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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC

Basic information

species Oryza sativa
transcript LOC_Os12g42884.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G149751_T02 (Zea mays), 3'ss of exon 9
gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC
                           | |||| |  | | |  | | | |   ||| | |||||        | | |  ||||  |    | |||      ||| | ||       ||||| || | |  | | |||| | | || |||||||||||||||||||||||||||| ||||||||||| || |||||||| || ||||||||||| |||||||| || ||||| ||  |||| |||||||| |
--------------------------gtcagtgctcttgaatccattctgc---tggtt-tttgatg------tctaagaagataaacc--cccataccatgagtgtagtc------gcatttaattgactttattggcctatgttctacagAGAAACGATATGGTTGAGTACTTCGGTGAGCAGCTCTCCGGTTTTGCGTTCACTGCCAATGGCTGGGTGCAGTCTTATGGGTCAAGGTGCGTCAAGCCTC

upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgca-ttgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC
                                                                                                    |   |||||    |||   |  |||  ||| |||  | |    | ||   ||||||||||| |||||||||||||| |||||||||||    |||||||| || || | ||| |||||||| || ||||| |||||||||||||| |||||||
--------------------------------------------------------------------------------------------------gtaggatttggcagattccataactgatctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

upper sequence: LOC_Os12g42884.3 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 8
gtcagtatcctcgtgtactacttgtgtttagtgtttattactagactttacacttggctgtttgagaaaacaatattattagatttattgactcattaacaaagtttggtttgttctgca-ttgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC
                                                                                                    |   |||||    |||   |  |||  ||| |||  | |    | ||   ||||||||||| |||||||||||||| |||||||||||    |||||||| || || | ||| |||||||| || ||||| |||||||||||||| |||||||
--------------------------------------------------------------------------------------------------gtaggatttggcagattccatagctgatctaatctacattgtcctttttcgccagAGAAACGACATGGTTGAGTACTTCGGTGAGCAGCTGCAAGGTTTTGCTTTCACCGTCAACGGATGGGTACAGTCCTACGGATCCCGGTGTGTAAAGCCAC

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|300215517|gb|HO088143.1|HO088143
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGA
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGA
EST: gi|218492493|gb|FG951515.1|FG951515
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|300216253|gb|HO088038.1|HO088038
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|11863315|gb|AU065792.2|AU065792
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTTGTGAGCAG-TTTCTNGTTT-GCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|29637650|gb|CB642659.1|CB642659
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|218478602|gb|FG965538.1|FG965538
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|571921|gb|D41432.1|D41432
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|218483058|gb|FG951439.1|FG951439
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|163927825|gb|EG709417.1|EG709417
EST:     TTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: TTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88724067|gb|CI749077.1|CI749077
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|571693|gb|D41204.1|D41204
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88718273|gb|CI741362.1|CI741362
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|570079|gb|D40928.1|D40928
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|88729113|gb|CI752623.1|CI752623
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|41884047|gb|BX928878.1|BX928878
EST:     AGAT-CAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58688902|gb|CK077589.1|CK077589
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58678399|gb|CK067086.1|CK067086
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCAGGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|428589|gb|D24741.1|D24741
EST:     CTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: CTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|33800724|gb|CF326232.1|CF326232
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
EST: gi|58661898|gb|CK050578.1|CK050578
EST:     AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAG                         AGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT
genomic: AGATCCAGGAAGAGCTTGACATTGATGTGCTTGTTCACGGCGAGCCTGAGgtcagtatcc ... tattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaagtttggtttgttctgcattgaagtaagctaactggcatgtattttacagAGAAACGATATGGTTGAGTACTTTGGTGAGCAGCTTTCTGGTTTTGCATTTACTGCCAATGGATGGGTGCAATCCTATGGATCCCGGTGTGTCAAGCCAC
                               agctaac  putative branch site (score: 2)
                                          atgtatttta  TA-rich tract