcta--attcttgaaaatgattcagttctcctaacctagcctttgtgt--gatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGACCGAGTGCATGCTAGAGGGGTAGGGCCTCTACCTATACCAGTTGATCAAT
   |||||     || || || ||||   |  |    ||| ||    |||   ||||| | |   | ||   |   |  ||  |||   | || |  |||||| |||| ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| |||||| |||||||||  ||||| ||||||||||| |
---ttgcattttgatgggatcaggcataagtctaaaataccttccttgctgttattctcgga---ggtttcttgtactcaatttagttgtagtctacgatttgcagTGTCCTACGACTATTGTACCTTTCTTTGGTGACCAACCTTTCTGGGGCGACCGGGTGCATGCAAGAGGGCTAGGGCCTCCGCCTATTCCAGTTGATCAGT
















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|218504178|gb|FG958866.1|FG958866
EST:     GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG                         TGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGAC
genomic: GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCGgtattccctc ... tgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaattcttgaaaatgattcagttctcctaacctagcctttgtgtgatttgtagTGCCCTACAACTATTGTACCTTTCTTTGGTGACCAACCATTCTGGGGAGACCGAGTGCATGCTAGAGGGGTAGGGCCTCTACCTATACCAGTTGATCAAT
                          tcctaac  putative branch site (score: 1)
           aaaatgatt  TA-rich tract