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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattcataattaatcatgaacagagcaaaattaaatggattggttcttcattacctagaaaacatgaagttctctgatgcaaaccaacttatatgcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC

Basic information

species Oryza sativa
transcript LOC_Os05g11140.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 4
-ttgattcataattaatcatgaacagagcaaaattaaatggattggttcttcattacctagaaaacatgaagttctctgatgcaaaccaacttatat-gcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC
  ||   | || ||   |       |  | ||       | |     ||     ||  |||      |||   | ||| | ||||   ||||| ||| ||||||||||||||||||||| |||||||| |||||||||||||||||||| || |||||
gctgggcc-tagttggcccgacttgggcccaacgcctccgtagcccatcacggctatttaggcc-tgtgacagtttctcacgcaatgtaacttctattgcagATTATGGACATGTTGGGGCCAAGCCTATGGGATGTTTGGAATAATAACTCTCACTC

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 4
------------ttgattcataattaatcatgaacagagcaaaattaaatggattggttcttca------ttacctagaaaacatgaagttc-tctgat-gcaaaccaacttatatgcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC
            ||| |   |  ||  | |||||   |      | || ||    | ||||| |      ||  |   ||   |  | ||   | |||| | |||||    |   ||||| ||||||||||| | || |||||| |||||||||||||||||||||| || ||| |
gtatgctatcatttgctgtcttgttggttatgaatttatggtggtcaactgtggagtttctttagtctgtttctccttaatttagaatgtctgtgtgatagaaaacctgaatggttgcagGTTATGGACATGCTTGGACCAAGCTTGTGGGATGTTTGGAATAATAACTCTCACAC
















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|29681938|gb|CB678213.1|CB678213
EST:     GTGTACCAAGAGTACATTATAAAGGGAGGCAGGGGGATTACTATATCATG                         ATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCC
genomic: GTGTACCAAGAGTACATTATAAAGGGAGGCAGGGGGATTACTATATCATGgtaacggagc ... ttatatgcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcattacctagaaaacatgaagttctctgatgcaaaccaacttatatgcagATTATGGACATGTTGGGTCCAAGCCTGTGGGATGTTTGGAATAATAATTCCCACTC
                            ctctgat  putative branch site (score: 4)
                                          aacttatat  TA-rich tract